diff --git a/BioModels/BIOMD0000000001/BIOMD0000000001_url.omex b/BioModels/BIOMD0000000001/BIOMD0000000001_url.omex new file mode 100644 index 00000000..3c241672 Binary files /dev/null and b/BioModels/BIOMD0000000001/BIOMD0000000001_url.omex differ diff --git a/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml b/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml new file mode 100644 index 00000000..03dd1b45 --- /dev/null +++ b/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml @@ -0,0 +1,634 @@ + + + + + + + + + + + + + + + + + auto_time_for_task1_var + + + + + + + + auto_dg_for_task1_BLL__x + + + + + + + + auto_dg_for_task1_IL__x + + + + + + + + auto_dg_for_task1_AL__x + + + + + + + + auto_dg_for_task1_A__x + + + + + + + + auto_dg_for_task1_BL__x + + + + + + + + auto_dg_for_task1_B__x + + + + + + + + auto_dg_for_task1_DLL__x + + + + + + + + auto_dg_for_task1_D__x + + + + + + + + auto_dg_for_task1_ILL__x + + + + + + + + auto_dg_for_task1_DL__x + + + + + + + + auto_dg_for_task1_I__x + + + + + + + + auto_dg_for_task1_ALL__x + + + + + + + + auto_dg_for_task1_kf_0__x + + + + + + + + auto_dg_for_task1_kr_0__x + + + + + + + + auto_dg_for_task1_kf_1__x + + + + + + + + auto_dg_for_task1_kr_1__x + + + + + + + + auto_dg_for_task1_kf_2__x + + + + + + + + auto_dg_for_task1_kr_2__x + + + + + + + + auto_dg_for_task1_kf_3__x + + + + + + + + auto_dg_for_task1_kr_3__x + + + + + + + + auto_dg_for_task1_kf_4__x + + + + + + + + auto_dg_for_task1_kr_4__x + + + + + + + + auto_dg_for_task1_kf_5__x + + + + + + + + auto_dg_for_task1_kr_5__x + + + + + + + + auto_dg_for_task1_kf_6__x + + + + + + + + auto_dg_for_task1_kr_6__x + + + + + + + + auto_dg_for_task1_kf_7__x + + + + + + + + auto_dg_for_task1_kr_7__x + + + + + + + + auto_dg_for_task1_kf_8__x + + + + + + + + auto_dg_for_task1_kr_8__x + + + + + + + + auto_dg_for_task1_kf_9__x + + + + + + + + auto_dg_for_task1_kr_9__x + + + + + + + + auto_dg_for_task1_kf_10__x + + + + + + + + auto_dg_for_task1_kr_10__x + + + + + + + + auto_dg_for_task1_kf_11__x + + + + + + + + auto_dg_for_task1_kr_11__x + + + + + + + + auto_dg_for_task1_kf_12__x + + + + + + + + auto_dg_for_task1_kr_12__x + + + + + + + + auto_dg_for_task1_kf_13__x + + + + + + + + auto_dg_for_task1_kr_13__x + + + + + + + + auto_dg_for_task1_kf_14__x + + + + + + + + auto_dg_for_task1_kr_14__x + + + + + + + + auto_dg_for_task1_kf_15__x + + + + + + + + auto_dg_for_task1_kr_15__x + + + + + + + + auto_dg_for_task1_kf_16__x + + + + + + + + auto_dg_for_task1_kr_16__x + + + + + + + + auto_dg_for_task1_t2__x + + + + + + + + auto_dg_for_task1_comp1__x + + + + + + + + auto_dg_for_task1_React0__x + + + + + + + + auto_dg_for_task1_React1__x + + + + + + + + auto_dg_for_task1_React2__x + + + + + + + + auto_dg_for_task1_React3__x + + + + + + + + auto_dg_for_task1_React4__x + + + + + + + + auto_dg_for_task1_React5__x + + + + + + + + auto_dg_for_task1_React6__x + + + + + + + + auto_dg_for_task1_React7__x + + + + + + + + auto_dg_for_task1_React8__x + + + + + + + + auto_dg_for_task1_React9__x + + + + + + + + auto_dg_for_task1_React10__x + + + + + + + + auto_dg_for_task1_React11__x + + + + + + + + auto_dg_for_task1_React12__x + + + + + + + + auto_dg_for_task1_React13__x + + + + + + + + auto_dg_for_task1_React14__x + + + + + + + + auto_dg_for_task1_React15__x + + + + + + + + auto_dg_for_task1_React16__x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/BioModels/BIOMD0000000001/BIOMD0000000001_url.xml b/BioModels/BIOMD0000000001/BIOMD0000000001_url.xml new file mode 100644 index 00000000..411e0c65 --- /dev/null +++ b/BioModels/BIOMD0000000001/BIOMD0000000001_url.xml @@ -0,0 +1,1343 @@ + + + + + +
Edelstein1996 - EPSP ACh event
+
+

Model of a nicotinic Excitatory Post-Synaptic Potential in a + Torpedo electric organ. Acetylcholine is not represented + explicitely, but by an event that changes the constants of + transition from unliganded to liganded.  +

+
+
+

This model has initially been encoded using StochSim.

+
+
+

This model is described in the article:

+
+ A kinetic mechanism for + nicotinic acetylcholine receptors based on multiple allosteric + transitions. +
+
Edelstein SJ, Schaad O, Henry E, + Bertrand D, Changeux JP.
+
Biol Cybern 1996 Nov; 75(5): + 361-379
+

Abstract:

+
+

Nicotinic acetylcholine receptors are transmembrane + oligomeric proteins that mediate interconversions between open + and closed channel states under the control of + neurotransmitters. Fast in vitro chemical kinetics and in vivo + electrophysiological recordings are consistent with the + following multi-step scheme. Upon binding of agonists, receptor + molecules in the closed but activatable resting state (the + Basal state, B) undergo rapid transitions to states of higher + affinities with either open channels (the Active state, A) or + closed channels (the initial Inactivatable and fully + Desensitized states, I and D). In order to represent the + functional properties of such receptors, we have developed a + kinetic model that links conformational interconversion rates + to agonist binding and extends the general principles of the + Monod-Wyman-Changeux model of allosteric transitions. The + crucial assumption is that the linkage is controlled by the + position of the interconversion transition states on a + hypothetical linear reaction coordinate. Application of the + model to the peripheral nicotine acetylcholine receptor (nAChR) + accounts for the main properties of ligand-gating, including + single-channel events, and several new relationships are + predicted. Kinetic simulations reveal errors inherent in using + the dose-response analysis, but justify its application under + defined conditions. The model predicts that (in order to + overcome the intrinsic stability of the B state and to produce + the appropriate cooperativity) channel activation is driven by + an A state with a Kd in the 50 nM range, hence some 140-fold + stronger than the apparent affinity of the open state deduced + previously. According to the model, recovery from the + desensitized states may occur via rapid transit through the A + state with minimal channel opening, thus without necessarily + undergoing a distinct recovery pathway, as assumed in the + standard 'cycle' model. Transitions to the desensitized states + by low concentration 'pre-pulses' are predicted to occur + without significant channel opening, but equilibrium values of + IC50 can be obtained only with long pre-pulse times. + Predictions are also made concerning allosteric effectors and + their possible role in coincidence detection. In terms of + future developments, the analysis presented here provides a + physical basis for constructing more biologically realistic + models of synaptic modulation that may be applied to artificial + neural networks.

