Add species_context_qualifier, remove closure expansion on most quali…

…fiers (#904) Schema tidying that is tightly coupled with the 2024-11 KG build
monarch-initiative · Nov 19, 2024 · 98cbf26 · 98cbf26
1 parent ce0851b
commit 98cbf26
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diff --git a/backend/src/monarch_py/cli.py b/backend/src/monarch_py/cli.py
@@ -83,9 +83,7 @@ def schema():
     """
     schema_name = "model"
     import_path = f"monarch_py.datamodels.{schema_name}"
-    schema_module_spec = importlib.util.find_spec(
-        f"monarch_py.datamodels.{schema_name}"
-    )
+    schema_module_spec = importlib.util.find_spec(f"monarch_py.datamodels.{schema_name}")
     if schema_module_spec is None or schema_module_spec.origin is None:
         print(f"No python module found at {import_path}")
         raise typer.Exit(code=1)

diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
@@ -662,16 +662,6 @@ class Association(ConfiguredBaseModel):
             "linkml_meta": {"alias": "qualifiers_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    qualifiers_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "qualifiers_closure", "domain_of": ["Association"]}},
-    )
-    qualifiers_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "qualifiers_closure_label", "domain_of": ["Association"]}},
-    )
     qualifier: Optional[List[str]] = Field(
         None, json_schema_extra={"linkml_meta": {"alias": "qualifier", "domain_of": ["Association"]}}
     )
@@ -692,16 +682,6 @@ class Association(ConfiguredBaseModel):
             "linkml_meta": {"alias": "qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "qualifier_closure", "domain_of": ["Association"]}},
-    )
-    qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     frequency_qualifier_label: Optional[str] = Field(
         None,
         description="""The name of the frequency_qualifier entity""",
@@ -721,16 +701,6 @@ class Association(ConfiguredBaseModel):
             "linkml_meta": {"alias": "frequency_qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    frequency_qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "frequency_qualifier_closure", "domain_of": ["Association"]}},
-    )
-    frequency_qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "frequency_qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     onset_qualifier_label: Optional[str] = Field(
         None,
         description="""The name of the onset_qualifier entity""",
@@ -750,16 +720,6 @@ class Association(ConfiguredBaseModel):
             "linkml_meta": {"alias": "onset_qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    onset_qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "onset_qualifier_closure", "domain_of": ["Association"]}},
-    )
-    onset_qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "onset_qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     sex_qualifier_label: Optional[str] = Field(
         None,
         description="""The name of the sex_qualifier entity""",
@@ -779,16 +739,6 @@ class Association(ConfiguredBaseModel):
             "linkml_meta": {"alias": "sex_qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    sex_qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "sex_qualifier_closure", "domain_of": ["Association"]}},
-    )
-    sex_qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "sex_qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     stage_qualifier_label: Optional[str] = Field(
         None,
         description="""The name of the stage_qualifier entity""",
@@ -808,16 +758,6 @@ class Association(ConfiguredBaseModel):
             "linkml_meta": {"alias": "stage_qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    stage_qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "stage_qualifier_closure", "domain_of": ["Association"]}},
-    )
-    stage_qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing stage_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "stage_qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     disease_context_qualifier: Optional[str] = Field(
         None,
         description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""",
@@ -866,6 +806,42 @@ class Association(ConfiguredBaseModel):
             "linkml_meta": {"alias": "disease_context_qualifier_closure_label", "domain_of": ["Association"]}
         },
     )
+    species_context_qualifier: Optional[str] = Field(
+        None,
+        description="""A context qualifier representing a species in which a relationship expressed in an association took place.""",
+        json_schema_extra={
+            "linkml_meta": {
+                "alias": "species_context_qualifier",
+                "domain_of": ["Association"],
+                "examples": [{"value": "NCBITaxon:9606"}],
+            }
+        },
+    )
+    species_context_qualifier_label: Optional[str] = Field(
+        None,
+        description="""The name of the species_context_qualifier entity""",
+        json_schema_extra={
+            "linkml_meta": {"alias": "species_context_qualifier_label", "domain_of": ["Association"], "is_a": "name"}
+        },
+    )
+    species_context_qualifier_namespace: Optional[str] = Field(
+        None,
+        description="""The namespace/prefix of the species_context_qualifier entity""",
+        json_schema_extra={
+            "linkml_meta": {"alias": "species_context_qualifier_namespace", "domain_of": ["Association"]}
+        },
+    )
+    species_context_qualifier_category: Optional[str] = Field(
+        None,
+        description="""The category of the species_context_qualifier entity""",
+        json_schema_extra={
+            "linkml_meta": {
+                "alias": "species_context_qualifier_category",
+                "domain_of": ["Association"],
+                "is_a": "category",
+            }
+        },
+    )
 
