From 56919dbc1ffc52604a74ad289fce133647cca79c Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Wed, 4 Dec 2024 11:04:18 +0100
Subject: [PATCH] Fix missing/incorrect yaml schemas

Closes #588.
---
 doc/conf.py                                   |  2 +-
 doc/v1/_static/petab_schema_v1.yaml           | 86 +++++++++++++++++++
 doc/v1/documentation_data_format.rst          |  9 +-
 .../_static/petab_schema_v2.yaml}             |  0
 doc/v2/documentation_data_format.rst          |  9 +-
 5 files changed, 99 insertions(+), 7 deletions(-)
 create mode 100644 doc/v1/_static/petab_schema_v1.yaml
 rename doc/{_static/petab_schema.yaml => v2/_static/petab_schema_v2.yaml} (100%)

diff --git a/doc/conf.py b/doc/conf.py
index e5c00715..832b8358 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -88,7 +88,7 @@ def setup(app):
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ['_static', 'v1/_static', 'v2/_static']
 
 html_context = {
     "display_github": True,
diff --git a/doc/v1/_static/petab_schema_v1.yaml b/doc/v1/_static/petab_schema_v1.yaml
new file mode 100644
index 00000000..bf012e57
--- /dev/null
+++ b/doc/v1/_static/petab_schema_v1.yaml
@@ -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
diff --git a/doc/v1/documentation_data_format.rst b/doc/v1/documentation_data_format.rst
index c3af75f9..a1d52874 100644
--- a/doc/v1/documentation_data_format.rst
+++ b/doc/v1/documentation_data_format.rst
@@ -709,9 +709,12 @@ to change in the future).
 Furthermore, this can be used to describe parameter estimation problems
 comprising multiple models (more details below).
 
-The format is described in the schema
-`../petab/petab_schema.yaml <_static/petab_schema.yaml>`_, which allows for
-easy validation.
+The format is described in the
+`jsonschema <../_static/petab_schema_v1.yaml>`_, which allows for
+easy validation:
+
+.. literalinclude:: _static/petab_schema_v1.yaml
+   :language: yaml
 
 
 Parameter estimation problems combining multiple models
diff --git a/doc/_static/petab_schema.yaml b/doc/v2/_static/petab_schema_v2.yaml
similarity index 100%
rename from doc/_static/petab_schema.yaml
rename to doc/v2/_static/petab_schema_v2.yaml
diff --git a/doc/v2/documentation_data_format.rst b/doc/v2/documentation_data_format.rst
index a969fbe9..3ed4df4d 100644
--- a/doc/v2/documentation_data_format.rst
+++ b/doc/v2/documentation_data_format.rst
@@ -805,9 +805,12 @@ This file also allows specifying a PEtab version and employed PEtab extensions.
 Furthermore, this can be used to describe parameter estimation problems
 comprising multiple models (more details below).
 
-The format is described in the schema
-`../petab/petab_schema.yaml <_static/petab_schema.yaml>`_, which allows for
-easy validation.
+The format is described in the
+`jsonschema <../_static/petab_schema_v2.yaml>`_, which allows for
+easy validation:
+
+.. literalinclude:: _static/petab_schema_v2.yaml
+   :language: yaml
 
 
 Parameter estimation problems combining multiple models