+
+
+
+

This model is hosted on + BioModels Database + and identified by: + BIOMD0000000001.

+

To cite BioModels Database, please use: + BioModels Database: + An enhanced, curated and annotated resource for published + quantitative kinetic models.

+
+
+

To the extent possible under law, all copyright and related or + neighbouring rights to this encoded model have been dedicated to + the public domain worldwide. Please refer to + CC0 + Public Domain Dedication for more information.

+
+ + + + + + + + + + Le Novère + Nicolas + + lenov@ebi.ac.uk + + EMBL-EBI + + + + + + 2005-02-02T14:56:11Z + + + 2017-05-19T14:33:51Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

biliganded basal state

+ + + + + + + + + + + + + + + + + + + +

monoliganded intermediate

+ + + + + + + + + + + + + + + + + + + +

monoliganded active state

+ + + + + + + + + + + + + + + + + + + +

unkiganded active state

+ + + + + + + + + + + + + + + + + + + +

monoliganded basal state

+ + + + + + + + + + + + + + + + + + + +

unliganded basal state

+ + + + + + + + + + + + + + + + + + + +

biliganded desensitised state

+ + + + + + + + + + + + + + + + + + + +

fully desensitised state

+ + + + + + + + + + + + + + + + + + + +

biliganded intermediate

+ + + + + + + + + + + + + + + + + + + +

monoliganded desensitised state

+ + + + + + + + + + + + + + + + + + + +

unliganted intermediate

+ + + + + + + + + + + + + + + + + + + +

biliganted active state

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

first ligand on basal

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_0 * B - kr_0 * BL

+ + + + + + comp1 + + + + + kf_0 + B + + + + kr_0 + BL + + + + + + + + + +

second ligand on basal

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_1 * BL - kr_1 * BLL

+ + + + + + comp1 + + + + + kf_1 + BL + + + + kr_1 + BLL + + + + + + + + + +

opening of biliganded

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_2 * BLL - kr_2 * ALL

+ + + + + + comp1 + + + + + kf_2 + BLL + + + + kr_2 + ALL + + + + + + + + + +

first ligand on active

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_3 * A - kr_3 * AL

+ + + + + + comp1 + + + + + kf_3 + A + + + + kr_3 + AL + + + + + + + + + +

second ligand on active

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_4 * AL - kr_4 * ALL

+ + + + + + comp1 + + + + + kf_4 + AL + + + + kr_4 + ALL + + + + + + + + + +

opening of unliganded

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_5 * B - kr_5 * A

+ + + + + + comp1 + + + + + kf_5 + B + + + + kr_5 + A + + + + + + + + + +

opening of monoliganded

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_6 * BL - kr_6 * AL

+ + + + + + comp1 + + + + + kf_6 + BL + + + + kr_6 + AL + + + + + + + + + +

first ligand on intermediate

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_7 * I - kr_7 * IL

+ + + + + + comp1 + + + + + kf_7 + I + + + + kr_7 + IL + + + + + + + + + +

second ligand on intermediate

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_8 * IL - kr_8 * ILL

+ + + + + + comp1 + + + + + kf_8 + IL + + + + kr_8 + ILL + + + + + + + + + +

unliganded active <=> unliganded intermediate

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_9 * A - kr_9 * I

+ + + + + + comp1 + + + + + kf_9 + A + + + + kr_9 + I + + + + + + + + + +

monoliganded active <=> monoliganded intermediate

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_10 * AL - kr_10 * IL

+ + + + + + comp1 + + + + + kf_10 + AL + + + + kr_10 + IL + + + + + + + + + +

biliganded active <=> biliganded intermediate

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_11 * ALL - kr_11 * ILL

+ + + + + + comp1 + + + + + kf_11 + ALL + + + + kr_11 + ILL + + + + + + + + + +

first ligand on desensitised

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_12 * D - kr_12 * DL

+ + + + + + comp1 + + + + + kf_12 + D + + + + kr_12 + DL + + + + + + + + + +

second ligand on desensitised

+ + + + + + + + + + + + + + + + + + + + + + + +

kf_13 * DL - kr_13 * DLL

+ + + + + + comp1 + + + + + kf_13 + DL + + + + kr_13 + DLL + + + + + + + + + +

unliganded intermediate <=> unliganded desensitised

+ + + + + + + + + + + +

kf_14 * I - kr_14 * D

+ + + + + + comp1 + + + + + kf_14 + I + + + + kr_14 + D + + + + + + + + + +

monoliganded intermediate <=> monoliganded desensitised

+ + + + + + + + + + + +

kf_15 * IL - kr_15 * DL

+ + + + + + comp1 + + + + + kf_15 + IL + + + + kr_15 + DL + + + + + + + + + +

biliganded intermediate <=> biliganded desensitised

+ + + + + + + + + + + +

kf_16 * ILL - kr_16 * DLL

+ + + + + + comp1 + + + + + kf_16 + ILL + + + + kr_16 + DLL + + + + + + + + + + + + + + + + + + + + + + + + + + time + t2 + + + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + + + \ No newline at end of file diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf new file mode 100644 index 00000000..ce985de5 Binary files /dev/null and b/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf new file mode 100644 index 00000000..284f1acc Binary files /dev/null and b/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf differ diff --git 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00000000..08c5e99f --- /dev/null +++ b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Could not load MassModel 'BIOMD0000000001'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

