Merge pull request #56 from PennChopMicrobiomeProgram/55-allow-explicit-sqlalchemy-uri-via-env

Define db URI directly in env

Author: Ulthran

app/metadatalib/src/metadatalib/__init__.py

@@ -6,20 +6,13 @@
 from sqlalchemy.orm import sessionmaker
 
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 
 try:
-    db_host = os.environ["METADATA_DB_HOST"]
-    db_user = os.environ["METADATA_DB_USER"]
-    db_name = os.environ["METADATA_DB_NAME"]
-    db_pswd = os.environ["METADATA_DB_PSWD"]
-    SQLALCHEMY_DATABASE_URI = f"postgresql://{db_user}:{db_pswd}@{db_host}/{db_name}"
+    SQLALCHEMY_DATABASE_URI = os.environ["METADATA_DB_URI"]
 except KeyError:
     sys.stderr.write(
-        "Missing database connection information in environment, using test SQLite database.\n"
-    )
-    sys.stderr.write(
-        f"METADATA_DB_HOST: {os.environ.get('METADATA_DB_HOST')}\nMETADATA_DB_USER: {os.environ.get('METADATA_DB_USER')}\nMETADATA_DB_NAME: {os.environ.get('METADATA_DB_NAME')}\nMETADATA_DB_PSWD: {os.environ.get('METADATA_DB_PSWD')}\n"
+        "Missing METADATA_DB_URI in environment, using test SQLite database.\n"
     )
     SQLALCHEMY_DATABASE_URI = f"sqlite:///{Path(__file__).parent.parent.parent.parent.parent.resolve()}/metadata.sqlite3"
 
@@ -29,5 +22,6 @@
     session = Session()
 except SQLAlchemyError as e:
     # Need to do handling here
+    sys.stderr.write(f"Error connecting to database: {SQLALCHEMY_DATABASE_URI}\n")
     raise e
     session = None