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cancervariants · Feb 4, 2025 · 3cacc2c · 3cacc2c
1 parent 1a0ffdc
commit 3cacc2c
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Showing 7 changed files with 176 additions and 134 deletions.
diff --git a/Pipfile b/Pipfile
@@ -4,11 +4,11 @@ verify_ssl = true
 name = "pypi"
 
 [packages]
-"ga4gh.vrs" = "~=2.0.0a10"
-gene-normalizer = {version = "~=0.4.1", extras = ["etl"]}
-variation-normalizer = "~=0.10.0"
-disease-normalizer = {version = "~=0.5.0", extras = ["etl"]}
-thera-py = {version = "~=0.6.0", extras = ["etl"]}
+"ga4gh.vrs" = "==2.0.0a13"
+gene-normalizer = {version = "~=0.7.0", extras = ["etl"]}
+variation-normalizer = "~=0.12.1"
+disease-normalizer = {version = "~=0.8.0", extras = ["etl"]}
+thera-py = {version = "~=0.8.0", extras = ["etl"]}
 civicpy = "~=3.1"
 requests = "*"
 pydantic = "==2.*"

diff --git a/pyproject.toml b/pyproject.toml
@@ -26,10 +26,10 @@ dependencies = [
     "ga4gh.vrs==2.0.0a13",
     "ga4gh.cat_vrs~=0.2.1",
     "ga4gh.va_spec @ git+https://github.com/ga4gh/va-spec-python.git@issue-10",
-    "gene-normalizer[etl]~=0.6.0",
-    "variation-normalizer~=0.12.0",
-    "disease-normalizer[etl]~=0.7.0",
-    "thera-py[etl]~=0.7.1",
+    "gene-normalizer[etl]~=0.7.0",
+    "variation-normalizer~=0.12.1",
+    "disease-normalizer[etl]~=0.8.0",
+    "thera-py[etl]~=0.8.0",
     "civicpy~=3.1",
     "requests",
     "pydantic==2.*",

diff --git a/src/metakb/transformers/base.py b/src/metakb/transformers/base.py
@@ -9,9 +9,6 @@
 from pathlib import Path
 from typing import ClassVar, TypeVar
 
-from disease.schemas import (
-    SYSTEM_URI_TO_NAMESPACE as DISEASE_SYSTEM_URI_TO_NAMESPACE,
-)
 from disease.schemas import (
     NamespacePrefix as DiseaseNamespacePrefix,
 )
@@ -591,13 +588,12 @@ def _add_merged_id_ext(
         normalizer_mappings = normalizer_resp_obj.mappings or []
         if isinstance(normalizer_resp, NormalizedDisease):
             for mapping in normalizer_mappings:
-                if (
-                    DISEASE_SYSTEM_URI_TO_NAMESPACE.get(mapping.coding.system)
-                    == DiseaseNamespacePrefix.MONDO.value
+                if mapping.coding.code.root.lower().startswith(
+                    DiseaseNamespacePrefix.MONDO.value
                 ):
                     mappings.append(_add_merged_id_ext(mapping, is_priority=False))
                 else:
-                    if normalized_id == mapping.coding.code.root:
+                    if normalized_id == mapping.coding.id:
                         mappings.append(
                             _add_merged_id_ext(
                                 mapping,
@@ -611,7 +607,7 @@ def _add_merged_id_ext(
                     mapping, label=normalizer_resp_obj.label, is_priority=True
                 )
                 for mapping in normalizer_mappings
-                if normalized_id == mapping.coding.code.root
+                if normalized_id == mapping.coding.id
             )
         return mappings