| ✅ PASS | | plot | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000001/tests/results_local.json b/BioModels/BIOMD0000000001/tests/results_local.json new file mode 100644 index 00000000..0dfb32c8 --- /dev/null +++ b/BioModels/BIOMD0000000001/tests/results_local.json @@ -0,0 +1,2167 @@ +{ + "amici": { + "exception_message": "", + "log_yml": { + "duration": 16.878883, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 16.395254, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 0.267185, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 0.432204, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000496", + "duration": 15.522015, + "exception": null, + "id": "task1", + "output": "", + "simulatorDetails": [ + { + "key": "solver", + "value": "amici.amici.CVodeSolver" + }, + { + "key": "method", + "value": "amici.swig_wrappers.runAmiciSimulation" + }, + { + "key": "arguments", + "value": {} + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.081759, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpzxessd2h/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpzxessd2h/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.160269, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp64y_xz8l/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.144054, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp5f1k93po/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.233937, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpllsy0tzm/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.145853, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpcnif1fxb/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 1.406639, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmplq5f15uj/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmplq5f15uj/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.081246, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 0.257525, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 0.499548, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 0.146259, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmplq5f15uj/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.14306, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp1cm368ul/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.156454, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmppsbjd98y/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.158375, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpev59pj1u/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.165867, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmpv87m0uvc/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.051762, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.12182, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpcvkt9vjo/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.083156, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmphs4vnr76/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.047416, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp_rolss6v/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "", + "log_yml": { + "duration": 1.484589, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpbh50myyf/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpbh50myyf/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.14505, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpc7l_eyuc.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpn2ifuf74.xml\r\nout: /tmp/tmpc7l_eyuc.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmpc7l_eyuc.psc loading ..... \r\nParsing file: /tmp/tmpc7l_eyuc.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\nCVODE time for 1001 points: 0.045973777770996094\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 0.298217, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 0.473628, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.178782, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "pysces.PyscesModel.Simulate" + }, + { + "key": "arguments", + "value": { + "cvode_abstol": 1e-09, + "cvode_access_solver": true, + "cvode_h0": 0.0, + "cvode_hmax": 0.0, + "cvode_hmin": 0.0, + "cvode_mxord": 5, + "cvode_mxstep": 5000, + "cvode_reltol": 1e-09, + "cvode_return_event_timepoints": false, + "cvode_stats": false, + "cvode_track_assignment_rules": true + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.141643, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpqlaao665/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "", + "log_yml": { + "duration": 1.493313, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpygc_3b8y/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpygc_3b8y/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 1.032751, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 0.261701, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 0.453212, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning:\r\n\r\n\u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n\r\n", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.134319, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable 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warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmpygc_3b8y/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "", + "log_yml": { + "duration": 13, + "exception": null, + "output": "Processing BIOMD0000000001_url.sedml. Done", + "sedDocuments": [ + { + "duration": null, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. Generating HDF5 file...", + "outputs": [ + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_plot_for_task1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_report_for_task1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 1, + "exception": null, + "id": "task1", + "output": "Initializing simulation job 0 ... done. Starting simulation... done.", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "xpp": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "log_yml": { + "duration": 0.056813, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmphu0i03yf/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/BioModels/BIOMD0000000001/tests/results_remote.json b/BioModels/BIOMD0000000001/tests/results_remote.json new file mode 100644 index 00000000..6f4be9b3 --- /dev/null +++ b/BioModels/BIOMD0000000001/tests/results_remote.json @@ -0,0 +1,2580 @@ +{ + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17a10d09353e8f0fc0b3", + "download": "https://api.biosimulations.org/results/672a17a10d09353e8f0fc0b3/download", + "logs": "https://api.biosimulations.org/logs/672a17a10d09353e8f0fc0b3?includeOutput=true", + "log_yml": { + "duration": 31.095497, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 30.69659, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": 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"autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 0.491604, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + 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"https://api.biosimulations.org/runs/672a17a75a60072d20f4c202", + "download": "https://api.biosimulations.org/results/672a17a75a60072d20f4c202/download", + "logs": "https://api.biosimulations.org/logs/672a17a75a60072d20f4c202?includeOutput=true", + "log_yml": { + "duration": 0.190837, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cbmpy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17a95a60072d20f4c205", + "download": "https://api.biosimulations.org/results/672a17a95a60072d20f4c205/download", + "logs": "https://api.biosimulations.org/logs/672a17a95a60072d20f4c205?includeOutput=true", + "log_yml": { + "duration": 0.28332, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cobrapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17ab0d09353e8f0fc0b9", + "download": "https://api.biosimulations.org/results/672a17ab0d09353e8f0fc0b9/download", + "logs": "https://api.biosimulations.org/logs/672a17ab0d09353e8f0fc0b9?includeOutput=true", + "log_yml": { + "duration": 0.18803, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "copasi": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17ad0d09353e8f0fc0bc", + "download": "https://api.biosimulations.org/results/672a17ad0d09353e8f0fc0bc/download", + "logs": "https://api.biosimulations.org/logs/672a17ad0d09353e8f0fc0bc?includeOutput=true", + "log_yml": { + "duration": 1.726035, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 1.387954, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml 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"value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "gillespy2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b05a60072d20f4c211", + "download": "https://api.biosimulations.org/results/672a17b05a60072d20f4c211/download", + "logs": "https://api.biosimulations.org/logs/672a17b05a60072d20f4c211?includeOutput=true", + "log_yml": { + "duration": 0.198661, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "ginsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b2b678b3883bb61539", + "download": "https://api.biosimulations.org/results/672a17b2b678b3883bb61539/download", + "logs": "https://api.biosimulations.org/logs/672a17b2b678b3883bb61539?includeOutput=true", + "log_yml": { + "duration": 0.184712, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "libsbmlsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b35a60072d20f4c218", + "download": "https://api.biosimulations.org/results/672a17b35a60072d20f4c218/download", + "logs": "https://api.biosimulations.org/logs/672a17b35a60072d20f4c218?includeOutput=true", + "log_yml": { + "duration": 0.188246, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "masspy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b5b678b3883bb6154b", + "download": "https://api.biosimulations.org/results/672a17b5b678b3883bb6154b/download", + "logs": "https://api.biosimulations.org/logs/672a17b5b678b3883bb6154b?includeOutput=true", + "log_yml": { + "duration": 1.428032, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Could not load MassModel 'BIOMD0000000001'", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.89302, + "exception": { + "message": "The SED document did not execute successfully:\n\n Could not load MassModel 'BIOMD0000000001'", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_BLL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_IL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_AL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_A", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_BL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_B", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_DLL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_D", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ILL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_DL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_I", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ALL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_t2", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_comp1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React0", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React2", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React3", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React4", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React5", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React6", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React7", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React8", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React9", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React10", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React11", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React12", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React13", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React14", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React15", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React16", + "status": "SKIPPED" + } + ], + "duration": 0.056867, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SKIPPED" + } + ], + "duration": 0.293776, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.322784, + "exception": { + "message": "Could not load MassModel 'BIOMD0000000001'", + "type": "MassSimulationError" + }, + "id": "task1", + "output": "\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML fbc package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML groups package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'BLL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'BLL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'IL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'IL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'AL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'AL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'A' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'A'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'BL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'BL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'B' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'B'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'DLL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'DLL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'D' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'D'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'ILL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'ILL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'DL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'DL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'I' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'I'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'ALL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'ALL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React0'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React1'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React2'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React3'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React4'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React5'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React6'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React7'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React8'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React9'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React10'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React11'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React12'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React13'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React14'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React15'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React16'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React0'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React1'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React2'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React3'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React4'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React5'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React6'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React7'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React8'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React9'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React10'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React11'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React12'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React13'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React14'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React15'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React16'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "netpyne": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b70d09353e8f0fc0d6", + "download": "https://api.biosimulations.org/results/672a17b70d09353e8f0fc0d6/download", + "logs": "https://api.biosimulations.org/logs/672a17b70d09353e8f0fc0d6?includeOutput=true", + "log_yml": { + "duration": 0.069968, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "neuron": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b95a60072d20f4c227", + "download": "https://api.biosimulations.org/results/672a17b95a60072d20f4c227/download", + "logs": "https://api.biosimulations.org/logs/672a17b95a60072d20f4c227?includeOutput=true", + "log_yml": { + "duration": 0.047913, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "opencor": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17ba5a60072d20f4c231", + "download": "https://api.biosimulations.org/results/672a17ba5a60072d20f4c231/download", + "logs": "https://api.biosimulations.org/logs/672a17ba5a60072d20f4c231?includeOutput=true", + "log_yml": { + "duration": 0.039026, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpzlgtc159/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pyneuroml": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17bc0d09353e8f0fc0e5", + "download": "https://api.biosimulations.org/results/672a17bc0d09353e8f0fc0e5/download", + "logs": "https://api.biosimulations.org/logs/672a17bc0d09353e8f0fc0e5?includeOutput=true", + "log_yml": { + "duration": 0.065451, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pysces": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17be0d09353e8f0fc0ea", + "download": "https://api.biosimulations.org/results/672a17be0d09353e8f0fc0ea/download", + "logs": "https://api.biosimulations.org/logs/672a17be0d09353e8f0fc0ea?includeOutput=true", + "log_yml": { + "duration": 1.795554, + "exception": null, + "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 1.425644, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpusbz_uk4.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmprqun8mcy.xml\r\nout: /tmp/tmpusbz_uk4.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpusbz_uk4.psc loading ..... \r\nParsing file: /tmp/tmpusbz_uk4.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\nCVODE time for 1001 points: 0.06746697425842285\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": 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a/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml b/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml new file mode 100644 index 00000000..13802d13 --- /dev/null +++ b/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml @@ -0,0 +1,425 @@ + + + + + + + + + + + + + + + + + auto_time_for_task1_var + + + + + + + + auto_dg_for_task1_c__x + + + + + + + + auto_dg_for_task1_vca__x + + + + + + + + auto_dg_for_task1_vk__x + + + + + + + + auto_dg_for_task1_Cm__x + + + + + + + + auto_dg_for_task1_gk__x + + + + + + + + auto_dg_for_task1_gcal__x + + + + + + + + auto_dg_for_task1_gsk__x + + + + + + + + auto_dg_for_task1_ga__x + + + + + + + + auto_dg_for_task1_gf__x + + + + + + + + auto_dg_for_task1_vn__x + + + + + + + + auto_dg_for_task1_va__x + + + + + + + + auto_dg_for_task1_vm__x + + + + + + + + auto_dg_for_task1_vh__x + + + + + + + + auto_dg_for_task1_vf__x + + + + + + + + auto_dg_for_task1_sn__x + + + + + + + + auto_dg_for_task1_sa__x + + + + + + + + auto_dg_for_task1_sm__x + + + + + + + + auto_dg_for_task1_sh__x + + + + + + + + auto_dg_for_task1_sf__x + + + + + + + + auto_dg_for_task1_taun__x + + + + + + + + auto_dg_for_task1_tauh__x + + + + + + + + auto_dg_for_task1_lambda__x + + + + + + + + auto_dg_for_task1_kc__x + + + + + + + + auto_dg_for_task1_ks__x + + + + + + + + auto_dg_for_task1_ff__x + + + + + + + + auto_dg_for_task1_alpha__x + + + + + + + + auto_dg_for_task1_phik__x + + + + + + + + auto_dg_for_task1_phia__x + + + + + + + + auto_dg_for_task1_phih__x + + + + + + + + auto_dg_for_task1_phif__x + + + + + + + + auto_dg_for_task1_phical__x + + + + + + + + auto_dg_for_task1_cinf__x + + + + + + + + auto_dg_for_task1_ica__x + + + + + + + + auto_dg_for_task1_isk__x + + + + + + + + auto_dg_for_task1_ibk__x + + + + + + + + auto_dg_for_task1_ikdr__x + + + + + + + + auto_dg_for_task1_ia__x + + + + + + + + auto_dg_for_task1_ik__x + + + + + + + + auto_dg_for_task1_n__x + + + + + + + + auto_dg_for_task1_h__x + + + + + + + + auto_dg_for_task1_V__x + + + + + + + + auto_dg_for_task1_cell__x + + + + + + + + auto_dg_for_task1_reaction_0000004__x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/BioModels/BIOMD0000000138/BIOMD0000000138_url.xml b/BioModels/BIOMD0000000138/BIOMD0000000138_url.xml new file mode 100644 index 00000000..c1212c7c --- /dev/null +++ b/BioModels/BIOMD0000000138/BIOMD0000000138_url.xml @@ -0,0 +1,539 @@ + + + + + +

