Refactor content fields to content_url and add metadata fields

Replaces 'content' with 'content_url' in Source and MappingSpecification classes and updates all related YAML and test files. Adds 'metadata_url' and 'metadata_type' fields to Source for improved metadata handling.

Author: matentzn

src/fair_mappings_schema/datamodel/fair_mappings_schema.py

@@ -1,5 +1,5 @@
 # Auto generated from fair_mappings_schema.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-10-06T23:07:21
+# Generation date: 2025-10-06T23:29:58
 # Schema: fair-mappings-schema
 #
 # id: https://w3id.org/mapping-commons/fair-mappings-schema
@@ -218,8 +218,10 @@ class Source(YAMLRoot):
     version: Optional[str] = None
     type: Optional[Union[str, "SourceTypeEnum"]] = None
     documentation: Optional[str] = None
-    content: Optional[str] = None
+    content_url: Optional[str] = None
     content_type: Optional[str] = None
+    metadata_url: Optional[str] = None
+    metadata_type: Optional[str] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self.id is not None and not isinstance(self.id, str):
@@ -237,12 +239,18 @@ def __post_init__(self, *_: str, **kwargs: Any):
         if self.documentation is not None and not isinstance(self.documentation, str):
             self.documentation = str(self.documentation)
 
-        if self.content is not None and not isinstance(self.content, str):
-            self.content = str(self.content)
+        if self.content_url is not None and not isinstance(self.content_url, str):
+            self.content_url = str(self.content_url)
 
         if self.content_type is not None and not isinstance(self.content_type, str):
             self.content_type = str(self.content_type)
 
+        if self.metadata_url is not None and not isinstance(self.metadata_url, str):
+            self.metadata_url = str(self.metadata_url)
+
+        if self.metadata_type is not None and not isinstance(self.metadata_type, str):
+            self.metadata_type = str(self.metadata_type)
+
         super().__post_init__(**kwargs)
 
 
@@ -271,7 +279,7 @@ class MappingSpecification(YAMLRoot):
     type: Optional[Union[str, "MappingSpecificationTypeEnum"]] = None
     mapping_method: Optional[str] = None
     documentation: Optional[str] = None
-    content: Optional[str] = None
+    content_url: Optional[str] = None
     subject_source: Optional[Union[dict, Source]] = None
     object_source: Optional[Union[dict, Source]] = None
 
@@ -312,8 +320,8 @@ def __post_init__(self, *_: str, **kwargs: Any):
         if self.documentation is not None and not isinstance(self.documentation, str):
             self.documentation = str(self.documentation)
 
-        if self.content is not None and not isinstance(self.content, str):
-            self.content = str(self.content)
+        if self.content_url is not None and not isinstance(self.content_url, str):
+            self.content_url = str(self.content_url)
 
         if self.subject_source is not None and not isinstance(self.subject_source, Source):
             self.subject_source = Source(**as_dict(self.subject_source))
@@ -372,6 +380,12 @@ class MappingSpecificationTypeEnum(EnumDefinitionImpl):
     sparql = PermissibleValue(
         text="sparql",
         description="SPARQL-based mapping")
+    yarrrml = PermissibleValue(
+        text="yarrrml",
+        description="YARRRML mapping file")
+    xslt = PermissibleValue(
+        text="xslt",
+        description="XSLT-based mapping")
     other = PermissibleValue(
         text="other",
         description="Other type of mapping specification")
@@ -424,12 +438,18 @@ class slots:
 slots.documentation = Slot(uri=FAIR_MAPPINGS_SCHEMA.documentation, name="documentation", curie=FAIR_MAPPINGS_SCHEMA.curie('documentation'),
                    model_uri=FAIR_MAPPINGS_SCHEMA.documentation, domain=None, range=Optional[str])
 
-slots.content = Slot(uri=FAIR_MAPPINGS_SCHEMA.content, name="content", curie=FAIR_MAPPINGS_SCHEMA.curie('content'),
-                   model_uri=FAIR_MAPPINGS_SCHEMA.content, domain=None, range=Optional[str])
+slots.content_url = Slot(uri=FAIR_MAPPINGS_SCHEMA.content_url, name="content_url", curie=FAIR_MAPPINGS_SCHEMA.curie('content_url'),
+                   model_uri=FAIR_MAPPINGS_SCHEMA.content_url, domain=None, range=Optional[str])
 
 slots.content_type = Slot(uri=FAIR_MAPPINGS_SCHEMA.content_type, name="content_type", curie=FAIR_MAPPINGS_SCHEMA.curie('content_type'),
                    model_uri=FAIR_MAPPINGS_SCHEMA.content_type, domain=None, range=Optional[str])
 
