Align model serialisation to handle api

.github/workflows/main.yaml

@@ -11,7 +11,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        # python-version: ["3.9", "3.10", "3.11", "3.12"]  # re-enable when linkml-runtime has https://github.com/linkml/linkml-runtime/pull/357
+        python-version: ["3.11", "3.12"]
       fail-fast: false
 
     steps:

.linkmllint.yaml

@@ -3,3 +3,6 @@ extends: recommended
 rules:
   standard_naming:
     permissible_values_upper_case: true
+  canonical_prefixes:
+    # Superfluous warnings for https-refixes, https://github.com/linkml/linkml/issues/2492
+    level: disabled

Makefile

@@ -150,7 +150,7 @@ test-schema:
 	$(RUN) gen-project ${CONFIG_YAML} -d tmp $(SOURCE_SCHEMA_PATH)
 
 test-python:
-	$(RUN) python -m unittest discover
+	$(RUN) python -m pytest
 
 lint:
 	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH)

examples/PID4CatRecord-001.yaml

@@ -1,26 +1,86 @@
-# Example data object
----
 contains_pids:
-- id: lik-123
-  landing_page_url: https://pid4cat.example.org/lik-123
-  status: REGISTERED
-  pid_schema_version: 0.1.0
-  record_version: 20240219v-0
-  resource_info:
-    label: Resource label
-    description: Resource description
-    resource_category: SAMPLE
-    rdf_url: https://example.org/resource
-    rdf_type: TURTLE
-    schema_url: https://example.org/schema
-    schema_type: XSD
-  dc_rights: CC0-1.0
-  curation_contact: [email protected]
-  change_log:
-  - datetime_log: '2024-02-19T00:00:00Z'
-    has_agent:
-      name: Data Fuzzi
-      person_orcid: 0000-0000-0000-0000
-      role: TRUSTEE
-    changed_field: STATUS
-    description: 'as requested in issue #123'
+- responseCode: 1
+  handle: 21.T12995/lik-1
+  values:
+  - index: 1
+    type: URL
+    data:
+      format: string
+      value: https://pid4cat.example.org/lik-1
+    ttl: 86400
+    timestamp: '2024-05-15T15:51:15Z'
+  - index: 2
+    type: STATUS
+    data:
+      format: string
+      value: REGISTERED
+    ttl: 86400
+    timestamp: '2024-05-15T15:51:15Z'
+  - index: 3
+    type: SCHEMA_VER
+    data:
+      format: string
+      value: v0.1.0
+    ttl: 86400
+    timestamp: '2024-05-15T15:51:15Z'
+  - index: 4
+    type: LICENSE
+    data:
+      format: string
+      value: CC0-1.0
+    ttl: 86400
+    timestamp: '2024-05-15T15:51:15Z'
+  - index: 5
+    type: EMAIL
+    data:
+      format: string
+      value: [email protected]
+    ttl: 86400
+    timestamp: '2024-05-15T15:51:15Z'
+  - index: 6
+    type: RESOURCE_INFO
+    data:
+      format: string
+      value:
+      - resource_info:
+          label: Resource label
+          description: Resource description
+          resource_category: SAMPLE
+          representation_variants:
+          - url: https://example.org/resource
+            media_type: text/turtle
+            encoding_format: UTF-8
+            size: 12345
+    ttl: 86400
+    timestamp: '2024-05-15T15:51:15Z'
+  - index: 7
+    type: RELATED
+    data:
+      format: string
+      value:
+      - related_identifiers:
+        - relation_type: IS_PART_OF
+          related_identifier: https://example.org/collection
+          datetime_log: '2024-02-19T00:00:00Z'
+        - relation_type: IS_REFERENCED_BY
+          related_identifier: https://example.org/referenced
+          datetime_log: '2024-02-19T00:00:00Z'
+    ttl: 86400
+    timestamp: '2024-05-15T15:51:15Z'
+  - index: 8
+    type: LOG
+    data:
+      format: string
+      value:
+      - change_log:
+        - datetime_log: '2024-02-19T00:00:00Z'
+          has_agent:
+            name: Data Fuzzi
+            email: [email protected]
+            orcid: 0000-0000-0000-0000
+            affiliation_ror: https://ror.org/029hg0311
+            role: TRUSTEE
+          changed_field: STATUS
+          description: 'as requested in issue #123'
+    ttl: 86400
+    timestamp: '2024-05-15T15:51:15Z'

examples/example_p1.json

@@ -1,60 +1,91 @@
 {
-  "id": "lik-1",
-  "landing_page_url": "https://pid4cat.example.org/lik-1",
-  "status": "REGISTERED",
-  "pid_schema_version": "0.1.0",
-  "license": "CC0-1.0",
-  "curation_contact_email": "[email protected]",
-  "resource_info": {
-    "label": "Resource label",
-    "description": "Resource description",
-    "resource_category": "SAMPLE",
-    "representation_variants": [
-      {
-        "url": "https://example.org/resource",
-        "media_type": "text/turtle",
-        "encoding_format": "UTF-8",
-        "size": 12345
-      }
-    ]
-  },
-  "related_identifiers": [
+  "contains_pids": [
     {
-      "relation_type": "IS_PART_OF",
-      "related_identifier": "https://example.org/collection",
-      "datetime_log": "2024-02-19T00:00:00+00:00"
-    },
-    {
-      "relation_type": "IS_REFERENCED_BY",
-      "related_identifier": "https://example.org/referenced",
-      "datetime_log": "2024-02-19T00:00:00+00:00"
-    }
-  ],
-  "change_log": [
-    {
-      "datetime_log": "2024-02-19T00:00:00+00:00",
-      "has_agent": {
-        "name": "Data Fuzzi",
-        "email": "[email protected]",
-        "orcid": "0000-0000-0000-0000",
-        "affiliation_ror": "https://ror.org/01abcde",
-        "role": "TRUSTEE"
-      },
-      "changed_field": "STATUS",
-      "description": "Registration completed."
-    },
-    {
-      "datetime_log": "2024-05-15T15:51:15+00:00",
-      "has_agent": {
-        "name": "Data Fuzzi",
-        "email": "[email protected]",
-        "orcid": "0000-0000-0000-0000",
-        "affiliation_ror": "https://ror.org/01abcde",
-        "role": "TRUSTEE"
-      },
-      "changed_field": "RESOURCE_INFO",
-      "description": "as requested in issue #234"
+      "responseCode": 1,
+      "handle": "21.T12995/lik-1",
+      "values": [
+        {
+          "index": 1,
+          "type": "URL",
+          "data": {
+            "format": "string",
+            "value": "https://pid4cat.example.org/lik-1"
+          },
+          "ttl": 86400,
+          "timestamp": "2024-05-15T15:51:15+00:00"
+        },
+        {
+          "index": 2,
+          "type": "STATUS",
+          "data": {
+            "format": "string",
+            "value": "PermissibleValue({\n  'text': 'REGISTERED',\n  'description': 'The PID4CatRecord links to a concrete resource.'\n})"
+          },
+          "ttl": 86400,
+          "timestamp": "2024-05-15T15:51:15+00:00"
+        },
+        {
+          "index": 3,
+          "type": "SCHEMA_VER",
+          "data": {
+            "format": "string",
+            "value": "v0.1.0"
+          },
+          "ttl": 86400,
+          "timestamp": "2024-05-15T15:51:15+00:00"
+        },
+        {
+          "index": 4,
+          "type": "LICENSE",
+          "data": {
+            "format": "string",
+            "value": "CC0-1.0"
+          },
+          "ttl": 86400,
+          "timestamp": "2024-05-15T15:51:15+00:00"
+        },
+        {
+          "index": 5,
+          "type": "EMAIL",
+          "data": {
+            "format": "string",
+            "value": "[email protected]"
+          },
+          "ttl": 86400,
+          "timestamp": "2024-05-15T15:51:15+00:00"
+        },
+        {
+          "index": 6,
+          "type": "RESOURCE_INFO",
+          "data": {
+            "format": "string",
+            "value": "ResourceInfo({\n  'label': 'Resource label',\n  'description': 'Resource description',\n  'resource_category': ResourceCategory(text='SAMPLE', description='A representative part of an entity of interest on which observations may be made.'),\n  'representation_variants': [RepresentationVariant({\n      'url': 'https://example.org/resource',\n      'media_type': 'text/turtle',\n      'encoding_format': 'UTF-8',\n      'size': 12345\n    })]\n})"
+          },
+          "ttl": 86400,
+          "timestamp": "2024-05-15T15:51:15+00:00"
+        },
+        {
+          "index": 7,
+          "type": "RELATED",
+          "data": {
+            "format": "string",
+            "value": "[PID4CatRelation({\n  'relation_type': RelationType(text='IS_PART_OF', description='The resource is part of another resource.', meaning='https://purl.org/dc/terms/isPartOf'),\n  'related_identifier': 'https://example.org/collection',\n  'datetime_log': '2024-02-19T00:00:00+00:00'\n}), PID4CatRelation({\n  'relation_type': RelationType(text='IS_REFERENCED_BY', description='The resource is referenced by another resource.', meaning='https://purl.org/dc/terms/isReferencedBy'),\n  'related_identifier': 'https://example.org/referenced',\n  'datetime_log': '2024-02-19T00:00:00+00:00'\n})]"
+          },
+          "ttl": 86400,
+          "timestamp": "2024-05-15T15:51:15+00:00"
+        },
+        {
+          "index": 8,
+          "type": "LOG",
+          "data": {
+            "format": "string",
+            "value": "[LogRecord({\n  'datetime_log': '2024-02-19T00:00:00+00:00',\n  'has_agent': Agent({\n      'name': 'Data Fuzzi',\n      'email': '[email protected]',\n      'orcid': '0000-0000-0000-0000',\n      'affiliation_ror': 'https://ror.org/01abcde',\n      'role': PID4CatAgentRole(text='TRUSTEE', description='The agent is the trustee of the resource.')\n    }),\n  'changed_field': ChangeLogField(text='STATUS', description='The status of the PID4CatRecord was changed.'),\n  'description': 'Registration completed.'\n}), LogRecord({\n  'datetime_log': '2024-05-15T15:51:15+00:00',\n  'has_agent': Agent({\n      'name': 'Data Fuzzi',\n      'email': '[email protected]',\n      'orcid': '0000-0000-0000-0000',\n      'affiliation_ror': 'https://ror.org/01abcde',\n      'role': PID4CatAgentRole(text='TRUSTEE', description='The agent is the trustee of the resource.')\n    }),\n  'changed_field': ChangeLogField(text='RESOURCE_INFO', description='The resource info of the PID4CatRecord was changed.'),\n  'description': 'as requested in issue #234'\n})]"
+          },
+          "ttl": 86400,
+          "timestamp": "2024-05-15T15:51:15+00:00"
+        }
+      ]
     }
   ],
-  "@type": "dict"
+  "@type": "HandleRecordContainer"
 }