The model is encoded according to the paper Low dose of dopamine may stimulate prolactin secretion by increasing fast potassium currents + Figure5 has been reproduced by MathSBML. One need to change the value of ga in order to get the three correct results.

+

the xppaut file of the model is avaiable on the following address offered by the author , http://www.math.fsu.edu/%7Ebertram/software/pituitary/JCNS_07.ode

+
+

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication + for more information.

+

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.

+
+

To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92. +

+ + + + + + + + + + + He + Enuo + + enuo@caltech.edu + + BNMC + + + + + + 2007-08-02T10:34:59Z + + + 2014-04-01T18:01:13Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ The concentration of Ca range can change from 0.1 to 0.3

+ + + + + + + + + + + + + + + + + + + + + + + + + + +

+ For figure 5A, ga=0, figure5B, ga=8, figure5C, ga=25

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + 1 + + + + + + + vn + V + + sn + + + + + + + + + + + 1 + + + 1 + + + + + + + va + V + + sa + + + + + + + + + + + 1 + + + 1 + + + + + + + V + vh + + sh + + + + + + + + + + + 1 + + + 1 + + + + + + + vf + V + + sf + + + + + + + + + + + 1 + + + 1 + + + + + + + vm + V + + sm + + + + + + + + + + + gcal + phical + + + V + vca + + + + + + + + + + + c + 2 + + + + + + c + 2 + + + + ks + 2 + + + + + + + + + + gsk + cinf + + + V + vk + + + + + + + + + gf + phif + + + V + vk + + + + + + + + + gk + n + + + V + vk + + + + + + + + + ga + phia + h + + + V + vk + + + + + + + + + isk + ibk + ikdr + ia + + + + + + + + + + + + + + + + + + + + + + + + ica + ik + + + Cm + + + + + + + + + + + + + + + + + + + + + + + lambda + + + phik + n + + + taun + + + + + + + + + + + + + + + + + + + + + + + phih + h + + tauh + + + + + + + + + + + + + + + + + + + + + + + + + + + + ff + + + + + + alpha + ica + + + + kc + c + + + cell 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100644 index 00000000..3d3250ad Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf new file mode 100644 index 00000000..bdd71b2a Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md b/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md new file mode 100644 index 00000000..3550c29d --- /dev/null +++ b/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
lambda * (phik - n) / taun

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
lambda * (phik - n) / taun

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AttributeError':'PysMod' object has no attribute 'lambda'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AttributeError':'PysMod' object has no attribute 'lambda'

