Fix/database

requirements.in

@@ -7,5 +7,4 @@ geode-common==33.11.0
 geode-viewables==3.3.0
 flask[async]==3.1.2
 flask-cors==6.0.1
-werkzeug==3.1.2
-flask-sqlalchemy==3.1.1
+werkzeug==3.1.2

requirements.txt

@@ -14,19 +14,14 @@ flask[async]>=3
     # via
     #   -r requirements.in
     #   flask-cors
-    #   flask-sqlalchemy
 flask-cors==6.0.1
     # via -r requirements.in
-flask-sqlalchemy==3.1.1
-    # via -r requirements.in
 geode-common==33.11.0
     # via
     #   -r requirements.in
     #   geode-viewables
 geode-viewables==3.3.0
     # via -r requirements.in
-greenlet>=3
-    # via sqlalchemy
 itsdangerous>=2
     # via flask
 jinja2>=3
@@ -59,14 +54,9 @@ opengeode-io==7.4.0
     #   -r requirements.in
     #   geode-viewables
     #   opengeode-geosciencesio
-sqlalchemy>=2
-    # via flask-sqlalchemy
-typing-extensions>=4
-    # via sqlalchemy
 werkzeug==3.1.2
     # via
     #   -r requirements.in
     #   flask
     #   flask-cors
 
-opengeodeweb-microservice==1.*,>=1.0.4rc7

src/opengeodeweb_back/app.py

@@ -140,12 +140,13 @@ def run_server() -> None:
         flush=True,
     )
 
-    db_filename: str = app.config.get("DATABASE_FILENAME") or "database.db"
+    db_filename: str = app.config.get("DATABASE_FILENAME") or "project.db"
     db_path = os.path.join(args.data_folder_path, db_filename)
     os.makedirs(os.path.dirname(db_path), exist_ok=True)
     app.config["SQLALCHEMY_DATABASE_URI"] = f"sqlite:///{db_path}"
     app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = False
-    init_database(app, db_filename)
+
+    init_database(db_path)
     print(f"Database initialized at: {db_path}", flush=True)
 
     app.run(debug=args.debug, host=args.host, port=args.port, ssl_context=SSL)

src/opengeodeweb_back/utils_functions.py

@@ -163,7 +163,7 @@ def create_data_folder_from_id(data_id: str) -> str:
 def save_all_viewables_and_return_info(
     geode_object: str,
     data: Any,
-    input_file: str,
+    input_file: str | None = None,
     additional_files: list[str] | None = None,
 ) -> dict[str, Any]:
     if additional_files is None:
@@ -227,6 +227,8 @@ def generate_native_viewable_and_light_viewable_from_object(
 def generate_native_viewable_and_light_viewable_from_file(
     geode_object: str, input_filename: str
 ) -> dict[str, Any]:
+
+    session = get_session()
     temp_data_entry = Data.create(
         geode_object=geode_object,
         input_file=input_filename,
@@ -258,10 +260,10 @@ def generate_native_viewable_and_light_viewable_from_file(
 
     data = geode_functions.load(geode_object, copied_full_path)
 
-    session = get_session()
     if session:
         session.delete(temp_data_entry)
         session.flush()
+        session.commit()
 
     return save_all_viewables_and_return_info(
         geode_object,

tests/conftest.py

@@ -36,7 +36,7 @@ def configure_test_environment() -> Generator[None, None, None]:
     print("Current working directory:", os.getcwd())
     print("Directory contents:", os.listdir("."))
 
-    init_database(app, db_path)
+    init_database(db_path)
     os.environ["TEST_DB_PATH"] = str(db_path)
 
     yield