Model changes to GenomeCoordinates, RepositoryId and ManuallyTyped

migrate_templates.sh

@@ -0,0 +1,3 @@
+rm -f src/data/templates/*/templates/*backup.json
+python -m opencloning_linkml.migrations.migrate --target-version 0.4.9 src/data/templates/*/templates/*.json
+rm -f src/data/templates/*/templates/*backup.json

project/graphql/opencloning_linkml.graphql

@@ -33,19 +33,6 @@ enum GatewayReactionType
     BP
   }
 
-enum RepositoryName
-  {
-    addgene
-    genbank
-    benchling
-    snapgene
-    euroscarf
-    igem
-    wekwikgene
-    seva
-    open_dna_collections
-  }
-
 enum SequenceFileFormat
   {
     fasta
@@ -62,7 +49,6 @@ type AddgeneIdSource
     databaseId: Integer
     input: [SourceInput]
     repositoryId: String!
-    repositoryName: RepositoryName!
     sequenceFileUrl: String
     addgeneSequenceType: AddgeneSequenceType
   }
@@ -118,7 +104,6 @@ type BenchlingUrlSource
     outputName: String
     databaseId: Integer
     input: [SourceInput]
-    repositoryName: RepositoryName!
     repositoryId: String!
   }
 
@@ -200,7 +185,6 @@ type EuroscarfSource
     outputName: String
     databaseId: Integer
     input: [SourceInput]
-    repositoryName: RepositoryName!
     repositoryId: String!
   }
 
@@ -223,13 +207,12 @@ type GenomeCoordinatesSource
     outputName: String
     databaseId: Integer
     input: [SourceInput]
+    coordinates: SimpleSequenceLocation
+    repositoryId: String!
     assemblyAccession: String
-    sequenceAccession: String!
     locusTag: String
     geneId: Integer
-    start: Integer!
-    end: Integer!
-    strand: Integer!
+    location: String!
   }
 
 type GibsonAssemblySource
@@ -259,7 +242,6 @@ type IGEMSource
     outputName: String
     databaseId: Integer
     input: [SourceInput]
-    repositoryName: RepositoryName!
     sequenceFileUrl: String!
     repositoryId: String!
   }
@@ -294,24 +276,41 @@ type LigationSource
     circular: Boolean
   }
 
+type ManuallyTypedSequence
+  {
+    id: Integer!
+    type: String
+    overhangCrick3prime: Integer
+    overhangWatson3prime: Integer
+    sequence: String!
+    circular: Boolean
+  }
+
 type ManuallyTypedSource
   {
     id: Integer!
     type: String
     outputName: String
     databaseId: Integer
     input: [SourceInput]
-    overhangCrick3prime: Integer
-    overhangWatson3prime: Integer
-    userInput: String!
-    circular: Boolean
   }
 
 type NamedThing
   {
     id: Integer!
   }
 
+type NCBISequenceSource
+  {
+    id: Integer!
+    type: String
+    outputName: String
+    databaseId: Integer
+    input: [SourceInput]
+    coordinates: SimpleSequenceLocation
+    repositoryId: String!
+  }
+
 type OligoHybridizationSource
   {
     id: Integer!
@@ -329,7 +328,6 @@ type OpenDNACollectionsSource
     outputName: String
     databaseId: Integer
     input: [SourceInput]
-    repositoryName: RepositoryName!
     sequenceFileUrl: String
     repositoryId: String!
   }
@@ -400,7 +398,6 @@ type RepositoryIdSource
     databaseId: Integer
     input: [SourceInput]
     repositoryId: String!
-    repositoryName: RepositoryName!
   }
 
 type RestrictionAndLigationSource
@@ -480,7 +477,6 @@ type SEVASource
     outputName: String
     databaseId: Integer
     input: [SourceInput]
-    repositoryName: RepositoryName!
     sequenceFileUrl: String
     repositoryId: String!
   }
@@ -492,7 +488,6 @@ type SnapGenePlasmidSource
     outputName: String
     databaseId: Integer
     input: [SourceInput]
-    repositoryName: RepositoryName!
     repositoryId: String!
   }
 
@@ -550,7 +545,6 @@ type WekWikGeneIdSource
     outputName: String
     databaseId: Integer
     input: [SourceInput]
-    repositoryName: RepositoryName!
     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": "2025-11-27T13:31:19",
+      "generation_date": "2025-12-06T00:30:23",
       "source": "opencloning_linkml.yaml"
    },
    "@context": {
@@ -163,35 +163,27 @@
       "assembly_accession": {
          "@id": "assembly_accession"
       },
-      "end": {
-         "@type": "xsd:integer",
-         "@id": "end"
-      },
       "gene_id": {
          "@type": "xsd:integer",
          "@id": "gene_id"
       },
       "locus_tag": {
          "@id": "locus_tag"
       },
-      "sequence_accession": {
-         "@id": "sequence_accession"
-      },
-      "start": {
-         "@type": "xsd:integer",
-         "@id": "start"
-      },
-      "strand": {
-         "@type": "xsd:integer",
-         "@id": "strand"
-      },
       "id": "@id",
-      "user_input": {
-         "@id": "user_input"
+      "location": {
+         "@id": "location"
+      },
+      "sequence": {
+         "@type": "@id",
+         "@id": "sequence"
       },
       "name": {
          "@id": "schema:name"
       },
+      "coordinates": {
+         "@id": "coordinates"
+      },
       "output_name": {
          "@id": "output_name"
       },
@@ -240,31 +232,23 @@
          "@type": "xsd:float",
          "@id": "percent_match_length"
       },
-      "sequence": {
-         "@type": "@id",
-         "@id": "sequence"
-      },
       "sseqid": {
          "@id": "sseqid"
       },
       "start_location": {
          "@type": "xsd:integer",
          "@id": "start_location"
       },
+      "strand": {
+         "@type": "xsd:integer",
+         "@id": "strand"
+      },
       "Type": {
          "@id": "Type"
       },
       "repository_id": {
          "@id": "repository_id"
       },
-      "repository_name": {
-         "@context": {
-            "text": "skos:notation",
-            "description": "skos:prefLabel",
-            "meaning": "@id"
-         },
-         "@id": "repository_name"
-      },
       "restriction_enzyme": {
          "@id": "restriction_enzyme"
       },
@@ -315,9 +299,6 @@
          "@type": "xsd:boolean",
          "@id": "circularize"
       },
-      "coordinates": {
-         "@id": "coordinates"
-      },
       "index_in_file": {
          "@type": "xsd:integer",
          "@id": "index_in_file"
@@ -391,12 +372,18 @@
       "LigationSource": {
          "@id": "LigationSource"
       },
+      "ManuallyTypedSequence": {
+         "@id": "ManuallyTypedSequence"
+      },
       "ManuallyTypedSource": {
          "@id": "ManuallyTypedSource"
       },
       "NamedThing": {
          "@id": "schema:Thing"
       },
+      "NCBISequenceSource": {
+         "@id": "NCBISequenceSource"
+      },
       "OligoHybridizationSource": {
          "@id": "OligoHybridizationSource"
       },