datasets field in metricsDatasetCollection may be empty (not required)

MontpellierRessourcesImagerie · Apr 29, 2024 · 4bae7e2 · 4bae7e2
1 parent 5560cf4
commit 4bae7e2
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Showing 11 changed files with 2,346 additions and 2,358 deletions.
diff --git a/project/excel/microscopemetrics_schema.xlsx b/project/excel/microscopemetrics_schema.xlsx
diff --git a/project/graphql/microscopemetrics_schema.graphql b/project/graphql/microscopemetrics_schema.graphql
@@ -343,7 +343,7 @@ type HarmonizedMetricsDatasetCollection
     description: String
     dataReference: DataReference
     linkedReferences: [DataReference]
-    datasets: [MetricsDataset]!
+    datasets: [MetricsDataset]
     datasetClass: String!
   }
 
@@ -453,7 +453,7 @@ type MetricsDatasetCollection
     description: String
     dataReference: DataReference
     linkedReferences: [DataReference]
-    datasets: [MetricsDataset]!
+    datasets: [MetricsDataset]
   }
 
 interface MetricsInput

diff --git a/project/jsonld/microscopemetrics_schema.context.jsonld b/project/jsonld/microscopemetrics_schema.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-04-23T13:43:14",
+      "generation_date": "2024-04-29T14:52:42",
       "source": "microscopemetrics_schema.yaml"
    },
    "@context": {

diff --git a/project/jsonld/microscopemetrics_schema.jsonld b/project/jsonld/microscopemetrics_schema.jsonld
@@ -2761,7 +2761,6 @@
         "MetricsDatasetCollection"
       ],
       "range": "MetricsDataset",
-      "required": true,
       "inlined": true,
       "inlined_as_list": true,
       "@type": "SlotDefinition"
@@ -5007,7 +5006,6 @@
           "description": "The datasets of the collection",
           "multivalued": true,
           "range": "MetricsDataset",
-          "required": true,
           "inlined": true,
           "inlined_as_list": true,
           "@type": "SlotDefinition"
@@ -6951,7 +6949,7 @@
   "source_file": "microscopemetrics_schema.yaml",
   "source_file_date": "2024-02-05T12:00:47",
   "source_file_size": 787,
-  "generation_date": "2024-04-23T13:43:15",
+  "generation_date": "2024-04-29T14:52:43",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/microscopemetrics_schema.context.jsonld",

diff --git a/project/jsonschema/microscopemetrics_schema.schema.json b/project/jsonschema/microscopemetrics_schema.schema.json
@@ -1696,8 +1696,7 @@
                 }
             },
             "required": [
-                "dataset_class",
-                "datasets"
+                "dataset_class"
             ],
             "title": "HarmonizedMetricsDatasetCollection",
             "type": "object"
@@ -2120,9 +2119,6 @@
                     "type": "string"
                 }
             },
-            "required": [
-                "datasets"
-            ],
             "title": "MetricsDatasetCollection",
             "type": "object"
         },

diff --git a/project/owl/microscopemetrics_schema.owl.ttl b/project/owl/microscopemetrics_schema.owl.ttl
diff --git a/project/shacl/microscopemetrics_schema.shacl.ttl b/project/shacl/microscopemetrics_schema.shacl.ttl
diff --git a/project/shex/microscopemetrics_schema.shex b/project/shex/microscopemetrics_schema.shex
@@ -752,7 +752,7 @@ CLOSED {
              &<https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema/core_schema/MetricsObject_tes> ;
              rdf:type [ <https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema/core_schema/MetricsObject> ] ? ;
              <https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema/core_schema/datasets>
-             @<https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema/core_schema/MetricsDataset> +
+             @<https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema/core_schema/MetricsDataset> *
           ) ;
           rdf:type [ <https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema/core_schema/MetricsDatasetCollection>
              ] ?