+slots.metadata_url = Slot(uri=FAIR_MAPPINGS_SCHEMA.metadata_url, name="metadata_url", curie=FAIR_MAPPINGS_SCHEMA.curie('metadata_url'),
+                   model_uri=FAIR_MAPPINGS_SCHEMA.metadata_url, domain=None, range=Optional[str])
+
+slots.metadata_type = Slot(uri=FAIR_MAPPINGS_SCHEMA.metadata_type, name="metadata_type", curie=FAIR_MAPPINGS_SCHEMA.curie('metadata_type'),
+                   model_uri=FAIR_MAPPINGS_SCHEMA.metadata_type, domain=None, range=Optional[str])
+
 slots.subject_source = Slot(uri=FAIR_MAPPINGS_SCHEMA.subject_source, name="subject_source", curie=FAIR_MAPPINGS_SCHEMA.curie('subject_source'),
                    model_uri=FAIR_MAPPINGS_SCHEMA.subject_source, domain=None, range=Optional[Union[dict, Source]])
 

src/fair_mappings_schema/datamodel/fair_mappings_schema_pydantic.py

@@ -82,7 +82,7 @@ def __contains__(self, key:str) -> bool:
                              'prefix_reference': 'http://schema.org/'}},
      'see_also': ['https://mapping-commons.github.io/fair-mappings-schema'],
      'source_file': 'src/fair_mappings_schema/schema/fair_mappings_schema.yaml',
-     'title': 'fair-mappings-schema'} )
+     'title': 'FAIR Mappings Schema'} )
 
 class SourceTypeEnum(str, Enum):
     """
@@ -138,6 +138,14 @@ class MappingSpecificationTypeEnum(str, Enum):
     """
     SPARQL-based mapping
     """
+    yarrrml = "yarrrml"
+    """
+    YARRRML mapping file
+    """
+    xslt = "xslt"
+    """
+    XSLT-based mapping
+    """
     other = "other"
     """
     Other type of mapping specification
@@ -221,8 +229,10 @@ class Source(ConfiguredBaseModel):
          'domain_of': ['Software', 'Source', 'MappingSpecification']} })
     type: Optional[SourceTypeEnum] = Field(default=None, description="""Type of the information entity""", json_schema_extra = { "linkml_meta": {'alias': 'type', 'domain_of': ['Agent', 'Source', 'MappingSpecification']} })
     documentation: Optional[str] = Field(default=None, description="""URL or reference to documentation for the mapping specification""", json_schema_extra = { "linkml_meta": {'alias': 'documentation', 'domain_of': ['Source', 'MappingSpecification']} })
-    content: Optional[str] = Field(default=None, description="""Reference to the actual content of the digital object""", json_schema_extra = { "linkml_meta": {'alias': 'content', 'domain_of': ['Source', 'MappingSpecification']} })
+    content_url: Optional[str] = Field(default=None, description="""Reference to the actual content of the digital object""", json_schema_extra = { "linkml_meta": {'alias': 'content_url', 'domain_of': ['Source', 'MappingSpecification']} })
     content_type: Optional[str] = Field(default=None, description="""The type of the content of the digital object""", json_schema_extra = { "linkml_meta": {'alias': 'content_type', 'domain_of': ['Source']} })
+    metadata_url: Optional[str] = Field(default=None, description="""Reference to metadata about the digital object""", json_schema_extra = { "linkml_meta": {'alias': 'metadata_url', 'domain_of': ['Source']} })
+    metadata_type: Optional[str] = Field(default=None, description="""The type of the metadata about the digital object""", json_schema_extra = { "linkml_meta": {'alias': 'metadata_type', 'domain_of': ['Source']} })
 
