Merge pull request #513 from djarecka/ga_rel_generate

updates to the release GA

Author: djarecka

.github/workflows/validate_and_release.yml

@@ -46,12 +46,32 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: 3.12
-
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install linkml astor pre-commit
+        pip install git+https://github.com/ReproNim/reproschema-py.git
+    - name: Generate pydantic  using linml and fixing it with reproschema specific script
+      run: |
+        gen-pydantic --pydantic-version 2 linkml-schema/reproschema.yaml > reproschema_model_autogen.py
+        python scripts/fix_pydantic.py reproschema_model_autogen.py reproschema_model.py
+        pre-commit run --files reproschema_model.py || true
+    - name: Generate jsonld format using linkml
+      run: |
+        gen-jsonld --context contexts/reproschema linkml-schema/reproschema.yaml > reproschema.jsonld
+    - name: Generate n-triples and turtle formats using reproschema
+      run: |
+        reproschema convert --format n-triples reproschema.jsonld > reproschema.nt
+        reproschema convert --format turtle reproschema.jsonld > reproschema.ttl
     - name: Make a release
       run: |
         echo "Making a release ${{ inputs.version }}"
         mkdir releases/${{ inputs.version }}
-        cp contexts/reproschema releases/${{ inputs.version }}/base
+        cp contexts/reproschema releases/${{ inputs.version }}/reproschema
+        cp reproschema_model.py releases/${{ inputs.version }}/reproschema_model.py
+        cp reproschema.jsonld releases/${{ inputs.version }}/reproschema.jsonld
+        cp reproschema.nt releases/${{ inputs.version }}/reproschema.nt
+        cp reproschema.ttl releases/${{ inputs.version }}/reproschema.ttl
     #     python scripts/makeRelease.py ${{ inputs.version }}
 
     -   name: Open pull requests to add files

linkml-schema/reproschema.yaml

@@ -55,7 +55,7 @@ slots:
     slot_uri: schema:associatedMedia
   audio:
     title: audio
-    description: TODO
+    description: An audio object.
     slot_uri: schema:audio
     any_of:
     - range: uri
@@ -101,12 +101,8 @@ slots:
   contentUrl:
     slot_uri: schema:contentUrl
     range: uriorcurie
-  creator:
-    slot_uri: schema:creator
-    range: Person
   cronTable:
     title: cronTable
-    description: TODO not described in reproschema
     slot_uri: reproschema:cronTable
   datumType:
     title: datumType
@@ -264,7 +260,7 @@ slots:
     range: OverrideProperty
   preamble:
     title: Preamble
-    description: The preamble for an assessment
+    description: The preamble for an assessment.
     slot_uri: reproschema:preamble
     multivalued: true
     range: langString
@@ -326,7 +322,7 @@ slots:
     range: datetime
     slot_uri: prov:startedAtTime
   subject_id:
-    slot_uri: nidm:subject_id #TODO check this @type:rdf:Property
+    slot_uri: nidm:subject_id
     range: string
   ui:
     title: UI
@@ -502,7 +498,7 @@ classes:
     class_uri: rdf:langString
   MediaObject:
     title: Media Object
-    description: Add description #TODO
+    description: A media object, such as an image, video, audio, or text object embedded in a web page or a downloadable dataset.
     is_a: Thing
     class_uri: schema:MediaObject
     slots:
@@ -542,7 +538,7 @@ classes:
       - id
       - subject_id
     class_uri: reproschema:Participant
-  Protocol: # TODO multiple types
+  Protocol:
     title: Protocol
     description: A representation of a study which comprises one or more assessments.
     is_a: Thing
@@ -555,6 +551,7 @@ classes:
     - description
     - landingPage
     - messages
+    - preamble
     - prefLabel
     - schemaVersion
     - ui
@@ -596,7 +593,7 @@ classes:
     - unitOptions
     - valueType
     class_uri: reproschema:ResponseOption
-  SoftwareAgent: # TODO multiple types
+  SoftwareAgent:
     title: Software Agent
     description:
       Captures information about some action that took place. It also links to information
@@ -616,9 +613,8 @@ classes:
       - category
     class_uri: schema:Thing
   UI:
-    title: todo
-    description:
-    - todo
+    title: UI properties
+    description: A group of properties related to UI.
     slots:
       - order
       - addProperties

scripts/fix_pydantic.py

@@ -0,0 +1,102 @@
+""" Using ast transformer to fix issues with automatic pydantic generation"""
+
+import ast
+import sys
+
+import astor
+
+
+class ClassRemover(ast.NodeTransformer):
+    def __init__(self, class_name):
+        self.class_name = class_name
+
+    def visit_ClassDef(self, node):
+        # Remove the class if its name matches the class_to_remove
+        if node.name == self.class_name:
+            return None
+        return node
+
+    def visit_Expr(self, node):
+        # Check if the node is a call expression
+        if isinstance(node.value, ast.Call):
+            # Check if the call expression is an attribute (method call)
+            if isinstance(node.value.func, ast.Attribute):
+                # Check if the method call matches the specified class
+                if (
+                    isinstance(node.value.func.value, ast.Name)
+                    and node.value.func.value.id == self.class_name
+                ):
+                    return None  # Remove this node
+        return self.generic_visit(node)
+
+
+class TypeReplacer(ast.NodeTransformer):
+    def __init__(self, old_type, new_type):
+        self.old_type = old_type
+        self.new_type = new_type
+
+    def visit_FunctionDef(self, node):
+        # Check all arguments in the function definition
+        for arg in node.args.args:
+            if arg.annotation:
+                arg.annotation = self.visit(arg.annotation)
+        return self.generic_visit(node)
+
+    def visit_AsyncFunctionDef(self, node):
+        # Handle async function definitions similarly
+        for arg in node.args.args:
+            if arg.annotation:
+                arg.annotation = self.visit(arg.annotation)
+        return self.generic_visit(node)
+
+    def visit_Name(self, node):
+        # Replace the old type with the new type
+        if node.id == self.old_type:
+            node.id = self.new_type
+        return node
+
+    def visit_Subscript(self, node):
+        # Handle Union, Optional, and other subscripted types
+        node.value = self.visit(node.value)
+        node.slice = self.visit(node.slice)
+        return node
+
+    def visit_Index(self, node):
+        # Handle the index part of subscripted types
+        node.value = self.visit(node.value)
+        return node
+
+    def visit_Tuple(self, node):
+        # Handle tuples in type annotations
+        node.elts = [self.visit(elt) for elt in node.elts]
+        return node
+
+
+def edit_pydantic(input_file, output_file):
+
+    with open(input_file, "r") as file:
+        tree = ast.parse(file.read())
+
+    transformer_class = ClassRemover(class_name="LangString")
+    tree_modclass = transformer_class.visit(tree)
+
+    transformer_tp = TypeReplacer(
+        old_type="LangString", new_type="Dict[str, str]"
+    )
+    tree_modclass_modtype = transformer_tp.visit(tree_modclass)
+
+    with open(output_file, "w") as file:
+        file.write(astor.to_source(tree_modclass_modtype))
+
+
+if __name__ == "__main__":
+    input_file = sys.argv[1]
+    if len(sys.argv) < 3:
+        output_file = input_file
+    else:
+        output_file = sys.argv[2]
+    print(
+        f"Fixing automatically generated pydantic file {input_file} "
+        f"and saving to {output_file}"
+    )
+    edit_pydantic(input_file, output_file)