Allow "built-in" controlled terms (such as Species.rattus_norvegicus) to be used as filters in queries

Author: apdavison

fairgraph/queries.py

@@ -50,6 +50,14 @@ def __init__(self, operation: str, parameter: Optional[str] = None, value: Optio
         self.parameter = parameter
         self.value = value
 
+    def __repr__(self):
+        repr = f"Filter(operation='{self.operation}'"
+        if self.parameter:
+            repr += f", parameter='{self.parameter}'"
+        if self.value:
+            repr += f", value='{self.value}'"
+        return repr + ")"
+
     def serialize(self):
         data = {"op": self.operation}
         if self.parameter:
@@ -406,7 +414,11 @@ def get_query_filter_property(property, context, filter: Any) -> QueryProperty:
         assert all(issubclass(_type, Node) for _type in property.types)
         prop = QueryProperty(expanded_path, name=f"Q{property.name}", required=True, reverse=property.reverse)
         if filter_obj:
-            prop.properties.append(QueryProperty("@id", filter=filter_obj))
+            if filter_obj.value.startswith("https://kg.ebrains.eu/api/instances"):
+                filter_path = "@id"
+            else:
+                filter_path = "http://schema.org/identifier"
+            prop.properties.append(QueryProperty(filter_path, filter=filter_obj))
         else:
             for cls in property.types:
                 child_properties = cls.generate_query_filter_properties(filter)

fairgraph/utility.py

@@ -549,10 +549,17 @@ def adapt_structure(structure, replacement):
             if "structure" in item:
                 adapt_structure(item["structure"], replacement)
 
+    def adapt_filters(structure, replacement):
+        for item in structure:
+            if "filter" in item and "value" in item["filter"]:
+                item["filter"]["value"] = item["filter"]["value"].replace(*replacement)
+            if "structure" in item:
+                adapt_filters(item["structure"], replacement)
+
     migrated_query = deepcopy(query)
     migrated_query["meta"]["type"] = adapt_type_4to3(migrated_query["meta"]["type"])
-    replacement = ("openminds.om-i.org/props", "openminds.ebrains.eu/vocab")
-    adapt_structure(migrated_query["structure"], replacement)
+    adapt_structure(migrated_query["structure"], ("openminds.om-i.org/props", "openminds.ebrains.eu/vocab"))
+    adapt_filters(migrated_query["structure"], ("openminds.om-i.org/instances", "openminds.ebrains.eu/instances"))
     return migrated_query
 
 

test/test_openminds_computation.py

@@ -73,7 +73,7 @@ def test_generate_query(self, mock_client):
                     "path": "https://openminds.om-i.org/props/hardware",
                     "propertyName": "Qhardware",
                     "required": True,
-                    "structure": [{"path": "@id", "filter": {"op": "CONTAINS", "value": "some_id"}}],
+                    "structure": [{"path": "http://schema.org/identifier", "filter": {"op": "CONTAINS", "value": "some_id"}}],
                 },
                 {
                     "path": "https://openminds.om-i.org/props/name",
@@ -85,7 +85,7 @@ def test_generate_query(self, mock_client):
                     "path": "https://openminds.om-i.org/props/software",
                     "propertyName": "Qsoftware",
                     "required": True,
-                    "structure": [{"path": "@id", "filter": {"op": "CONTAINS", "value": "another_id"}}],
+                    "structure": [{"path": "http://schema.org/identifier", "filter": {"op": "CONTAINS", "value": "another_id"}}],
                 },
             ],
         }

test/test_openminds_core.py

@@ -68,6 +68,21 @@ def test_retrieve_released_models_filter_species_by_obj(kg_client):
             assert rat in study_targets
 
 
+@skip_if_no_connection
+def test_retrieve_released_datasets_filter_species_by_openminds_obj(kg_client):
+    rat = omterms.Species.by_name("Rattus norvegicus", kg_client)
+    rat_om = omterms.Species.rattus_norvegicus
+    assert rat.name == rat_om.name == "Rattus norvegicus"
+    follow_links = {"study_targets": {}}
+    datasets = omcore.DatasetVersion.list(kg_client, space="dataset", study_targets=rat, follow_links=follow_links)
+    datasets_om = omcore.DatasetVersion.list(kg_client, space="dataset", study_targets=rat_om, follow_links=follow_links)
+    assert len(datasets) > 0
+    assert len(datasets) == len(datasets_om)
+    assert [ds.id for ds in datasets] == [ds.id for ds in datasets_om]
+    for dataset in datasets_om:
+        assert rat in dataset.study_targets
+
+
 @skip_if_no_connection
 def test_retrieve_released_models_filter_species_by_uuid(kg_client):
     human = omterms.Species.by_name("Homo sapiens", kg_client)