 
 class MappingSpecification(ConfiguredBaseModel):
@@ -247,7 +257,7 @@ class MappingSpecification(ConfiguredBaseModel):
     type: Optional[MappingSpecificationTypeEnum] = Field(default=None, description="""Type of the information entity""", json_schema_extra = { "linkml_meta": {'alias': 'type', 'domain_of': ['Agent', 'Source', 'MappingSpecification']} })
     mapping_method: Optional[str] = Field(default=None, description="""Method used to create the mapping specification""", json_schema_extra = { "linkml_meta": {'alias': 'mapping_method', 'domain_of': ['MappingSpecification']} })
     documentation: Optional[str] = Field(default=None, description="""URL or reference to documentation for the mapping specification""", json_schema_extra = { "linkml_meta": {'alias': 'documentation', 'domain_of': ['Source', 'MappingSpecification']} })
-    content: Optional[str] = Field(default=None, description="""Reference to the actual content of the digital object""", json_schema_extra = { "linkml_meta": {'alias': 'content', 'domain_of': ['Source', 'MappingSpecification']} })
+    content_url: Optional[str] = Field(default=None, description="""Reference to the actual content of the digital object""", json_schema_extra = { "linkml_meta": {'alias': 'content_url', 'domain_of': ['Source', 'MappingSpecification']} })
     subject_source: Optional[Source] = Field(default=None, description="""The source from which the subject entities are drawn""", json_schema_extra = { "linkml_meta": {'alias': 'subject_source', 'domain_of': ['MappingSpecification']} })
     object_source: Optional[Source] = Field(default=None, description="""The source from which the object entities are drawn""", json_schema_extra = { "linkml_meta": {'alias': 'object_source', 'domain_of': ['MappingSpecification']} })
 

src/fair_mappings_schema/schema/fair_mappings_schema.yaml

@@ -102,8 +102,10 @@ classes:
       - version
       - type
       - documentation
-      - content
+      - content_url
       - content_type
+      - metadata_url
+      - metadata_type
     slot_usage:
       type:
         range: SourceTypeEnum
@@ -125,7 +127,7 @@ classes:
       - type
       - mapping_method
       - documentation
-      - content
+      - content_url
       - subject_source
       - object_source
     slot_usage:
@@ -176,12 +178,18 @@ slots:
   documentation:
     description: URL or reference to documentation for the mapping specification
     range: string
-  content:
+  content_url:
     description: Reference to the actual content of the digital object
     range: string
   content_type:
     description: The type of the content of the digital object
     range: string
+  metadata_url:
+    description: Reference to metadata about the digital object
+    range: string
+  metadata_type:
+    description: The type of the metadata about the digital object
+    range: string
   subject_source:
     description: The source from which the subject entities are drawn
     range: Source

tests/data/valid/MappingSpecification-001.yaml

@@ -7,18 +7,18 @@ description: Mappings between disease ontologies DO and MONDO
 type: sssom
 mapping_method: manual curation
 documentation: https://example.org/do-mondo-mappings/docs
-content: https://example.org/mappings/do-mondo.sssom.tsv
+content_url: https://example.org/mappings/do-mondo.sssom.tsv
 subject_source:
   name: Disease Ontology
   version: "2024-01-01"
   type: owl_ontology
   documentation: https://disease-ontology.org/
-  content: http://purl.obolibrary.org/obo/doid.owl
+  content_url: http://purl.obolibrary.org/obo/doid.owl
   content_type: application/rdf+xml
 object_source:
   name: Mondo Disease Ontology
   version: "2024-01-10"
   type: owl_ontology
   documentation: https://mondo.monarchinitiative.org/
-  content: http://purl.obolibrary.org/obo/mondo.owl
+  content_url: http://purl.obolibrary.org/obo/mondo.owl
   content_type: application/rdf+xml

tests/data/valid/MappingSpecification-002.yaml

@@ -8,18 +8,18 @@ description: R2RML mapping from legacy patient database to FHIR RDF
 type: r2rml
 mapping_method: automated generation with manual review
 documentation: https://example.org/patient-fhir-mapping
-content: https://example.org/mappings/patient-db-to-fhir.r2rml.ttl
+content_url: https://example.org/mappings/patient-db-to-fhir.r2rml.ttl
 subject_source:
   name: Patient Database
   version: "v5.2"
   type: database
   documentation: https://example.org/db-schema
-  content: postgresql://example.org:5432/patients
+  content_url: postgresql://example.org:5432/patients
   content_type: application/sql
 object_source:
   name: FHIR RDF Ontology
   version: "4.0.1"
   type: rdf_vocabulary
   documentation: http://hl7.org/fhir/
-  content: http://hl7.org/fhir/fhir.ttl
+  content_url: http://hl7.org/fhir/fhir.ttl
   content_type: text/turtle

tests/data/valid/MappingSpecification-003.yaml

@@ -1,11 +1,11 @@
 # Valid MappingSpecification example - minimal required fields only
 ---
-content: https://example.org/minimal-mapping.txt
+content_url: https://example.org/minimal-mapping.txt
 subject_source:
   name: Source A
-  content: https://example.org/source-a
+  content_url: https://example.org/source-a
   content_type: text/plain
 object_source:
   name: Source B
-  content: https://example.org/source-b
+  content_url: https://example.org/source-b
   content_type: text/plain