fix disease references per PR suggestsions

cancervariants · Oct 26, 2023 · 22a0938 · 22a0938
1 parent cc704e9
commit 22a0938
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/therapy/cli.py b/therapy/cli.py
@@ -7,8 +7,8 @@
 import click
 from botocore.exceptions import ClientError
 from boto3.dynamodb.conditions import Key
-from disease.database import Database as DiseaseDatabase
-from disease.cli import CLI as DiseaseCLI
+from disease.database.dynamodb import DynamoDbDatabase as DiseaseDatabase
+from disease.cli import update_db as update_disease_db
 from disease.schemas import SourceName as DiseaseSources
 
 from therapy import SOURCES
@@ -134,7 +134,7 @@ def _check_disease_normalizer(self, normalizers: List[str],
                 logger.debug(msg)
                 click.echo(msg)
                 try:
-                    DiseaseCLI().update_normalizer_db(
+                    update_disease_db(
                         ["--update_all", "--update_merged", "--db_url", endpoint_url]
                     )
                 except Exception as e:

diff --git a/therapy/etl/base.py b/therapy/etl/base.py
@@ -14,6 +14,7 @@
 from pydantic import ValidationError
 import requests
 import bioversions
+from disease.database.dynamodb import DynamoDbDatabase
 from disease.query import QueryHandler as DiseaseNormalizer
 
 from therapy import APP_ROOT, ITEM_TYPES, DownloadException
@@ -318,7 +319,8 @@ def __init__(self, database: Database, data_path: Path = DEFAULT_DATA_PATH):
         :param Path data_path: path to normalizer data directory
         """
         super().__init__(database, data_path)
-        self.disease_normalizer = DiseaseNormalizer(self.database.endpoint_url)
+        db = DynamoDbDatabase(self.database.endpoint_url)
+        self.disease_normalizer = DiseaseNormalizer(db)
 
     @lru_cache(maxsize=64)
     def _normalize_disease(self, query: str) -> Optional[str]: