Add pydantic model gen; improve schema

Schema
- add slot: pid_schema_version
- fix: Make ResourceInfo single-valued
- style: Gave enums singular name

Makefile

@@ -104,7 +104,8 @@ gen-examples:
 
 gen-project: $(PYMODEL)
 	$(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
-
+	# addition vs. template
+	$(RUN) gen-pydantic --pydantic_version 2 $(SOURCE_SCHEMA_PATH) > $(PYMODEL)/pid4cat_model_pydantic.py
 
 test: test-schema test-python test-examples
 

config.yaml

@@ -24,6 +24,9 @@ generator_args:
     mergeimports: true
   python:
     mergeimports: true
+  pydantic:
+    mergeimports: true
+    pydantic-version: 2
   prefixmap:
     mergeimports: true
   proto:

explore_pydantic.py

@@ -0,0 +1,48 @@
+from linkml_runtime.dumpers import json_dumper, yaml_dumper
+from pid4cat_model.datamodel import pid4cat_model_pydantic as p4c
+
+p1_Agent = p4c.Agent(
+    name="Data Fuzzi",
+    contact_information=None,
+    person_orcid="0000-0000-0000-0000",
+    affiliation_ror=None,
+    role=p4c.PID4CatAgentRole.TRUSTEE,
+)
+
+p1_log = p4c.LogRecord(
+    datetime_log="2024-02-19T00:00:00Z",
+    has_agent=p1_Agent,
+    changed_field=p4c.ChangeLogField.STATUS,
+    description="as requested in issue #123",
+)
+
+p1_ressource_info = p4c.ResourceInfo(
+    label="Resource label",
+    description="Resource description",
+    resource_category=p4c.ResourceCategory.SAMPLE,
+    rdf_url="https://example.org/resource",
+    rdf_type="TURTLE",
+    schema_url="https://example.org/schema",
+    schema_type="XSD",
+)
+
+p1 = p4c.PID4CatRecord(
+    id="lik-123",
+    change_log=[p1_log],
+    landing_page_url="https://pid4cat.example.org/lik-123",
+    status=p4c.PID4CatStatus.REGISTERED,
+    pid_schema_version="0.1.0",
+    record_version="20240219v-0",
+    resource_info=p1_ressource_info,
+    related_identifiers=None,
+    dc_rights="CC0-1.0",
+    curation_contact="[email protected]",
+)
+
+c = p4c.Container(contains_pids=[p1])
+
+print(p1)
+
+print(json_dumper.dumps(p1))
+
+print(yaml_dumper.dumps(c))

explore_python.py

@@ -0,0 +1,34 @@
+from linkml_runtime.dumpers import json_dumper
+from pid4cat_model.datamodel import pid4cat_model as p4c
+
+
+p1_Agent = p4c.Agent(
+    person_orcid="0000-0000-0000-0000",
+    name="Data Fuzzi",
+    role="TRUSTEE",
+)
+
+p1_log = p4c.LogRecord(
+    datetime_log="2024-02-19T00:00:00Z",
+    has_agent=p1_Agent,
+    changed_field=p4c.ChangeLogField.STATUS,  # "STATUS",
+    description="as requested in issue #123",
+)
+
+p1 = p4c.PID4CatRecord(
+    id="lik-1",
+    change_log=p1_log,
+    landing_page_url="https://pid4cat.example.org/lik-1",
+    status=p4c.PID4CatStatus.REGISTERED,  # "REGISTERED",
+    record_version="20240219v-0",
+    resource_info={},
+    related_identifiers=None,
+    dc_rights="CC0-1.0",
+    curation_contact="[email protected]",
+)
+
+print(p1)
+
+print(json_dumper.dumps(p1))
+
+c = p4c.Container(contains_pids=[p1])

project/graphql/pid4cat_model.graphql

@@ -4,14 +4,19 @@ type Agent
     contactInformation: String
     personOrcid: String
     affiliationRor: String
-    role: PID4CatAgentRoles
+    role: PID4CatAgentRole
+  }
+
+type Container
+  {
+    containsPids: [PID4CatRecord]
   }
 
 type LogRecord
   {
     datetimeLog: String
-    agent: Agent
-    changedField: ChangeLogFields
+    hasAgent: Agent
+    changedField: ChangeLogField
     description: String
   }
 
@@ -20,26 +25,28 @@ type PID4CatRecord
     id: Uriorcurie!
     landingPageUrl: String
     status: PID4CatStatus
-    resourceInfo: [ResourceInfo]
-    relatedIdentifiers: [Uriorcurie]
+    recordVersion: String
+    pidSchemaVersion: String
     dcRights: String
     curationContact: String
+    resourceInfo: ResourceInfo
+    relatedIdentifiers: [Uriorcurie]
     changeLog: [LogRecord]!
   }
 
 type PID4CatRelation
   {
-    relationType: [RelationTypes]
+    relationType: [RelationType]
     relatedIdentifier: String
     datetimeLog: String
-    agent: Agent
+    hasAgent: Agent
   }
 
 type ResourceInfo
   {
     label: String
     description: String
-    resourceCategory: ResourceCategories
+    resourceCategory: ResourceCategory
     rdfUrl: String
     rdfType: String
     schemaUrl: String

project/jsonld/pid4cat_model.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2023-12-07T18:08:50",
+      "generation_date": "2024-02-25T23:40:28",
       "source": "pid4cat_model.yaml"
    },
    "@context": {
@@ -16,10 +16,6 @@
       "affiliation_ror": {
          "@id": "schema:identifier"
       },
-      "agent": {
-         "@type": "@id",
-         "@id": "schema:Agent"
-      },
       "change_log": {
          "@type": "@id",
          "@id": "schema:identifier"
@@ -36,6 +32,9 @@
       "contact_information": {
          "@id": "schema:email"
       },
+      "contains_pids": {
+         "@type": "@id"
+      },
       "curation_contact": {
          "@id": "schema:email"
       },
@@ -48,6 +47,10 @@
       "description": {
          "@id": "schema:description"
       },
+      "has_agent": {
+         "@type": "@id",
+         "@id": "schema:Agent"
+      },
       "id": "@id",
       "label": {
          "@id": "schema:name"
@@ -61,12 +64,18 @@
       "person_orcid": {
          "@id": "schema:identifier"
       },
+      "pid_schema_version": {
+         "@id": "schema:identifier"
+      },
       "rdf_type": {
          "@id": "schema:additionalType"
       },
       "rdf_url": {
          "@id": "schema:additionalType"
       },
+      "record_version": {
+         "@id": "schema:identifier"
+      },
       "related_identifier": {
          "@id": "schema:identifier"
       },