diff --git a/project/sqlschema/microscopemetrics_schema.sql b/project/sqlschema/microscopemetrics_schema.sql
@@ -275,7 +275,7 @@ CREATE TABLE "HarmonizedMetricsDatasetCollection" (
 	description TEXT, 
 	data_reference TEXT, 
 	linked_references TEXT, 
-	datasets TEXT NOT NULL, 
+	datasets TEXT, 
 	dataset_class TEXT NOT NULL, 
 	PRIMARY KEY (name, description, data_reference, linked_references, datasets, dataset_class)
 );
@@ -358,7 +358,7 @@ CREATE TABLE "MetricsDatasetCollection" (
 	description TEXT, 
 	data_reference TEXT, 
 	linked_references TEXT, 
-	datasets TEXT NOT NULL, 
+	datasets TEXT, 
 	PRIMARY KEY (name, description, data_reference, linked_references, datasets)
 );
 

diff --git a/src/microscopemetrics_schema/datamodel/microscopemetrics_schema.py b/src/microscopemetrics_schema/datamodel/microscopemetrics_schema.py
@@ -1,5 +1,5 @@
 # Auto generated from microscopemetrics_schema.yaml by pythongen.py version: 0.0.1
-# Generation date: 2024-04-23T13:43:21
+# Generation date: 2024-04-29T14:52:50
 # Schema: microscopemetrics-schema
 #
 # id: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
@@ -341,11 +341,9 @@ class MetricsDatasetCollection(MetricsObject):
     class_name: ClassVar[str] = "MetricsDatasetCollection"
     class_model_uri: ClassVar[URIRef] = MICROSCOPEMETRICS_SCHEMA.MetricsDatasetCollection
 
-    datasets: Union[Union[dict, "MetricsDataset"], List[Union[dict, "MetricsDataset"]]] = None
+    datasets: Optional[Union[Union[dict, "MetricsDataset"], List[Union[dict, "MetricsDataset"]]]] = empty_list()
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
-        if self._is_empty(self.datasets):
-            self.MissingRequiredField("datasets")
         if not isinstance(self.datasets, list):
             self.datasets = [self.datasets] if self.datasets is not None else []
         self.datasets = [v if isinstance(v, MetricsDataset) else MetricsDataset(**as_dict(v)) for v in self.datasets]
@@ -366,7 +364,6 @@ class HarmonizedMetricsDatasetCollection(MetricsDatasetCollection):
     class_name: ClassVar[str] = "HarmonizedMetricsDatasetCollection"
     class_model_uri: ClassVar[URIRef] = MICROSCOPEMETRICS_SCHEMA.HarmonizedMetricsDatasetCollection
 
-    datasets: Union[Union[dict, "MetricsDataset"], List[Union[dict, "MetricsDataset"]]] = None
     dataset_class: str = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
@@ -3006,7 +3003,7 @@ class slots:
                    model_uri=MICROSCOPEMETRICS_SCHEMA.comment__text, domain=None, range=str)
 
 slots.metricsDatasetCollection__datasets = Slot(uri=MICROSCOPEMETRICS_SCHEMA['core_schema/datasets'], name="metricsDatasetCollection__datasets", curie=MICROSCOPEMETRICS_SCHEMA.curie('core_schema/datasets'),
-                   model_uri=MICROSCOPEMETRICS_SCHEMA.metricsDatasetCollection__datasets, domain=None, range=Union[Union[dict, MetricsDataset], List[Union[dict, MetricsDataset]]])
+                   model_uri=MICROSCOPEMETRICS_SCHEMA.metricsDatasetCollection__datasets, domain=None, range=Optional[Union[Union[dict, MetricsDataset], List[Union[dict, MetricsDataset]]]])
 
 slots.harmonizedMetricsDatasetCollection__dataset_class = Slot(uri=MICROSCOPEMETRICS_SCHEMA['core_schema/dataset_class'], name="harmonizedMetricsDatasetCollection__dataset_class", curie=MICROSCOPEMETRICS_SCHEMA.curie('core_schema/dataset_class'),
                    model_uri=MICROSCOPEMETRICS_SCHEMA.harmonizedMetricsDatasetCollection__dataset_class, domain=None, range=str)

diff --git a/src/microscopemetrics_schema/schema/core_schema.yaml b/src/microscopemetrics_schema/schema/core_schema.yaml
@@ -186,7 +186,6 @@ classes:
       datasets:
         range: MetricsDataset
         description: The datasets of the collection
-        required: true
         multivalued: true
         inlined: true
         inlined_as_list: true