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

| ✅ PASS | | plot | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000138/tests/results_local.json b/BioModels/BIOMD0000000138/tests/results_local.json new file mode 100644 index 00000000..a8ec0304 --- /dev/null +++ b/BioModels/BIOMD0000000138/tests/results_local.json @@ -0,0 +1,1491 @@ +{ + "amici": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/amici' returned non-zero exit status 1", + "log_yml": { + "duration": 0.850246, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.52011, + "exception": { + "message": "The SED document did not execute successfully:\n\n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.058425, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.276489, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.091858, + "exception": { + "message": "rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\nTokenError: Starred arguments in lambda not supported.", + "type": "SBMLException" + }, + "id": "task1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.056218, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpu6r4hu1y/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpu6r4hu1y/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.180791, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpeshio693/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.164126, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpgkng3_hy/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.24882, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp8l4hbgu5/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.127481, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjxguzzyz/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 1.22201, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpiylro8bg/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpiylro8bg/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.921278, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 0.258751, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 0.42799, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 0.107382, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000138_url` may be invalid.\r\n - The model file `/tmp/tmpiylro8bg/./BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.14345, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpfzgeabsg/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.130563, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp_hz6rgwd/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.153092, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpxa6bvyzf/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.142051, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmpl5_adwtl/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.041781, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.045526, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpodjpnvas/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.062107, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpimbuyk1m/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.05475, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpmsah6p4v/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1", + "log_yml": { + "duration": 2.142324, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :'PysMod' object has no attribute 'lambda'", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp7egu9upf/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp7egu9upf/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.820202, + "exception": { + "message": "The SED document did not execute successfully:\n\n :'PysMod' object has no attribute 'lambda'", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V1\r\nlambda is a reserved symbol, replacing with Lambda\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmph6bvy05t.xml\r\n*******************************************************************\r\n\r\nReserved symbol lambda replaced with Lambda \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"reaction_0000004\" in default compartment\r\nWriting file: /tmp/tmp7kw5rkpa.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmph6bvy05t.xml\r\nout: /tmp/tmp7kw5rkpa.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmp7kw5rkpa.psc loading ..... \r\nParsing file: /tmp/tmp7kw5rkpa.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"vca\" has been initialised but does not occur in a rate equation\r\nInfo: \"vk\" has been initialised but does not occur in a rate equation\r\nInfo: \"Cm\" has been initialised but does not occur in a rate equation\r\nInfo: \"gk\" has been initialised but does not occur in a rate equation\r\nInfo: \"gcal\" has been initialised but does not occur in a rate equation\r\nInfo: \"gsk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ga\" has been initialised but does not occur in a rate equation\r\nInfo: \"gf\" has been initialised but does not occur in a rate equation\r\nInfo: \"vn\" has been initialised but does not occur in a rate equation\r\nInfo: \"va\" has been initialised but does not occur in a rate equation\r\nInfo: \"vm\" has been initialised but does not occur in a rate equation\r\nInfo: \"vh\" has been initialised but does not occur in a rate equation\r\nInfo: \"vf\" has been initialised but does not occur in a rate equation\r\nInfo: \"sn\" has been initialised but does not occur in a rate equation\r\nInfo: \"sa\" has been initialised but does not occur in a rate equation\r\nInfo: \"sm\" has been initialised but does not occur in a rate equation\r\nInfo: \"sh\" has been initialised but does not occur in a rate equation\r\nInfo: \"sf\" has been initialised but does not occur in a rate equation\r\nInfo: \"taun\" has been initialised but does not occur in a rate equation\r\nInfo: \"tauh\" has been initialised but does not occur in a rate equation\r\nInfo: \"Lambda\" has been initialised but does not occur in a rate equation\r\nInfo: \"ks\" has been initialised but does not occur in a rate equation\r\nInfo: \"phik\" has been initialised but does not occur in a rate equation\r\nInfo: \"phia\" has been initialised but does not occur in a rate equation\r\nInfo: \"phih\" has been initialised but does not occur in a rate equation\r\nInfo: \"phif\" has been initialised but does not occur in a rate equation\r\nInfo: \"phical\" has been initialised but does not occur in a rate equation\r\nInfo: \"cinf\" has been initialised but does not occur in a rate equation\r\nInfo: \"isk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ibk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ikdr\" has been initialised but does not occur in a rate equation\r\nInfo: \"ia\" has been initialised but does not occur in a rate equation\r\nInfo: \"ik\" has been initialised but does not occur in a rate equation\r\nInfo: \"n\" has been initialised but does not occur in a rate equation\r\nInfo: \"h\" has been initialised but does not occur in a rate equation\r\nInfo: \"V\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nRate rule(s) detected.\r\nINFO: RateRules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 1001 points: 0.02880549430847168\r\nRateRules evaluated and added to mod.data_sim.\r\n \u001b[31mfailed - 'PysMod' object has no attribute 'lambda'\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.116927, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.371212, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 1.134029, + "exception": { + "message": "'PysMod' object has no attribute 'lambda'", + "type": "AttributeError" + }, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.18608, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpt51vbuiz/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "", + "log_yml": { + "duration": 1.193888, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmp370xud5o/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmp370xud5o/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 0.791637, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 0.207648, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 0.312604, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.124152, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `BIOMD0000000138_url` may be invalid.\r\n - The model file `/tmp/tmp370xud5o/./BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "", + "log_yml": { + "duration": 9, + "exception": null, + "output": "Processing BIOMD0000000138_url.sedml. Done", + "sedDocuments": [ + { + "duration": null, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. Generating HDF5 file...", + "outputs": [ + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_plot_for_task1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_report_for_task1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 1, + "exception": null, + "id": "task1", + "output": "Initializing simulation job 0 ... done. Starting simulation... done.", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "xpp": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "log_yml": { + "duration": 0.049408, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp1k_stn43/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/BioModels/BIOMD0000000138/tests/results_remote.json b/BioModels/BIOMD0000000138/tests/results_remote.json new file mode 100644 index 00000000..2268395c --- /dev/null +++ b/BioModels/BIOMD0000000138/tests/results_remote.json @@ -0,0 +1,1772 @@ +{ + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c8c0d09353e8f106b51", + "download": "https://api.biosimulations.org/results/67323c8c0d09353e8f106b51/download", + "logs": "https://api.biosimulations.org/logs/67323c8c0d09353e8f106b51?includeOutput=true", + "log_yml": { + "duration": 1.059903, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.629425, + "exception": { + "message": "The SED document did not execute successfully:\n\n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.060745, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.341835, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.104082, + "exception": { + "message": "rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\nTokenError: Starred arguments in lambda not supported.", + "type": "SBMLException" + }, + "id": "task1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "brian2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c8eb678b3883bb6c1d2", + "download": "https://api.biosimulations.org/results/67323c8eb678b3883bb6c1d2/download", + "logs": "https://api.biosimulations.org/logs/67323c8eb678b3883bb6c1d2?includeOutput=true", + "log_yml": { + "duration": 0.048472, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "bionetgen": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c900d09353e8f106b54", + "download": "https://api.biosimulations.org/results/67323c900d09353e8f106b54/download", + "logs": "https://api.biosimulations.org/logs/67323c900d09353e8f106b54?includeOutput=true", + "log_yml": { + "duration": 