feat!: rename study --> study statement / statement

docs/source/reference/index.rst

@@ -34,11 +34,8 @@ Data Schemas
    :toctree: api/
    :template: module_summary.rst
 
-   metakb.schemas.annotation
    metakb.schemas.api
    metakb.schemas.app
-   metakb.schemas.categorical_variation
-   metakb.schemas.variation_statement
 
 Harvesters
 ----------

pyproject.toml

@@ -23,7 +23,9 @@ requires-python = ">=3.10"
 description = "A search interface for cancer variant interpretations assembled by aggregating and harmonizing across multiple cancer variant interpretation knowledgebases."
 license = {file = "LICENSE"}
 dependencies = [
-    "ga4gh.vrs~=2.0.0a10",
+    "ga4gh.vrs~=2.0.0a12",
+    "ga4gh.cat_vrs~=0.1.0",
+    "ga4gh.va_spec~=0.1.0",
     "gene-normalizer[etl]~=0.4.1",
     "variation-normalizer~=0.10.0",
     "disease-normalizer[etl]~=0.5.0",
@@ -42,7 +44,7 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-tests = ["pytest", "pytest-cov", "mock", "pytest-asyncio"]
+tests = ["pytest", "pytest-cov", "mock", "pytest-asyncio", "deepdiff"]
 dev = ["pre-commit>=3.7.1", "ruff==0.5.0"]
 notebooks = ["ipykernel", "jupyterlab"]
 docs = [

src/metakb/database.py

@@ -74,15 +74,15 @@ def _get_credentials(
 
 _CONSTRAINTS = {
     "coding_constraint": "CREATE CONSTRAINT coding_constraint IF NOT EXISTS FOR (c:Coding) REQUIRE (c.code, c.label, c.system) IS UNIQUE;",
-    "gene_id_constraint": "CREATE CONSTRAINT gene_id_constraint IF NOT EXISTS FOR (n:Gene}) REQUIRE n.id IS UNIQUE;",
+    "gene_id_constraint": "CREATE CONSTRAINT gene_id_constraint IF NOT EXISTS FOR (n:Gene) REQUIRE n.id IS UNIQUE;",
     "disease_id_constraint": "CREATE CONSTRAINT disease_id_constraint IF NOT EXISTS FOR (n:Disease) REQUIRE n.id IS UNIQUE;",
     "therapeuticprocedure_id_constraint": "CREATE CONSTRAINT therapeuticprocedure_id_constraint IF NOT EXISTS FOR (n:TherapeuticProcedure) REQUIRE n.id IS UNIQUE;",
     "variation_id_constraint": "CREATE CONSTRAINT variation_id_constraint IF NOT EXISTS FOR (n:Variation) REQUIRE n.id IS UNIQUE;",
-    "categoricalvariation_id_constraint": "CREATE CONSTRAINT categoricalvariation_id_constraint IF NOT EXISTS FOR (n:CategoricalVariation) REQUIRE n.id IS UNIQUE;",
+    "categoricalvariant_id_constraint": "CREATE CONSTRAINT categoricalvariant_id_constraint IF NOT EXISTS FOR (n:CategoricalVariant) REQUIRE n.id IS UNIQUE;",
     "variantgroup_id_constraint": "CREATE CONSTRAINT variantgroup_id_constraint IF NOT EXISTS FOR (n:VariantGroup) REQUIRE n.id IS UNIQUE;",
     "location_id_constraint": "CREATE CONSTRAINT location_id_constraint IF NOT EXISTS FOR (n:Location) REQUIRE n.id IS UNIQUE;",
     "document_id_constraint": "CREATE CONSTRAINT document_id_constraint IF NOT EXISTS FOR (n:Document) REQUIRE n.id IS UNIQUE;",
-    "study_id_constraint": "CREATE CONSTRAINT study_id_constraint IF NOT EXISTS FOR (n:Study) REQUIRE n.id IS UNIQUE;",
+    "statement_id_constraint": "CREATE CONSTRAINT statement_id_constraint IF NOT EXISTS FOR (n:Statement) REQUIRE n.id IS UNIQUE;",
     "method_id_constraint": "CREATE CONSTRAINT method_id_constraint IF NOT EXISTS FOR (n:Method) REQUIRE n.id IS UNIQUE;",
 }