Merge pull request #259 from alliance-genome/assembly_component_tweak

Assembly component tweak
alliance-genome · Jul 10, 2024 · b622740 · b622740
2 parents aa8f5c6 + fe924fc
commit b622740
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Showing 3 changed files with 23 additions and 15 deletions.
diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json
@@ -5311,9 +5311,6 @@
                     "format": "date-time",
                     "type": "string"
                 },
-                "display_name": {
-                    "type": "string"
-                },
                 "genome_assembly": {
                     "$ref": "#/$defs/GenomeAssembly",
                     "description": "The GenomeAssembly to which a AssemblyComponent belongs."
@@ -5322,6 +5319,10 @@
                     "description": "Classifies the entity as private (for internal use) or not (for public use).",
                     "type": "boolean"
                 },
+                "maps_to_chromosome": {
+                    "$ref": "#/$defs/Chromosome",
+                    "description": "The chromosome(s) to which a chromosome assembly or unlocalized scaffold or contig maps."
+                },
                 "mod_entity_id": {
                     "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.",
                     "type": "string"
@@ -5330,6 +5331,10 @@
                     "description": "The model organism database (MOD) internal identifier for the object",
                     "type": "string"
                 },
+                "name": {
+                    "description": "a human-readable name for an entity",
+                    "type": "string"
+                },
                 "obsolete": {
                     "description": "Entity is no longer current.",
                     "type": "boolean"
@@ -5344,11 +5349,10 @@
                 }
             },
             "required": [
-                "display_name",
+                "name",
                 "genome_assembly",
                 "taxon",
                 "data_provider",
-                "curie",
                 "internal"
             ],
             "title": "AssemblyComponent",
@@ -5392,9 +5396,6 @@
                     "format": "date-time",
                     "type": "string"
                 },
-                "display_name": {
-                    "type": "string"
-                },
                 "genome_assembly_identifier": {
                     "description": "The identifier for the GenomeAssembly. This can be a MOD curie, a MOD internal ID or an external (3rd party) identifier.",
                     "type": "string"
@@ -5411,6 +5412,10 @@
                     "description": "The model organism database (MOD) internal identifier for the object",
                     "type": "string"
                 },
+                "name": {
+                    "description": "a human-readable name for an entity",
+                    "type": "string"
+                },
                 "obsolete": {
                     "description": "Entity is no longer current.",
                     "type": "boolean"
@@ -5425,7 +5430,7 @@
                 }
             },
             "required": [
-                "display_name",
+                "name",
                 "genome_assembly_identifier",
                 "data_provider_dto",
                 "taxon_curie",

diff --git a/model/schema/core.yaml b/model/schema/core.yaml
@@ -476,24 +476,27 @@ classes:
       In the context of this model, this entity is used as a landmark for the
       location of other genomic entities.
     slots:
-      - display_name
+      - name
       - genome_assembly
+      - maps_to_chromosome
     slot_usage:
-      curie:
+      name:
         required: true
     defining_slots:
-      - display_name
+      - name
       - genome_assembly
-      - maps_to_chromosome
 
   AssemblyComponentDTO:
     is_a: GenomicEntityDTO
     description: >-
       Ingest class for assembly components
     slots:
-      - display_name
+      - name
       - genome_assembly_identifier
       - data_provider_dto
+    slot_usage:
+      name:
+        required: true
 
   GenomeAssembly:
     is_a: BiologicalEntity

diff --git a/test/data/assembly_component_test.json b/test/data/assembly_component_test.json
@@ -7,7 +7,7 @@
       "created_by_curie": "WB:WBPerson2987",
       "updated_by_curie": "WB:WBPerson2987",
       "genome_assembly_identifier": "WB:WBcel235",
-      "display_name": "W02C12",
+      "name": "W02C12",
       "internal": false,
       "obsolete": false,
       "data_provider_dto": {