0.19821, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "boolnet": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c92b678b3883bb6c1d6", + "download": "https://api.biosimulations.org/results/67323c92b678b3883bb6c1d6/download", + "logs": "https://api.biosimulations.org/logs/67323c92b678b3883bb6c1d6?includeOutput=true", + "log_yml": { + "duration": 0.182139, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cbmpy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c930d09353e8f106b57", + "download": "https://api.biosimulations.org/results/67323c930d09353e8f106b57/download", + "logs": "https://api.biosimulations.org/logs/67323c930d09353e8f106b57?includeOutput=true", + "log_yml": { + "duration": 0.31853, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cobrapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c95b678b3883bb6c1dc", + "download": "https://api.biosimulations.org/results/67323c95b678b3883bb6c1dc/download", + "logs": "https://api.biosimulations.org/logs/67323c95b678b3883bb6c1dc?includeOutput=true", + "log_yml": { + "duration": 0.176861, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "copasi": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c980d09353e8f106b5b", + "download": "https://api.biosimulations.org/results/67323c980d09353e8f106b5b/download", + "logs": "https://api.biosimulations.org/logs/67323c980d09353e8f106b5b?includeOutput=true", + "log_yml": { + "duration": 1.265494, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 0.950286, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml 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"autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 0.24725, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 0.395308, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 0.17546, + "exception": null, + "id": "task1", + "output": "", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "gillespy2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c9a5a60072d20f56d8d", + "download": "https://api.biosimulations.org/results/67323c9a5a60072d20f56d8d/download", + "logs": "https://api.biosimulations.org/logs/67323c9a5a60072d20f56d8d?includeOutput=true", + "log_yml": { + "duration": 0.211598, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "ginsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c9c5a60072d20f56d90", + "download": "https://api.biosimulations.org/results/67323c9c5a60072d20f56d90/download", + "logs": "https://api.biosimulations.org/logs/67323c9c5a60072d20f56d90?includeOutput=true", + "log_yml": { + "duration": 0.185889, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "libsbmlsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c9eb678b3883bb6c1ec", + "download": "https://api.biosimulations.org/results/67323c9eb678b3883bb6c1ec/download", + "logs": "https://api.biosimulations.org/logs/67323c9eb678b3883bb6c1ec?includeOutput=true", + "log_yml": { + "duration": 0.193056, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "masspy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca05a60072d20f56da2", + "download": "https://api.biosimulations.org/results/67323ca05a60072d20f56da2/download", + "logs": "https://api.biosimulations.org/logs/67323ca05a60072d20f56da2?includeOutput=true", + "log_yml": { + "duration": 1.181274, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.612617, + "exception": { + "message": "The SED document did not execute successfully:\n\n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.061385, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.319179, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.083462, + "exception": { + "message": "Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n\t`(model, errors) = validate_sbml_model(filename)`\nIf the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "MassSBMLError" + }, + "id": "task1", + "output": "\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML fbc package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML groups package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "netpyne": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca1b678b3883bb6c200", + "download": "https://api.biosimulations.org/results/67323ca1b678b3883bb6c200/download", + "logs": "https://api.biosimulations.org/logs/67323ca1b678b3883bb6c200?includeOutput=true", + "log_yml": { + "duration": 0.05409, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "neuron": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca30d09353e8f106b76", + "download": "https://api.biosimulations.org/results/67323ca30d09353e8f106b76/download", + "logs": "https://api.biosimulations.org/logs/67323ca30d09353e8f106b76?includeOutput=true", + "log_yml": { + "duration": 0.049106, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "opencor": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca40d09353e8f106b7d", + "download": "https://api.biosimulations.org/results/67323ca40d09353e8f106b7d/download", + "logs": "https://api.biosimulations.org/logs/67323ca40d09353e8f106b7d?includeOutput=true", + "log_yml": { + "duration": 0.02749, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpnh9ii2_u/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pyneuroml": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca60d09353e8f106b82", + "download": "https://api.biosimulations.org/results/67323ca60d09353e8f106b82/download", + "logs": "https://api.biosimulations.org/logs/67323ca60d09353e8f106b82?includeOutput=true", + "log_yml": { + "duration": 0.050187, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pysces": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca80d09353e8f106b87", + "download": "https://api.biosimulations.org/results/67323ca80d09353e8f106b87/download", + "logs": "https://api.biosimulations.org/logs/67323ca80d09353e8f106b87?includeOutput=true", + "log_yml": { + "duration": 2.233287, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :'PysMod' object has no attribute 'lambda'", + "type": "CombineArchiveExecutionError" + }, + "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 1.882373, + "exception": { + "message": "The SED document did not execute successfully:\n\n :'PysMod' object has no attribute 'lambda'", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V1\r\nlambda is a reserved symbol, replacing with Lambda\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpzhjj07jb.xml\r\n*******************************************************************\r\n\r\nReserved symbol lambda replaced with Lambda \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"reaction_0000004\" in default compartment\r\nWriting file: /tmp/tmpdr5eja8y.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpzhjj07jb.xml\r\nout: /tmp/tmpdr5eja8y.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpdr5eja8y.psc loading ..... \r\nParsing file: /tmp/tmpdr5eja8y.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"vca\" has been initialised but does not occur in a rate equation\r\nInfo: \"vk\" has been initialised but does not occur in a rate equation\r\nInfo: \"Cm\" has been initialised but does not occur in a rate equation\r\nInfo: \"gk\" has been initialised but does not occur in a rate equation\r\nInfo: \"gcal\" has been initialised but does not occur in a rate equation\r\nInfo: \"gsk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ga\" has been initialised but does not occur in a rate equation\r\nInfo: \"gf\" has been initialised but does not occur in a rate equation\r\nInfo: \"vn\" has been initialised but does not occur in a rate equation\r\nInfo: \"va\" has been initialised but does not occur in a rate equation\r\nInfo: \"vm\" has been initialised but does not occur in a rate equation\r\nInfo: \"vh\" has been initialised but does not occur in a rate equation\r\nInfo: \"vf\" has been initialised but does not occur in a rate equation\r\nInfo: \"sn\" has been initialised but does not occur in a rate equation\r\nInfo: \"sa\" has been initialised but does not occur in a rate equation\r\nInfo: \"sm\" has been initialised but does not occur in a rate equation\r\nInfo: \"sh\" has been initialised but does not occur in a rate equation\r\nInfo: \"sf\" has been initialised but does not occur in a rate equation\r\nInfo: \"taun\" has been initialised but does not occur in a rate equation\r\nInfo: \"tauh\" has been initialised but does not occur in a rate equation\r\nInfo: \"Lambda\" has been initialised but does not occur in a rate equation\r\nInfo: \"ks\" has been initialised but does not occur in a rate equation\r\nInfo: \"phik\" has been initialised but does not occur in a rate equation\r\nInfo: \"phia\" has been initialised but does not occur in a rate equation\r\nInfo: \"phih\" has been initialised but does not occur in a rate equation\r\nInfo: \"phif\" has been initialised but does not occur in a rate equation\r\nInfo: \"phical\" has been initialised but does not occur in a rate equation\r\nInfo: \"cinf\" has been initialised but does not occur in a rate equation\r\nInfo: \"isk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ibk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ikdr\" has been initialised but does not occur in a rate equation\r\nInfo: \"ia\" has been initialised but does not occur in a rate equation\r\nInfo: \"ik\" has been initialised but does not occur in a rate equation\r\nInfo: \"n\" has been initialised but does not occur in a rate equation\r\nInfo: \"h\" has been initialised but does not occur in a rate equation\r\nInfo: \"V\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nRate rule(s) detected.\r\nINFO: RateRules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 1001 points: 0.048134565353393555\r\nRateRules evaluated and added to mod.data_sim.\r\n \u001b[31mfailed - 'PysMod' object has no attribute 'lambda'\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": 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"skipReason": null, + "status": "FAILED" + } + }, + "rbapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca9b678b3883bb6c229", + "download": "https://api.biosimulations.org/results/67323ca9b678b3883bb6c229/download", + "logs": "https://api.biosimulations.org/logs/67323ca9b678b3883bb6c229?includeOutput=true", + "log_yml": { + "duration": 0.191135, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "smoldyn": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323cab0d09353e8f106b90", + "download": "https://api.biosimulations.org/results/67323cab0d09353e8f106b90/download", + "logs": 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"autogen_task1_V", + "status": "QUEUED" + }, + { + "id": "autogen_task1_cell", + "status": "QUEUED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_report_for_task1", + "output": null, + "skipReason": null, + "status": "QUEUED" + } + ], + "skipReason": null, + "status": "QUEUED", + "tasks": [ + { + "algorithm": null, + "duration": null, + "exception": null, + "id": "task1", + "output": null, + "simulatorDetails": null, + "skipReason": null, + "status": "QUEUED" + } + ] + } + ], + "skipReason": null, + "status": "QUEUED" + } + }, + "xpp": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323cb15a60072d20f56ddf", + "download": "https://api.biosimulations.org/results/67323cb15a60072d20f56ddf/download", + "logs": "https://api.biosimulations.org/logs/67323cb15a60072d20f56ddf?includeOutput=true", + "log_yml": { + "duration": 0.048852, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + } +} \ No newline at end of file diff --git a/BioModels/parse_biomodels.py b/BioModels/parse_biomodels.py index d5b0a6dd..b14bf041 100755 --- a/BioModels/parse_biomodels.py +++ b/BioModels/parse_biomodels.py @@ -24,6 +24,8 @@ sys.path.append("..") import utils +matplotlib.use('Agg') #prevent matplotlib from trying to open a window + API_URL: str = "https://www.ebi.ac.uk/biomodels" out_format="json" @@ -181,7 +183,7 @@ def main(): #caching is used to prevent the need to download the same responses from the remote server multiple times during testing #mode="off" to disable caching, "store" to wipe and store fresh results, "reuse" to use the stored cache - cache = utils.RequestCache(mode="auto",direc="cache") + cache = utils.RequestCache(mode="store",direc="cache") #accumulate results in columns defined by keys which correspond to the local variable names to be used below #to allow automated loading into the columns diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py new file mode 100644 index 00000000..2acbe56d --- /dev/null +++ b/BioModels/test_biomodels_compatibility_biosimulators.py @@ -0,0 +1,253 @@ +#!