Gen3SchemaDev 2.3.4__tar.gz → 2.3.6__tar.gz

{gen3schemadev-2.3.4 → gen3schemadev-2.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Gen3SchemaDev
-Version: 2.3.4
+Version: 2.3.6
 Summary: Tool for data modelling in Gen3
 License: Apache 2.0
 License-File: LICENSE

{gen3schemadev-2.3.4 → gen3schemadev-2.3.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "Gen3SchemaDev"
-version = "2.3.4"
+version = "2.3.6"
 description = "Tool for data modelling in Gen3"
 authors = [
     {name = "JoshuaHarris391",email = "harjo391@gmail.com"}

{gen3schemadev-2.3.4 → gen3schemadev-2.3.6}/src/gen3schemadev/converter.py

@@ -307,6 +307,10 @@ def create_link_prop(target_node: str, multiplicity: str) -> dict:
     """
     Create a property dictionary for a link to another node.
 
+    Links targeting 'project' use the special 'to_one_project' / 'to_many_project'
+    definitions because the project foreign key is identified by 'id' or 'code'
+    (foreign_key_project), not the standard 'id' or 'submitter_id' (foreign_key).
+
     Args:
         target_node: The name of the target node.
         multiplicity: The multiplicity of the link (e.g., 'one_to_one', 'one_to_many').
@@ -314,9 +318,14 @@ def create_link_prop(target_node: str, multiplicity: str) -> dict:
     Returns:
         A dictionary representing the link property for the schema.
     """
+    formatted = format_multiplicity(multiplicity)
+    if target_node == "project":
+        ref = f"_definitions.yaml#/{formatted}_project"
+    else:
+        ref = f"_definitions.yaml#/{formatted}"
     link_prop = {
         link_suffix(target_node): {
-            "$ref": f"_definitions.yaml#/{format_multiplicity(multiplicity)}"
+            "$ref": ref
         }
     }
     return link_prop
@@ -623,21 +632,20 @@ def construct_props(node_name: str, data: DataSourceProtocol) -> dict:
 
     # if it's an Enum, add the enum values
     if category == "data_file":
-        props_dict['core_metadata_collections'] = {"$ref": "_definitions.yaml#/to_one"}
         props_dict['$ref'] = "_definitions.yaml#/data_file_properties"
-
-        props_dict['data_category'] = {
+        props_dict.setdefault('core_metadata_collections', {"$ref": "_definitions.yaml#/to_one"})
+        props_dict.setdefault('data_category', {
             "description": "Broad categorization of the contents of the data file.",
             "enum": ['data_category_1', 'data_category_2', 'data_category_3']
-        }
-        props_dict['data_format'] = {
+        })
+        props_dict.setdefault('data_format', {
             "description": "The format of the data in this data file",
             "enum": ['data_format_1', 'data_format_2', 'data_format_3']
-        }
-        props_dict['data_type'] = {
+        })
+        props_dict.setdefault('data_type', {
             "description": "The type of data in this data file",
             "enum": ['data_type_1', 'data_type_2', 'data_type_3']
-        }
+        })
 
     return props_dict
 

{gen3schemadev-2.3.4 → gen3schemadev-2.3.6}/src/gen3schemadev/validators/rule_validator.py

@@ -17,6 +17,7 @@ class RuleValidator:
         self.type_array_needs_items()
         self.core_metadata_required_link()
         self.data_file_props_need_data_props()
+        self.project_must_require_code()
 
     def _get_links(self):
         links = self.schema.get("links", [])
@@ -239,6 +240,22 @@ class RuleValidator:
         return True
 
 
+    def project_must_require_code(self):
+        """If the schema is for the project node (id: project),
+        then 'code' must be in the required list. Gen3 uses 'code'
+        as the unique project identifier.
+        """
+        if self.schema.get('id', '') != 'project':
+            return True
+
+        required = self.schema.get('required', [])
+        if 'code' not in required:
+            raise ValueError(
+                f"Schema 'project' must include 'code' in the 'required' list. "
+                f"Please add 'code' to the 'required' section."
+            )
+        return True
+
     def core_metadata_required_link(self):
         """Core metadata collection schema needs at least one required link
         """