Skip to content
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
86 changes: 86 additions & 0 deletions doc/_static/petab_schema.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
# For syntax see: https://json-schema.org/understanding-json-schema/index.html
#$schema: "https://json-schema.org/draft/2019-09/meta/core"
$schema: "http://json-schema.org/draft-06/schema"
description: PEtab parameter estimation problem config file schema

properties:

format_version:
type: integer
description: Version of the PEtab format (e.g. 1).

parameter_file:
oneOf:
- type: string
- type: array
description: |
File name (absolute or relative) or URL to PEtab parameter table
containing parameters of all models listed in `problems`. A single
table may be split into multiple files and described as an array here.

problems:
type: array
description: |
One or multiple PEtab problems (sets of model, condition, observable
and measurement files). If different model and data files are
independent, they can be specified as separate PEtab problems, which
may allow more efficient handling. Files in one problem cannot refer
to models entities or data specified inside another problem.
items:

type: object
description: |
A set of PEtab model, condition, observable and measurement
files and optional visualization files.
properties:

sbml_files:
type: array
description: List of PEtab SBML files.

items:
type: string
description: PEtab SBML file name or URL.

measurement_files:
type: array
description: List of PEtab measurement files.

items:
type: string
description: PEtab measurement file name or URL.

condition_files:
type: array
description: List of PEtab condition files.

items:
type: string
description: PEtab condition file name or URL.

observable_files:
type: array
description: List of PEtab observable files.

items:
type: string
description: PEtab observable file name or URL.

visualization_files:
type: array
description: List of PEtab visualization files.

items:
type: string
description: PEtab visualization file name or URL.

required:
- sbml_files
- observable_files
- measurement_files
- condition_files

required:
- format_version
- parameter_file
- problems