 
 class AssociationCountList(ConfiguredBaseModel):
@@ -1372,16 +1348,6 @@ class DirectionalAssociation(Association):
             "linkml_meta": {"alias": "qualifiers_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    qualifiers_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "qualifiers_closure", "domain_of": ["Association"]}},
-    )
-    qualifiers_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "qualifiers_closure_label", "domain_of": ["Association"]}},
-    )
     qualifier: Optional[List[str]] = Field(
         None, json_schema_extra={"linkml_meta": {"alias": "qualifier", "domain_of": ["Association"]}}
     )
@@ -1402,16 +1368,6 @@ class DirectionalAssociation(Association):
             "linkml_meta": {"alias": "qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "qualifier_closure", "domain_of": ["Association"]}},
-    )
-    qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     frequency_qualifier_label: Optional[str] = Field(
         None,
         description="""The name of the frequency_qualifier entity""",
@@ -1431,16 +1387,6 @@ class DirectionalAssociation(Association):
             "linkml_meta": {"alias": "frequency_qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    frequency_qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "frequency_qualifier_closure", "domain_of": ["Association"]}},
-    )
-    frequency_qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "frequency_qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     onset_qualifier_label: Optional[str] = Field(
         None,
         description="""The name of the onset_qualifier entity""",
@@ -1460,16 +1406,6 @@ class DirectionalAssociation(Association):
             "linkml_meta": {"alias": "onset_qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    onset_qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "onset_qualifier_closure", "domain_of": ["Association"]}},
-    )
-    onset_qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "onset_qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     sex_qualifier_label: Optional[str] = Field(
         None,
         description="""The name of the sex_qualifier entity""",
@@ -1489,16 +1425,6 @@ class DirectionalAssociation(Association):
             "linkml_meta": {"alias": "sex_qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    sex_qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "sex_qualifier_closure", "domain_of": ["Association"]}},
-    )
-    sex_qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "sex_qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     stage_qualifier_label: Optional[str] = Field(
         None,
         description="""The name of the stage_qualifier entity""",
@@ -1518,16 +1444,6 @@ class DirectionalAssociation(Association):
             "linkml_meta": {"alias": "stage_qualifier_category", "domain_of": ["Association"], "is_a": "category"}
         },
     )
-    stage_qualifier_closure: Optional[List[str]] = Field(
-        None,
-        description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "stage_qualifier_closure", "domain_of": ["Association"]}},
-    )
-    stage_qualifier_closure_label: Optional[List[str]] = Field(
-        None,
-        description="""Field containing stage_qualifier name and the names of all of it's ancestors""",
-        json_schema_extra={"linkml_meta": {"alias": "stage_qualifier_closure_label", "domain_of": ["Association"]}},
-    )
     disease_context_qualifier: Optional[str] = Field(
         None,
         description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""",
@@ -1576,6 +1492,42 @@ class DirectionalAssociation(Association):
             "linkml_meta": {"alias": "disease_context_qualifier_closure_label", "domain_of": ["Association"]}
         },
     )
+    species_context_qualifier: Optional[str] = Field(
+        None,
+        description="""A context qualifier representing a species in which a relationship expressed in an association took place.""",
+        json_schema_extra={
+            "linkml_meta": {
+                "alias": "species_context_qualifier",
+                "domain_of": ["Association"],
+                "examples": [{"value": "NCBITaxon:9606"}],
+            }
+        },
+    )
+    species_context_qualifier_label: Optional[str] = Field(
+        None,
+        description="""The name of the species_context_qualifier entity""",
+        json_schema_extra={
+            "linkml_meta": {"alias": "species_context_qualifier_label", "domain_of": ["Association"], "is_a": "name"}
+        },
+    )
+    species_context_qualifier_namespace: Optional[str] = Field(
+        None,
+        description="""The namespace/prefix of the species_context_qualifier entity""",
+        json_schema_extra={
+            "linkml_meta": {"alias": "species_context_qualifier_namespace", "domain_of": ["Association"]}
+        },
+    )
+    species_context_qualifier_category: Optional[str] = Field(
+        None,
+        description="""The category of the species_context_qualifier entity""",
+        json_schema_extra={
+            "linkml_meta": {
+                "alias": "species_context_qualifier_category",
+                "domain_of": ["Association"],
+                "is_a": "category",
+            }
+        },
+    )
 
 
 class ExpandedCurie(ConfiguredBaseModel):