Add Demo Mode

.github/workflows/build-windows-executable-app.yaml

@@ -14,7 +14,7 @@ env:
   OPENMS_VERSION: 3.2.0 
   PYTHON_VERSION: 3.11.0
   # Name of the installer
-  APP_NAME: FLASHApp-0.7.4
+  APP_NAME: FLASHApp-0.8.0
   APP_UpgradeCode: "69ae44ad-d554-4e3c-8715-7c4daf60f8bb"
 
 jobs:

.gitignore

@@ -8,7 +8,6 @@ clean-up-workspaces.log
 gdpr_consent/node_modules/
 
 # FLASHApp
-workspaces
 Pipfile
 workspaces-flashtaggerviewer
 

content/FLASHDeconv/FLASHDeconvLayoutManager.py

@@ -36,6 +36,15 @@
     Path(st.session_state['workspace'], 'flashdeconv', 'cache')
 )
 
+def get_sequence():
+    # Check if layout has been set
+    if not file_manager.result_exists('sequence', 'sequence'):
+        return None
+    # fetch layout from cache
+    sequence = file_manager.get_results('sequence', 'sequence')['sequence']
+
+    return sequence['input_sequence'], sequence['fixed_mod_cysteine'], sequence['fixed_mod_methionine']
+
 def set_layout(layout, side_by_side=False):
     file_manager.store_data('layout', 'layout', 
         {
@@ -205,7 +214,7 @@ def handleSettingButtons():
 
 
 def setSequenceView():
-    if 'input_sequence' in st.session_state and st.session_state.input_sequence:
+    if get_sequence() is not None:
         global COMPONENT_OPTIONS
         COMPONENT_OPTIONS = COMPONENT_OPTIONS + ['Sequence view (Mass table needed)',
                                                  'Internal fragment map (Mass table needed)']

content/FLASHDeconv/FLASHDeconvSequenceInput.py

@@ -1,6 +1,38 @@
 import streamlit as st
 import re
 from src.common.common import page_setup, save_params, v_space
+from src.workflow.FileManager import FileManager
+from pathlib import Path
+
+
+# Setup cache access
+file_manager = FileManager(
+    st.session_state["workspace"],
+    Path(st.session_state['workspace'], 'flashdeconv', 'cache')
+)
+
+def set_sequence(input_sequence, fixed_mod_cysteine=None, fixed_mod_methionine=None):
+    file_manager.store_data('sequence', 'sequence', 
+        {
+            'input_sequence' : input_sequence, 
+            'fixed_mod_cysteine' : fixed_mod_cysteine, 
+            'fixed_mod_methionine' : fixed_mod_methionine
+        }
+    )
+
+def get_sequence():
+    # Check if layout has been set
+    if not file_manager.result_exists('sequence', 'sequence'):
+        return None
+    # fetch layout from cache
+    sequence = file_manager.get_results('sequence', 'sequence')['sequence']
+
+    return sequence['input_sequence'], sequence['fixed_mod_cysteine'], sequence['fixed_mod_methionine'] 
+
+def emptySequenceInput():
+    if file_manager.result_exists('sequence', 'sequence'):
+        file_manager.remove_results('sequence')
+    st.session_state['reset_sequence_input'] = True
 
 fixed_mod_cysteine = ['No modification',
                       'Carbamidomethyl (+57)',
@@ -26,14 +58,6 @@ def validateSequenceInput(input_seq):
         return False
     return True
 
-
-def emptySequenceInput():
-    for key in ['input_sequence', 'fixed_mod_cysteine', 'fixed_mod_methionine']:
-        if key in st.session_state:
-            del st.session_state[key]
-    st.session_state['reset_sequence_input'] = True
-
-
 # page initialization
 params = page_setup()
 
@@ -48,17 +72,22 @@ def emptySequenceInput():
 if c2.button('Reset'):
     emptySequenceInput()
 
-# if any sequence was submitted before
-if 'input_sequence' in st.session_state and st.session_state.input_sequence \
-        and 'sequence_text' not in st.session_state:
-    st.session_state['sequence_text'] = st.session_state.input_sequence
-# if any modification was submitted before
-if 'fixed_mod_cysteine' in st.session_state and st.session_state.fixed_mod_cysteine \
-        and 'selected_fixed_mod_cysteine' not in st.session_state:
-    st.session_state['selected_fixed_mod_cysteine'] = st.session_state.fixed_mod_cysteine
-if 'fixed_mod_methionine' in st.session_state and st.session_state.fixed_mod_methionine \
-        and 'selected_fixed_mod_methionine' not in st.session_state:
-    st.session_state['selected_fixed_mod_methionine'] = st.session_state.fixed_mod_methionine
+cached_data = get_sequence() 
+if cached_data is not None:
+    seq, cys_mod, met_mod = cached_data
+
+    if 'sequence_text' not in st.session_state:
+        st.session_state['sequence_text'] = seq
+    if (
+        (cys_mod is not None) 
+        and ('selected_fixed_mod_cysteine' not in st.session_state)
+    ):
+        st.session_state['selected_fixed_mod_cysteine'] = cys_mod
+    if (
+        (met_mod is not None)
+        and ('selected_fixed_mod_methionine' not in st.session_state)
+    ):
+        st.session_state['selected_fixed_mod_methionine'] = met_mod
 
