Merge pull request #90 from SCAI-BIO/refactor-url

Refactor url

CITATION.cff

@@ -10,14 +10,29 @@ type: software
 authors:
   - given-names: Mehmet Can
     family-names: Ay
+    email: [email protected]
+    affiliation: Fraunhofer Institute for Algorithms and Scientific Computing
+    orcid: https://orcid.org/0000-0002-2977-7695
   - given-names: Tim
     family-names: Adams
+    email: [email protected]
+    affiliation: Fraunhofer Institute for Algorithms and Scientific Computing
+    orcid: https://orcid.org/0000-0002-2823-0102
   - given-names: Yasamin
     family-names: Salimi
+    email: [email protected]
+    affiliation: Fraunhofer Institute for Algorithms and Scientific Computing
+    orcid: https://orcid.org/0000-0002-7773-7786
   - given-names: Marjan
     family-names: Niazpoor
+    email: [email protected]
+    affiliation: Fraunhofer Institute for Algorithms and Scientific Computing
+    orcid: https://orcid.org/0009-0000-1455-6569
   - given-names: Marc
     family-names: Jacobs
+    email: [email protected]
+    affiliation: Fraunhofer Institute for Algorithms and Scientific Computing
+    orcid: https://orcid.org/0000-0003-4153-3930
 identifiers:
   - type: doi
     value: 10.5281/zenodo.13629128
@@ -33,7 +48,7 @@ keywords:
   - Interoperability
   - FAIR principles
 license: Apache-2.0
-version: 0.0.8
+version: 0.0.9
 date-released: "2024-09-02"
 preferred-citation:
   title: On the Utility of Large Language Model Embeddings for Revolutionizing Semantic Data Harmonization in Alzheimer's and Parkinson's Disease

backend/api/routes.py

@@ -10,6 +10,7 @@
 from datastew import DataDictionarySource
 from datastew.embedding import GPT4Adapter, MPNetAdapter
 from datastew.repository.weaviate import WeaviateRepository
+from dotenv import load_dotenv
 from fastapi import Depends, FastAPI, File, Form, HTTPException, UploadFile
 from fastapi.responses import RedirectResponse
 from fastapi.security import HTTPBasicCredentials
@@ -22,12 +23,13 @@
 
 from api.auth import authenticate_user, init_credentials
 
+load_dotenv()
+
 resources = {}
 logger = logging.getLogger("uvicorn.info")
+weaviate_url = os.getenv("WEAVIATE_URL", "http://weaviate:8080")
 database = SQLLiteRepository()
-weaviate = WeaviateRepository(
-    mode="remote", path="http://ww8.index.k8s.bio.scai.fraunhofer.de"
-)
+weaviate = WeaviateRepository(mode="remote", path=weaviate_url)
 
 
 @asynccontextmanager