/usr/bin/env python3 + +md_description = \ +''' +Download and and create results table for curated models from BioModels https://www.ebi.ac.uk/biomodels. + +''' + +import pyneuroml.sbml #for validate_sbml_files +import pyneuroml.sedml #for validate_sedml_files + +import re +import os +import urllib +import sys +import matplotlib + +sys.path.append("..") +import utils + +matplotlib.use('Agg') #prevent plotting from trying to open a window + +API_URL: str = "https://www.ebi.ac.uk/biomodels" + +out_format="json" +max_count = 0 #0 for unlimited + +#local temporary storage of the model files +#this is independent of caching, and still happens when caching is turned off +#this allows the model to be executed and the files manually examined etc +tmp_dir = "tmplocalfiles" + +#suppress stdout/err output from validation functions to make progress counter readable +suppress_stdout = True +suppress_stderr = True + +#whether to replace "model.xml" in the sedml file with the name of the actual sbml file +fix_broken_ref = True + +#skip tests that cause the script to be killed due to lack of RAM +#needs at least 8GB +skip = {} + +def download_file(model_id,filename,output_file,cache): + ''' + request the given file and save it to disk + ''' + + qfilename = urllib.parse.quote_plus(filename) + + response = cache.do_request(f'{API_URL}/model/download/{model_id}?filename={qfilename}').content + + with open(output_file,"wb") as fout: + fout.write(response) + +def replace_model_xml(sedml_path,sbml_filename): + ''' + if the SEDML refers to a generic "model.xml" file + and the SBML file is not called this + replace the SEDML reference with the actual SBML filename + + method used assumes 'source="model.xml"' will only + occur in the SBML file reference + which was true at time of testing on current BioModels release + + returns True if the SBML reference already seemed valid + ''' + + if sbml_filename == "model.xml": return True + + with open(sedml_path,encoding='utf-8') as f: + data = f.read() + + if not 'source="model.xml"' in data: return True + + data = data.replace('source="model.xml"',f'source="{sbml_filename}"') + + with open(f'{sedml_path}',"w",encoding="utf-8") as fout: + fout.write(data) + + return False + +def validate_sbml_file(model_id,mtab,info,cache,sup): + ''' + tasks relating to validating the SBML file + return None to indicate aborting any further tests on this model + otherwise return the SBML filename + ''' + + #handle only single SBML files + if not info['format']['name'] == "SBML": + mtab['valid_sbml'] = ['NonSBML', f"{info['format']['name']}:{info['files']['main']}"] + return None + + if len(info['files']['main']) > 1: + mtab['valid_sbml'] = ['MultipleSBMLs',f"{info['files']['main']}"] + return None + + if len(info['files']['main']) < 1: + mtab['valid_sbml'] = ['NoSBMLs',f"{info['files']['main']}"] + return None + + #download the sbml file + sbml_file = info['files']['main'][0]['name'] + try: + download_file(model_id,sbml_file,sbml_file,cache) + except Exception as e: + mtab['valid_sbml'] = ['DownloadFail',f"{sbml_file} {e}"] + return None + + #validate the sbml file + sup.suppress() #suppress validation warning/error messages + valid_sbml = pyneuroml.sbml.validate_sbml_files([sbml_file], strict_units=False) + valid_sbml_units = pyneuroml.sbml.validate_sbml_files([sbml_file], strict_units=True) + sup.restore() + + mtab['valid_sbml'] = ['pass' if valid_sbml else 'FAIL', f'[{sbml_file}]({API_URL}/{model_id}#Files)'] + mtab['valid_sbml_units'] = 'pass' if valid_sbml_units else 'FAIL' + + return sbml_file + +def validate_sedml_file(model_id,mtab,info,cache,sup,sbml_file): + ''' + tasks relating to validating the SEDML file + return None to indicate aborting any further tests on this model + otherwise return the SEDML filename + ''' + + #must have a SEDML file as well in order to be executed + if not 'additional' in info['files']: + mtab['valid_sedml'] = f"NoSEDML" + return None + + sedml_file = [] + for file_info in info['files']['additional']: + pattern = 'SED[-]?ML' + target = f"{file_info['name']}|{file_info['description']}".upper() + if re.search(pattern,target): + sedml_file.append(file_info['name']) + + #require exactly one SEDML file + if len(sedml_file) == 0: + mtab['valid_sedml'] = "NoSEDML" + return None + + if len(sedml_file) > 1: + mtab['valid_sedml'] = ["MultipleSEDMLs",f"{sedml_file}"] + return None + + #download sedml file + sedml_file = sedml_file[0] + try: + download_file(model_id,sedml_file,sedml_file,cache) + except: + mtab['valid_sedml'] = ["DownloadFail",f"{sedml_file}"] + return None + + #if the sedml file contains a generic 'source="model.xml"' replace it with the sbml filename + if fix_broken_ref: + broken_ref = replace_model_xml(sedml_file,sbml_file) + mtab['broken_ref'] = 'pass' if broken_ref else 'FAIL' + else: + mtab['broken_ref'] = 'NA' + + sup.suppress() + valid_sedml = pyneuroml.sedml.validate_sedml_files([sedml_file]) + sup.restore() + mtab['valid_sedml'] = ['pass' if valid_sedml else 'FAIL', f'[{sedml_file}]({API_URL}/{model_id}#Files)'] + + return sedml_file + +def main(): + ''' + download the BioModel model files, run various validation steps + report the results as a markdown table README file with a summary row at the top + ''' + + #caching is used to prevent the need to download the same responses from the remote server multiple times during testing + #mode="off" to disable caching, "store" to wipe and store fresh results, "reuse" to use the stored cache + cache = utils.RequestCache(mode="store",direc="cache") + + #accumulate results in columns defined by keys which correspond to the local variable names to be used below + #to allow automated loading into the columns + column_labels = "Model |valid-sbml|valid-sbml-units|valid-sedml|broken-ref|tellurium" + column_keys = "model_desc|valid_sbml|valid_sbml_units|valid_sedml|broken_ref|tellurium_outcome" + mtab = utils.MarkdownTable(column_labels,column_keys) + + #allow stdout/stderr from validation tests to be suppressed to improve progress count visibility + sup = utils.SuppressOutput(stdout=suppress_stdout,stderr=suppress_stderr) + + #get list of all available models + model_ids = cache.do_request(f"{API_URL}/model/identifiers?format={out_format}").json()['models'] + count = 0 + starting_dir = os.getcwd() + + if cases != None: + model_ids = cases + + for model_id in model_ids: + #allow testing on a small sample of models + if max_count > 0 and count >= max_count: + break + count += 1 + print(f"\r{model_id} {count}/{len(model_ids)}",end='') + + #only process curated models + #BIOMD ids should be the curated models + if not 'BIOMD' in model_id: + continue + + #skip if on the list to be skipped + if count in skip or model_id in skip: + continue + + #from this point the model will create an output row even if not all tests are run + mtab.new_row() #append empty placeholder row + info = cache.do_request(f"{API_URL}/{model_id}?format={out_format}").json() + + if len(info['name']) > 36: + model_summary = f"[{model_id}]({API_URL}/{model_id})
{info['name'][:30]}" + model_details = f"{info['name']}" + mtab['model_desc'] = mtab.make_fold(model_summary,model_details) + else: + mtab['model_desc'] = f"[{model_id}]({API_URL}/{model_id})
{info['name']}" + + #make temporary downloads of the sbml and sedml files + model_dir = os.path.join(starting_dir,model_id) + os.makedirs(model_dir,exist_ok=True) + os.chdir(model_dir) + + #sbml file validation tasks, includes downloading a local copy + sbml_file = validate_sbml_file(model_id,mtab,info,cache,sup) + if not sbml_file: continue # no further tests possible + + sedml_file = validate_sedml_file(model_id,mtab,info,cache,sup,sbml_file) + if not sedml_file: continue # no further tests possible + + test_folder = 'tests' + # engine_list = list(utils.ENGINES.keys()) + + utils.run_biosimulators_remotely_and_locally(engine_list, + os.path.basename(sedml_file), + os.path.basename(sbml_file), + os.path.join(test_folder,'d1_plots_remote'), + os.path.join(test_folder,'d1_plots_local'), + test_folder=test_folder, + remove_output=remove_output) + +if __name__ == "__main__": + cases = ["BIOMD0000000001","BIOMD0000000138"] + remove_output = False + engine_list = ['copasi'] + main() \ No newline at end of file diff --git a/utils/__init__.py b/utils/__init__.py index 1b7e4eaf..3053d4ca 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -461,17 +461,20 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): if file_extensions in engine_filetypes_tuple_list: file_types = [TYPES[i] for i in file_extensions] return 'pass', (f"The file extensions {file_extensions} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}.") + if 'xml' in file_extensions: - if 'sbml' in model_filepath and 'sedml' not in model_filepath: - if 'sbml' in experiment_filepath and 'sedml' in experiment_filepath: - file_types = ('sbml', 'sedml') - if file_types in engine_filetypes_tuple_list: - return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") - else: - return 'unsure', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is not compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + model_sbml = 'sbml' in model_filepath + model_sedml = 'sedml' in model_filepath + experiment_sbml = 'sbml' in experiment_filepath + experiment_sedml = 'sedml' in experiment_filepath + + if model_sbml and experiment_sbml and experiment_sedml and not model_sedml: + file_types = [TYPES[i] for i in ('sbml', 'sedml') ] + return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {file_types} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + else: + return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may be compatibe with {engine}.