 # clean up the entries of form, if needed
 if st.session_state['reset_sequence_input']:
@@ -80,23 +109,26 @@ def emptySequenceInput():
     _, c2 = st.columns([8, 1])
     submitted = c2.form_submit_button("Save")
     if submitted:
-        if 'input_sequence' in st.session_state:  # initialize
-            del st.session_state['input_sequence']
         if st.session_state['sequence_text'] == '':
             emptySequenceInput()
             st.rerun()
         elif validateSequenceInput(st.session_state['sequence_text']):
+
             st.success('Proteoform sequence is submitted: ' + st.session_state['sequence_text'])
-            # save information for sequence view
-            st.session_state['input_sequence'] = ''.join(st.session_state['sequence_text'].split()).upper()
 
-            st.session_state['fixed_mod_cysteine'], st.session_state['fixed_mod_methionine'] = '', ''
+            # save information for sequence view
+            seq = ''.join(st.session_state['sequence_text'].split()).upper()
+            cys_mod = None
+            met_mod = None
             if 'selected_fixed_mod_cysteine' in st.session_state \
                     and st.session_state['selected_fixed_mod_cysteine'] != 'No modification':
-                st.session_state['fixed_mod_cysteine'] = st.session_state.selected_fixed_mod_cysteine
+                cys_mod = st.session_state.selected_fixed_mod_cysteine
             if 'selected_fixed_mod_methionine' in st.session_state \
                     and st.session_state['selected_fixed_mod_methionine'] != 'No modification':
-                st.session_state['fixed_mod_methionine'] = st.session_state.selected_fixed_mod_methionine
+                met_mod = st.session_state.selected_fixed_mod_methionine
+
+            set_sequence(seq, cys_mod, met_mod)
+
         else:
             st.error('Error: sequence input is not valid')
 

content/FLASHDeconv/FLASHDeconvViewer.py

@@ -8,8 +8,6 @@
 
 DEFAULT_LAYOUT = [['ms1_deconv_heat_map'], ['scan_table', 'mass_table'],
                   ['anno_spectrum', 'deconv_spectrum'], ['3D_SN_plot']]
-if 'input_sequence' in st.session_state and st.session_state.input_sequence:
-    DEFAULT_LAYOUT = DEFAULT_LAYOUT + [['sequence_view']]
 
 def select_experiment():
     st.session_state.selected_experiment0 = st.session_state.selected_experiment_dropdown
@@ -19,6 +17,15 @@ def select_experiment():
                 continue
             st.session_state[f"selected_experiment{exp_index}"] = st.session_state[f'selected_experiment_dropdown_{exp_index}']
 
+def validate_selected_index(file_manager, selected_experiment):
+    results = file_manager.get_results_list(['deconv_dfs', 'anno_dfs'])
+    if selected_experiment in st.session_state:
+        if st.session_state[selected_experiment] in results:
+            return name_to_index[st.session_state[selected_experiment]]
+        else:
+            del st.session_state[selected_experiment]
+    return None
+
 # page initialization
 params = page_setup()
 
@@ -27,6 +34,19 @@ def select_experiment():
     st.session_state["workspace"],
     Path(st.session_state['workspace'], 'flashdeconv', 'cache')
 )
+
+def get_sequence():
+    # Check if layout has been set
+    if not file_manager.result_exists('sequence', 'sequence'):
+        return None
+    # fetch layout from cache
+    sequence = file_manager.get_results('sequence', 'sequence')['sequence']
+
+    return sequence['input_sequence'], sequence['fixed_mod_cysteine'], sequence['fixed_mod_methionine'] 
+
+if get_sequence() is not None:
+    DEFAULT_LAYOUT = DEFAULT_LAYOUT + [['sequence_view']]
+
 results = file_manager.get_results_list(['deconv_dfs', 'anno_dfs'])
 
 if file_manager.result_exists('layout', 'layout'):
@@ -52,7 +72,7 @@ def select_experiment():
         st.selectbox(
             "choose experiment", results, 
             key="selected_experiment_dropdown", 
-            index=name_to_index[st.session_state.selected_experiment0] if 'selected_experiment0' in st.session_state else None,
+            index=validate_selected_index(file_manager, 'selected_experiment0'),
             on_change=select_experiment
         )
         if 'selected_experiment0' in st.session_state:
@@ -64,7 +84,7 @@ def select_experiment():
         st.selectbox(
             "choose experiment", results, 
             key=f'selected_experiment_dropdown_1',
-            index = name_to_index[st.session_state[f'selected_experiment1']] if f'selected_experiment1' in st.session_state else None,
+            index=validate_selected_index(file_manager, 'selected_experiment1'),
             on_change=select_experiment
         )
         if f"selected_experiment1" in st.session_state:
@@ -80,7 +100,7 @@ def select_experiment():
     st.selectbox(
         "choose experiment", results, 
         key="selected_experiment_dropdown", 
-        index=name_to_index[st.session_state.selected_experiment0] if 'selected_experiment0' in st.session_state else None,
+        index=validate_selected_index(file_manager, 'selected_experiment0'),
         on_change=select_experiment
     )
 
