update ga4gh va spec imports

cancervariants · Jan 23, 2025 · 2553f46 · 2553f46
1 parent d7420ae
commit 2553f46
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Showing 5 changed files with 16 additions and 18 deletions.
diff --git a/src/metakb/query.py b/src/metakb/query.py
@@ -7,13 +7,12 @@
 
 from ga4gh.cat_vrs.models import CategoricalVariant, DefiningAlleleConstraint
 from ga4gh.core.models import Extension, MappableConcept
-from ga4gh.va_spec.aac_2017.models import (
+from ga4gh.va_spec.aac_2017 import (
     VariantDiagnosticStudyStatement,
     VariantPrognosticStudyStatement,
     VariantTherapeuticResponseStudyStatement,
 )
-from ga4gh.va_spec.base.core import Document, Method
-from ga4gh.va_spec.base.domain_entities import TherapyGroup
+from ga4gh.va_spec.base import Document, Method, TherapyGroup
 from ga4gh.vrs.models import Expression, Variation
 from neo4j import Driver
 from neo4j.graph import Node

diff --git a/src/metakb/schemas/api.py b/src/metakb/schemas/api.py
@@ -2,7 +2,7 @@
 
 from typing import Literal
 
-from ga4gh.va_spec.aac_2017.models import (
+from ga4gh.va_spec.aac_2017 import (
     VariantDiagnosticStudyStatement,
     VariantPrognosticStudyStatement,
     VariantTherapeuticResponseStudyStatement,

diff --git a/src/metakb/transformers/base.py b/src/metakb/transformers/base.py
@@ -23,13 +23,12 @@
     Extension,
     MappableConcept,
 )
-from ga4gh.va_spec.aac_2017.models import (
+from ga4gh.va_spec.aac_2017 import (
     VariantDiagnosticStudyStatement,
     VariantPrognosticStudyStatement,
     VariantTherapeuticResponseStudyStatement,
 )
-from ga4gh.va_spec.base.core import Document, Method
-from ga4gh.va_spec.base.domain_entities import TherapyGroup
+from ga4gh.va_spec.base import Document, Method, TherapyGroup
 from ga4gh.vrs.models import Allele
 from gene.schemas import NormalizeService as NormalizedGene
 from pydantic import BaseModel, StrictStr, ValidationError

diff --git a/src/metakb/transformers/civic.py b/src/metakb/transformers/civic.py
@@ -13,22 +13,22 @@
     MappableConcept,
     Relation,
 )
-from ga4gh.va_spec.aac_2017.models import (
-    VariantDiagnosticProposition,
+from ga4gh.va_spec.aac_2017 import (
     VariantDiagnosticStudyStatement,
-    VariantPrognosticProposition,
     VariantPrognosticStudyStatement,
-    VariantTherapeuticResponseProposition,
     VariantTherapeuticResponseStudyStatement,
 )
-from ga4gh.va_spec.base.core import (
+from ga4gh.va_spec.base import (
     DiagnosticPredicate,
     Direction,
     Document,
     PrognosticPredicate,
     TherapeuticResponsePredicate,
+    TherapyGroup,
+    VariantDiagnosticProposition,
+    VariantPrognosticProposition,
+    VariantTherapeuticResponseProposition,
 )
-from ga4gh.va_spec.base.domain_entities import TherapyGroup
 from ga4gh.vrs.models import Expression, Syntax, Variation
 from pydantic import BaseModel, ValidationError
 

diff --git a/src/metakb/transformers/moa.py b/src/metakb/transformers/moa.py
@@ -14,19 +14,19 @@
     MappableConcept,
     Relation,
 )
-from ga4gh.va_spec.aac_2017.models import (
-    VariantPrognosticProposition,
+from ga4gh.va_spec.aac_2017 import (
     VariantPrognosticStudyStatement,
-    VariantTherapeuticResponseProposition,
     VariantTherapeuticResponseStudyStatement,
 )
-from ga4gh.va_spec.base.core import (
+from ga4gh.va_spec.base import (
     Direction,
     Document,
     PrognosticPredicate,
     TherapeuticResponsePredicate,
+    TherapyGroup,
+    VariantPrognosticProposition,
+    VariantTherapeuticResponseProposition,
 )
-from ga4gh.va_spec.base.domain_entities import TherapyGroup
 from ga4gh.vrs.models import Variation
 
 from metakb import APP_ROOT