property is added to the schema through count references transformati…

…on (#79) * property is added to the schema through count references transformation
ghga-de · Sep 3, 2024 · f8e543a · f8e543a
1 parent 080432e
commit f8e543a
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Showing 6 changed files with 40 additions and 54 deletions.
diff --git a/src/metldata/builtin_transformations/add_content_properties/model_transform.py b/src/metldata/builtin_transformations/add_content_properties/model_transform.py
@@ -47,7 +47,7 @@ def add_content_properties(
 
         for cls_instruction in cls_instructions:
             try:
-                target_object = resolve_schema_object_path(
+                target_schema = resolve_schema_object_path(
                     content_schema, cls_instruction.target_content.object_path
                 )
             except KeyError as e:
@@ -58,12 +58,12 @@ def add_content_properties(
             ):
                 raise EvitableTransformationError()
 
-            target_object.setdefault("properties", {})[
+            target_schema.setdefault("properties", {})[
                 cls_instruction.target_content.property_name
             ] = deepcopy(cls_instruction.content_schema)
 
             if cls_instruction.required:
-                target_object.setdefault("required", []).append(
+                target_schema.setdefault("required", []).append(
                     cls_instruction.target_content.property_name
                 )
 

diff --git a/src/metldata/builtin_transformations/count_references/assumptions.py b/src/metldata/builtin_transformations/count_references/assumptions.py
@@ -165,10 +165,8 @@ def assert_object_path_exists(
             + f" in class {class_name}."
         ) from exc
 
-    # Check if the propert_name already exists in the model
-    if instruction.target_content.property_name not in target_schema.get(
-        "properties", {}
-    ):
+    # Check if the propert_name already exists in the model and raise an error if so
+    if instruction.target_content.property_name in target_schema.get("properties", {}):
         raise ModelAssumptionError(
             f"Property {
                 instruction.target_content.property_name} does not exist"

diff --git a/src/metldata/builtin_transformations/count_references/model_transform.py b/src/metldata/builtin_transformations/count_references/model_transform.py
@@ -15,6 +15,7 @@
 """Model transformation logic for the 'count references' transformation"""
 
 from schemapack.spec.schemapack import (
+    ClassDefinition,
     SchemaPack,
 )
 
@@ -26,16 +27,18 @@
 )
 from metldata.transform.base import EvitableTransformationError
 
+DEFAULT_PROPERTY_SCHEMA = {"type": "integer"}
+
 
 def add_count_references(
     *,
     model: SchemaPack,
     instructions_by_class: dict[str, list[AddReferenceCountPropertyInstruction]],
 ) -> SchemaPack:
-    """The content properties are added to the model with the 'add_content_properties
-    step of the workflow. Thus, this function applies no transformation.
-    It only checks for EvitableTransformationError.
+    """The target content - object_names are added to the model with the 'add_content_properties
+    step of the workflow. Thus, this function only adds the property_name to a content schema.
     """
+    updated_class_defs: dict[str, ClassDefinition] = {}
     for class_name, cls_instructions in instructions_by_class.items():
         class_def = model.classes.get(class_name)
 
@@ -45,15 +48,24 @@ def add_count_references(
         content_schema = class_def.content.json_schema_dict
 
         for cls_instruction in cls_instructions:
+            object_path = cls_instruction.target_content.object_path
+            property_name = cls_instruction.target_content.property_name
             try:
-                resolve_schema_object_path(
-                    content_schema, cls_instruction.target_content.object_path
-                )
-            except KeyError as e:
-                raise EvitableTransformationError() from e
-
-            if cls_instruction.target_content.property_name in content_schema.get(
-                "properties", {}
-            ):
+                target_schema = resolve_schema_object_path(content_schema, object_path)
+            except KeyError as exc:
+                raise EvitableTransformationError() from exc
+
+            if property_name in target_schema.get("properties", {}):
                 raise EvitableTransformationError()
-    return model
+
+            target_schema.setdefault("properties", {})[property_name] = (
+                DEFAULT_PROPERTY_SCHEMA
+            )
+
+        updated_class_defs[class_name] = class_def.model_validate(
+            {**class_def.model_dump(), "content": content_schema}
+        )
+
+    model_dict = model.model_dump()
+    model_dict["classes"].update(updated_class_defs)
+    return SchemaPack.model_validate(model_dict)
diff --git a/tests/fixtures/example_transformations/count_references/multiple/input.datapack.yaml b/tests/fixtures/example_transformations/count_references/multiple/input.datapack.yaml
@@ -23,8 +23,7 @@ resources:
     dataset_1:
       content:
         dac_contact: dac@example.org
-        file_summary: # <-
-          count: 0
+        file_summary: {} # <-
       relations:
         files:
           - file_a
@@ -34,24 +33,21 @@ resources:
     sample_x:
       content:
         description: Some sample.
-        file_summary: # <-
-          count: 0
+        file_summary: {} # <-
       relations:
         files:
           - file_a
           - file_b
     sample_y:
       content:
-        file_summary: # <-
-          count: 0
+        file_summary: {} # <-
       relations:
         files:
           - file_c
   Experiment:
     experiment_i:
       content:
-        sample_summary: # <-
-          count: 0
+        sample_summary: {} # <-
       relations:
         samples:
           - sample_x

diff --git a/tests/fixtures/example_transformations/count_references/multiple/input.schemapack.yaml b/tests/fixtures/example_transformations/count_references/multiple/input.schemapack.yaml
@@ -16,13 +16,7 @@ classes:
         "properties":
           {
             "dac_contact": { "type": "string" },
-            "file_summary":
-              {
-                "type": "object",
-                "additionalProperties": false,
-                "properties": { "count": { "type": "integer" } },
-                "required": ["count"],
-              },
+            "file_summary": { "type": "object", "additionalProperties": true },
           },
         "type": "object",
       }
@@ -46,13 +40,7 @@ classes:
         "properties":
           {
             "description": { "type": "string" },
-            "file_summary":
-              {
-                "type": "object",
-                "additionalProperties": false,
-                "properties": { "count": { "type": "integer" } },
-                "required": ["count"],
-              },
+            "file_summary": { "type": "object", "additionalProperties": true },
           },
         "type": "object",
       }
@@ -77,12 +65,7 @@ classes:
           {
             "description": { "type": "string" },
             "sample_summary":
-              {
-                "type": "object",
-                "additionalProperties": false,
-                "properties": { "count": { "type": "integer" } },
-                "required": ["count"],
-              },
+              { "type": "object", "additionalProperties": true },
           },
         "type": "object",
       }

diff --git a/tests/fixtures/example_transformations/count_references/multiple/transformed.schemapack.yaml b/tests/fixtures/example_transformations/count_references/multiple/transformed.schemapack.yaml
@@ -19,9 +19,8 @@ classes:
             "file_summary":
               {
                 "type": "object",
-                "additionalProperties": false,
+                "additionalProperties": true,
                 "properties": { "count": { "type": "integer" } },
-                "required": ["count"],
               },
           },
         "type": "object",
@@ -49,9 +48,8 @@ classes:
             "file_summary":
               {
                 "type": "object",
-                "additionalProperties": false,
+                "additionalProperties": true,
                 "properties": { "count": { "type": "integer" } },
-                "required": ["count"],
               },
           },
         "type": "object",
@@ -79,9 +77,8 @@ classes:
             "sample_summary":
               {
                 "type": "object",
-                "additionalProperties": false,
+                "additionalProperties": true,
                 "properties": { "count": { "type": "integer" } },
-                "required": ["count"],
               },
           },
         "type": "object",