{compatible_filetypes} are compatible with {engine}.") else: return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatibe with {engine}.

{compatible_filetypes} are compatible with {engine}.") - def collapsible_content(content, title='Details'): """ @@ -1185,7 +1188,8 @@ def run_biosimulators_remotely(engine_keys, sedml_file_name, sbml_file_name, d1_plots_remote_dir, - test_folder='tests'): + test_folder='tests', + remove_output_remote=True): """ run with directory pointing towards the location of the sedml and sbml files""" @@ -1217,10 +1221,10 @@ def run_biosimulators_remotely(engine_keys, file_paths = find_files(remote_output_dir, '.pdf') move_d1_files(file_paths, d1_plots_remote_dir) - # remove the remote results directory - if os.path.exists(remote_output_dir): - shutil.rmtree(remote_output_dir) - print('Removed ' + remote_output_dir + ' folder') + if remove_output_remote == True:# remove the remote results directory + if os.path.exists(remote_output_dir): + shutil.rmtree(remote_output_dir) + print('Removed ' + remote_output_dir + ' folder') return results_remote @@ -1228,7 +1232,8 @@ def run_biosimulators_locally(engine_keys, sedml_file_name, sbml_file_name, d1_plots_local_dir, - test_folder='tests'): + test_folder='tests', + remove_output_local=True): engines = {k: v for k, v in ENGINES.items() if k in engine_keys} results_local = {} @@ -1247,9 +1252,10 @@ def run_biosimulators_locally(engine_keys, move_d1_files(file_paths, d1_plots_local_dir) # if it exists remove the output folder - if os.path.exists(local_output_dir): - shutil.rmtree(local_output_dir) - print('Removed ' + local_output_dir + ' folder') + if remove_output_local == True: + if os.path.exists(local_output_dir): + shutil.rmtree(local_output_dir) + print('Removed ' + local_output_dir + ' folder') return results_local @@ -1313,19 +1319,22 @@ def run_biosimulators_remotely_and_locally(engine_keys, sbml_file_name, d1_plots_remote_dir, d1_plots_local_dir, - test_folder='tests'): + test_folder='tests', + remove_output=True): results_remote = run_biosimulators_remotely(engine_keys, sedml_file_name=sedml_file_name, sbml_file_name=sbml_file_name, d1_plots_remote_dir=d1_plots_remote_dir, - test_folder=test_folder) + test_folder=test_folder, + remove_output_remote = remove_output) results_local = run_biosimulators_locally(engine_keys, sedml_file_name=sedml_file_name, sbml_file_name=sbml_file_name, d1_plots_local_dir=d1_plots_local_dir, - test_folder=test_folder) + test_folder=test_folder, + remove_output_local = remove_output) results_table = create_combined_results_table(results_remote, results_local,