@@ -102,7 +122,7 @@ def select_experiment():
             st.selectbox(
                 "choose experiment", results, 
                 key=f'selected_experiment_dropdown_{exp_index}',
-                index = name_to_index[st.session_state[f'selected_experiment{exp_index}']] if f'selected_experiment{exp_index}' in st.session_state else None,
+                index=validate_selected_index(file_manager, f'selected_experiment{exp_index}'),
                 on_change=select_experiment
             )
             # if #experiment input files are less than #layouts, all the pre-selection will be the first experiment

content/FLASHDeconv/FLASHDeconvWorkflow.py

@@ -85,57 +85,35 @@ def process_uploaded_files(uploaded_files):
             for k, v in parsed_data.items():
                 wf.file_manager.store_data(unparsed_dataset, k, v)
 
-    # make directory to store deconv and anno mzML files & initialize data storage
-    tabs = st.tabs(["File Upload", "Example Data"])
+    st.subheader("**Upload FLASHDeconv output files (\*_annotated.mzML & \*_deconv.mzML) or spec1/2 TSV files (Qscore Density Plot only)**")
+    st.info(
+        """
+        **💡 How to upload files**
 
-    # Load Example Data
-    with tabs[1]:
-        st.markdown("An example truncated file from the ThermoFisher Pierce Intact Protein Standard Mix dataset.")
-        _, c2, _ = st.columns(3)
-        if c2.button("Load Example Data", type="primary"):
-            # loading and copying example files into default workspace
-            for filename_postfix, name_tag in zip(
-                ['*_deconv.mzML', '*_annotated.mzML', '*_spec1.tsv'],
-                ["out_deconv_mzML", "anno_annotated_mzML", "spec1_tsv"]
-            ):
-                for file in Path("example-data", "flashdeconv").glob(filename_postfix):
-                    wf.file_manager.store_file(
-                        file.name.replace(filename_postfix[1:], ''), 
-                        name_tag, file, remove=False
-                    )
-            process_uploaded_files([])
-            st.success("Example files loaded!")
-
-    with tabs[0]:
-        st.subheader("**Upload FLASHDeconv output files (\*_annotated.mzML & \*_deconv.mzML) or spec1/2 TSV files (Qscore Density Plot only)**")
-        st.info(
-            """
-            **💡 How to upload files**
-
-            1. Browse files on your computer or drag and drops files
-            2. Click the **Add the uploaded files** button to use them in the workflows
+        1. Browse files on your computer or drag and drops files
+        2. Click the **Add the uploaded files** button to use them in the workflows
 
-            Select data for analysis from the uploaded files shown below.
+        Select data for analysis from the uploaded files shown below.
 
-            **💡 Make sure that the same number of deconvolved and annotated mzML files are uploaded!**
-            """
+        **💡 Make sure that the same number of deconvolved and annotated mzML files are uploaded!**
+        """
+    )
+    with st.form('input_files', clear_on_submit=True):
+        uploaded_files = st.file_uploader(
+            "FLASHDeconv output mzML files or TSV files", accept_multiple_files=True, type=["mzML", "tsv"]
         )
-        with st.form('input_files', clear_on_submit=True):
-            uploaded_files = st.file_uploader(
-                "FLASHDeconv output mzML files or TSV files", accept_multiple_files=True, type=["mzML", "tsv"]
-            )
-            _, c2, _ = st.columns(3)
-            if c2.form_submit_button("Add files to workspace", type="primary"):
-                if uploaded_files:
-                    # A list of files is required, since online allows only single upload, create a list
-                    if type(uploaded_files) != list:
-                        uploaded_files = [uploaded_files]
-
-                    # opening file dialog and closing without choosing a file results in None upload
-                    process_uploaded_files(uploaded_files)
-                    st.success("Successfully added uploaded files!")
-                else:
-                    st.warning("Upload some files before adding them.")
+        _, c2, _ = st.columns(3)
+        if c2.form_submit_button("Add files to workspace", type="primary"):
+            if uploaded_files:
+                # A list of files is required, since online allows only single upload, create a list
+                if type(uploaded_files) != list:
+                    uploaded_files = [uploaded_files]
+
+                # opening file dialog and closing without choosing a file results in None upload
+                process_uploaded_files(uploaded_files)
+                st.success("Successfully added uploaded files!")
+            else:
+                st.warning("Upload some files before adding them.")
 
     # File Upload Table
     experiments = (