Initialise git with minimal project

Author: RobertJCarroll

src/include_access_model/datamodel/include_access_model.py

@@ -1,5 +1,5 @@
 # Auto generated from include_access_model.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-11-10T19:04:46
+# Generation date: 2025-11-10T19:22:06
 # Schema: include-access-model
 #
 # id: https://includedcc.org/include-access-model
@@ -103,6 +103,10 @@ class InvestigatorId(RecordId):
     pass
 
 
+class PublicationId(RecordId):
+    pass
+
+
 @dataclass(repr=False)
 class Record(YAMLRoot):
     """
@@ -170,7 +174,7 @@ class Study(Record):
     vbr: Optional[Union[str, VirtualBiorepositoryId]] = None
     selection_criteria: Optional[str] = None
     website: Optional[Union[str, URI]] = None
-    publication: Optional[Union[Union[dict, "Publication"], list[Union[dict, "Publication"]]]] = empty_list()
+    publication: Optional[Union[Union[str, PublicationId], list[Union[str, PublicationId]]]] = empty_list()
     acknowledgments: Optional[str] = None
     citation_statement: Optional[str] = None
 
@@ -274,7 +278,7 @@ def __post_init__(self, *_: str, **kwargs: Any):
 
         if not isinstance(self.publication, list):
             self.publication = [self.publication] if self.publication is not None else []
-        self.publication = [v if isinstance(v, Publication) else Publication(**as_dict(v)) for v in self.publication]
+        self.publication = [v if isinstance(v, PublicationId) else PublicationId(v) for v in self.publication]
 
         if self.acknowledgments is not None and not isinstance(self.acknowledgments, str):
             self.acknowledgments = str(self.acknowledgments)
@@ -405,7 +409,7 @@ def __post_init__(self, *_: str, **kwargs: Any):
 
 
 @dataclass(repr=False)
-class Publication(YAMLRoot):
+class Publication(Record):
     """
     Information about a specific publication.
     """
@@ -416,10 +420,17 @@ class Publication(YAMLRoot):
     class_name: ClassVar[str] = "Publication"
     class_model_uri: ClassVar[URIRef] = INCLUDEDCC.Publication
 
+    id: Union[str, PublicationId] = None
+    uuid: str = None
     bibliographic_reference: Optional[str] = None
     website: Optional[Union[str, URI]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
+        if self._is_empty(self.id):
+            self.MissingRequiredField("id")
+        if not isinstance(self.id, PublicationId):
+            self.id = PublicationId(self.id)
+
         if self.bibliographic_reference is not None and not isinstance(self.bibliographic_reference, str):
             self.bibliographic_reference = str(self.bibliographic_reference)
 
@@ -724,7 +735,7 @@ class slots:
                    model_uri=INCLUDEDCC.clinical_data_source_type, domain=None, range=Union[Union[str, "EnumClinicalDataSourceType"], list[Union[str, "EnumClinicalDataSourceType"]]])
 
 slots.publication = Slot(uri=INCLUDEDCC.publication, name="publication", curie=INCLUDEDCC.curie('publication'),
-                   model_uri=INCLUDEDCC.publication, domain=None, range=Optional[Union[Union[dict, Publication], list[Union[dict, Publication]]]])
+                   model_uri=INCLUDEDCC.publication, domain=None, range=Optional[Union[Union[str, PublicationId], list[Union[str, PublicationId]]]])
 
 slots.expected_number_of_participants = Slot(uri=INCLUDEDCC.expected_number_of_participants, name="expected_number_of_participants", curie=INCLUDEDCC.curie('expected_number_of_participants'),
                    model_uri=INCLUDEDCC.expected_number_of_participants, domain=None, range=int)

src/include_access_model/datamodel/include_access_model_pydantic.py

@@ -260,7 +260,7 @@ class Study(Record):
     clinical_data_source_type: list[EnumClinicalDataSourceType] = Field(default=..., title="Clinical Data Source Type", description="""Source(s) of data collected from study participants""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} })
     data_category: list[EnumDataCategory] = Field(default=..., title="Data Category", description="""General category of data in this Record (e.g. Clinical, Genomics, etc)""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} })
     website: Optional[str] = Field(default=None, title="Website", description="""Website for the Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'VirtualBiorepository', 'Publication']} })
-    publication: Optional[list[Publication]] = Field(default=[], title="Publication", description="""Publications associated with this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} })
+    publication: Optional[list[str]] = Field(default=[], title="Publication", description="""Publications associated with this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} })
     expected_number_of_participants: int = Field(default=..., title="Expected Number of Participants", description="""Total expected number of participants to be recruited.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} })
     actual_number_of_participants: int = Field(default=..., title="Actual Number of Participants", description="""Total participants included at this time.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} })
     acknowledgments: Optional[str] = Field(default=None, title="Acknowledgments", description="""Funding statement and acknowledgments for this study""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study']} })
@@ -317,7 +317,7 @@ class Investigator(Record):
     external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} })
 
 
-class Publication(ConfiguredBaseModel):
+class Publication(Record):
     """
     Information about a specific publication.
     """
@@ -326,6 +326,9 @@ class Publication(ConfiguredBaseModel):
 
     bibliographic_reference: Optional[str] = Field(default=None, title="Bibiliographic Reference", description="""Text use to reference this Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['DOI', 'Publication']} })
     website: Optional[str] = Field(default=None, title="Website", description="""Website for the Record.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Study', 'VirtualBiorepository', 'Publication']} })
+    uuid: str = Field(default=..., title="UUID", description="""Internally assigned UUID for data management and QC purposes""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} })
+    id: str = Field(default=..., title="ID", description="""INLCUDE Global ID for this record""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} })
+    external_id: Optional[list[str]] = Field(default=[], title="External Identifiers", description="""Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP""", json_schema_extra = { "linkml_meta": {'domain_of': ['Record']} })
 
 
 # Model rebuild

src/include_access_model/schema/include_access_model.yaml

@@ -104,6 +104,7 @@ classes:
   Publication:
     title: Publication
     description: Information about a specific publication.
+    is_a: Record
     #Could add more here
     slots:
       - bibliographic_reference

tests/data/valid/Record-000.yaml

@@ -0,0 +1,2 @@
+uuid: e9d804b4-9d51-4c82-be25-876839de744e
+id: 000