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cancervariants · Jul 11, 2024 · fee46cb · fee46cb
1 parent d9ac25f
commit fee46cb
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Showing 5 changed files with 29 additions and 167 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -31,13 +31,13 @@ dependencies = [
     "uvicorn",
     "click",
     "boto3",
-    "ga4gh.vrs~=2.0.0a1",
+    # "ga4gh.vrs~=2.0.0a1",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 etl = [
-    "disease-normalizer[etl]~=0.4.0.dev0",
+    # "disease-normalizer[etl]~=0.4.0.dev0",
     "owlready2",
     "rdflib",
     "wikibaseintegrator>=0.12.0",

diff --git a/src/therapy/query.py b/src/therapy/query.py
@@ -5,7 +5,7 @@
 from typing import Any, Callable, Dict, List, Optional, Set, Tuple, TypeVar, Union
 
 from botocore.exceptions import ClientError
-from ga4gh.core import core_models
+from ga4gh.core import domain_models, entity_models
 from uvicorn.config import logger
 
 from therapy import NAMESPACE_LUIS, PREFIX_LOOKUP, SOURCES
@@ -391,7 +391,7 @@ def _add_therapeutic_agent(
         :param MatchType match_type: type of match achieved
         :return: completed response object ready to return to user
         """
-        therapeutic_agent_obj = core_models.TherapeuticAgent(
+        therapeutic_agent_obj = domain_models.TherapeuticAgent(
             id=f"normalize.therapy.{record['concept_id']}", label=record.get("label")
         )
 
@@ -400,18 +400,18 @@ def _add_therapeutic_agent(
         for source_id in source_ids:
             system, code = source_id.split(":")
             mappings.append(
-                core_models.Mapping(
-                    coding=core_models.Coding(
-                        code=core_models.Code(code), system=system.lower()
+                entity_models.ConceptMapping(
+                    coding=entity_models.Coding(
+                        code=entity_models.Code(code), system=system.lower()
                     ),
-                    relation=core_models.Relation.RELATED_MATCH,
+                    relation=entity_models.Relation.RELATED_MATCH,
                 )
             )
         if mappings:
             therapeutic_agent_obj.mappings = mappings
 
         if "aliases" in record:
-            therapeutic_agent_obj.aliases = record["aliases"]
+            therapeutic_agent_obj.alternativeLabels = record["aliases"]
 
         extensions = []
         if any(
@@ -438,39 +438,39 @@ def _add_therapeutic_agent(
                 if indication.normalized_disease_id:
                     system, code = indication.normalized_disease_id.split(":")
                     mappings = [
-                        core_models.Mapping(
-                            coding=core_models.Coding(
-                                code=core_models.Code(code), system=system.lower()
+                        entity_models.ConceptMapping(
+                            coding=entity_models.Coding(
+                                code=entity_models.Code(code), system=system.lower()
                             ),
-                            relation=core_models.Relation.RELATED_MATCH,
+                            relation=entity_models.Relation.RELATED_MATCH,
                         )
                     ]
                 else:
                     mappings = []
-                ind_disease_obj = core_models.Disease(
+                ind_disease_obj = domain_models.Disease(
                     id=indication.disease_id,
                     label=indication.disease_label,
                     mappings=mappings or None,
                 )
 
                 if indication.supplemental_info:
                     ind_disease_obj.extensions = [
-                        core_models.Extension(name=k, value=v)
+                        entity_models.Extension(name=k, value=v)
                         for k, v in indication.supplemental_info.items()
                     ]
                 inds_list.append(ind_disease_obj.model_dump(exclude_none=True))
             if inds_list:
                 approv_value["has_indication"] = inds_list
 
-            approv = core_models.Extension(
+            approv = entity_models.Extension(
                 name="regulatory_approval", value=approv_value
             )
             extensions.append(approv)
 
         trade_names = record.get("trade_names")
         if trade_names:
             extensions.append(
-                core_models.Extension(name="trade_names", value=trade_names)
+                entity_models.Extension(name="trade_names", value=trade_names)
             )
 
         if extensions:

diff --git a/src/therapy/schemas.py b/src/therapy/schemas.py
@@ -3,7 +3,7 @@
 from enum import Enum, IntEnum
 from typing import Any, Dict, List, Literal, Optional, Set, Union
 
-from ga4gh.core import core_models
+from ga4gh.core import domain_models
 from pydantic import BaseModel, ConfigDict, StrictBool, constr
 
 from therapy.version import __version__
@@ -484,7 +484,7 @@ class NormalizationService(BaseNormalizationService):
     """Response containing one or more merged records and source data."""
 
     normalized_id: Optional[str] = None
-    therapeutic_agent: Optional[core_models.TherapeuticAgent] = None
+    therapeutic_agent: Optional[domain_models.TherapeuticAgent] = None
     source_meta_: Optional[Dict[SourceName, SourceMeta]] = None
 
     model_config = ConfigDict(
@@ -560,7 +560,7 @@ class NormalizationService(BaseNormalizationService):
                             "relation": "relatedMatch",
                         },
                     ],
-                    "aliases": [
+                    "alternativeLabels": [
                         "CIS-DDP",
                         "cis Platinum",
                         "DDP",
@@ -583,7 +583,6 @@ class NormalizationService(BaseNormalizationService):
                     ],
                     "extensions": [
                         {
-                            "type": "Extension",
                             "name": "trade_names",
                             "value": ["Platinol", "Cisplatin"],
                         },