Merge pull request #87 from SCAI-BIO/fix-sql

Fix SQL database
SCAI-BIO · Sep 2, 2024 · d41973e · d41973e
2 parents 40478df + 40853d5
commit d41973e
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Showing 16 changed files with 2 additions and 773 deletions.
diff --git a/backend/api/routes.py b/backend/api/routes.py
@@ -24,12 +24,7 @@
 
 resources = {}
 logger = logging.getLogger("uvicorn.info")
-database = SQLLiteRepository(
-    db_path="./db/cdm.db",
-    data_path="./data",
-    initiate_with_data=True,
-    replace_if_exists=True,
-)
+database = SQLLiteRepository()
 weaviate = WeaviateRepository(
     mode="remote", path="http://ww8.index.k8s.bio.scai.fraunhofer.de"
 )
@@ -414,7 +409,7 @@ async def import_data(
                 if (
                     filename.startswith("longitudinal_")
                     or filename.startswith("biomarkers_")
-                    or filename == "metadata"
+                    or filename.startswith("metadata")
                 ):
                     database.store_upload(csv_data, table_name)
 

diff --git a/backend/data/cdm/APOE.csv b/backend/data/cdm/APOE.csv
diff --git a/backend/data/cdm/CSF.csv b/backend/data/cdm/CSF.csv