Small changes to adapt to pydna usage

project/graphql/opencloning_linkml.graphql

@@ -481,7 +481,7 @@ type SEVASource
     databaseId: Integer
     input: [SourceInput]
     repositoryName: RepositoryName!
-    sequenceFileUrl: String!
+    sequenceFileUrl: String
     repositoryId: String!
   }
 

project/jsonld/opencloning_linkml.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2025-11-17T18:53:28",
+      "generation_date": "2025-11-26T10:36:02",
       "source": "opencloning_linkml.yaml"
    },
    "@context": {

project/jsonld/opencloning_linkml.jsonld

@@ -1981,7 +1981,6 @@
       "is_usage_slot": true,
       "usage_slot_name": "sequence_file_url",
       "range": "string",
-      "required": true,
       "pattern": "^https?:\\/\\/(www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b([-a-zA-Z0-9()@:%_\\+.~#?&//=]*)$",
       "@type": "SlotDefinition"
     },
@@ -3542,9 +3541,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "opencloning_linkml.yaml",
-  "source_file_date": "2025-11-17T18:34:01",
-  "source_file_size": 26051,
-  "generation_date": "2025-11-17T18:53:29",
+  "source_file_date": "2025-11-26T10:35:56",
+  "source_file_size": 26028,
+  "generation_date": "2025-11-26T10:36:03",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/opencloning_linkml.context.jsonld",

project/jsonschema/opencloning_linkml.schema.json

@@ -2621,7 +2621,10 @@
                 "sequence_file_url": {
                     "description": "The URL of the sequence file, which can refer to a a gb file hosted on the SEVA website or an entry in the NCBI.",
                     "pattern": "^https?:\\/\\/(www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b([-a-zA-Z0-9()@:%_\\+.~#?&//=]*)$",
-                    "type": "string"
+                    "type": [
+                        "string",
+                        "null"
+                    ]
                 },
                 "type": {
                     "description": "Designates the class",
@@ -2635,7 +2638,6 @@
                 }
             },
             "required": [
-                "sequence_file_url",
                 "repository_id",
                 "repository_name",
                 "id"

project/python/opencloning_linkml.py

@@ -1,5 +1,5 @@
 # Auto generated from opencloning_linkml.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-11-17T18:53:30
+# Generation date: 2025-11-26T10:36:04
 # Schema: OpenCloning_LinkML
 #
 # id: https://opencloning.github.io/OpenCloning_LinkML
@@ -908,25 +908,23 @@ class SEVASource(RepositoryIdSource):
 
     id: Union[int, SEVASourceId] = None
     repository_name: Union[str, "RepositoryName"] = None
-    sequence_file_url: str = None
     repository_id: str = None
+    sequence_file_url: Optional[str] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
             self.MissingRequiredField("id")
         if not isinstance(self.id, SEVASourceId):
             self.id = SEVASourceId(self.id)
 
-        if self._is_empty(self.sequence_file_url):
-            self.MissingRequiredField("sequence_file_url")
-        if not isinstance(self.sequence_file_url, str):
-            self.sequence_file_url = str(self.sequence_file_url)
-
         if self._is_empty(self.repository_id):
             self.MissingRequiredField("repository_id")
         if not isinstance(self.repository_id, str):
             self.repository_id = str(self.repository_id)
 
+        if self.sequence_file_url is not None and not isinstance(self.sequence_file_url, str):
+            self.sequence_file_url = str(self.sequence_file_url)
+
         super().__post_init__(**kwargs)
         self.type = str(self.class_name)
 
@@ -2970,7 +2968,7 @@ class slots:
     curie=OPENCLONING_LINKML.curie("sequence_file_url"),
     model_uri=OPENCLONING_LINKML.SEVASource_sequence_file_url,
     domain=SEVASource,
-    range=str,
+    range=Optional[str],
     pattern=re.compile(
         r"^https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*)$"
     ),

project/shex/opencloning_linkml.shex

@@ -485,7 +485,7 @@ linkml:Sparqlpath xsd:string
 <SEVASource> CLOSED {
     (  $<SEVASource_tes> (  &<RepositoryIdSource_tes> ;
           rdf:type [ <RepositoryIdSource> ] ? ;
-          <sequence_file_url> @linkml:String ;
+          <sequence_file_url> @linkml:String ? ;
           <repository_id> @linkml:String
        ) ;
        rdf:type [ <SEVASource> ]

project/sqlschema/opencloning_linkml.sql

@@ -483,7 +483,7 @@ CREATE TABLE "WekWikGeneIdSource" (
 	PRIMARY KEY (id)
 );
 CREATE TABLE "SEVASource" (
-	sequence_file_url TEXT NOT NULL,
+	sequence_file_url TEXT,
 	repository_id TEXT NOT NULL,
 	repository_name VARCHAR(20) NOT NULL,
 	type TEXT,

src/opencloning_linkml/datamodel/_models.py

@@ -1382,14 +1382,13 @@ class SEVASource(RepositoryIdSource):
                     "the SEVA website or an "
                     "entry in the NCBI.",
                     "name": "sequence_file_url",
-                    "required": True,
                 },
             },
         }
     )
 
-    sequence_file_url: str = Field(
-        default=...,
+    sequence_file_url: Optional[str] = Field(
+        default=None,
         description="""The URL of the sequence file, which can refer to a a gb file hosted on the SEVA website or an entry in the NCBI.""",
         json_schema_extra={
             "linkml_meta": {

src/opencloning_linkml/schema/opencloning_linkml.yaml

@@ -368,7 +368,6 @@ classes:
         description: >-
           The URL of the sequence file, which can refer to a a gb file hosted on the SEVA website or an
           entry in the NCBI.
-        required: true
 
   BenchlingUrlSource:
     is_a: RepositoryIdSource