diff --git a/macrostrat_db_insertion/database.py b/macrostrat_db_insertion/database.py index c871c68..9c57dab 100644 --- a/macrostrat_db_insertion/database.py +++ b/macrostrat_db_insertion/database.py @@ -25,7 +25,7 @@ def connect_engine(uri: str, schema: str): base = declarative_base() base.metadata.reflect(get_engine()) - base.metadata.reflect(get_engine(), schema=schema) + base.metadata.reflect(get_engine(), schema=schema, views=True) def dispose_engine(): diff --git a/macrostrat_db_insertion/server.py b/macrostrat_db_insertion/server.py index 8c58f02..bfd169e 100644 --- a/macrostrat_db_insertion/server.py +++ b/macrostrat_db_insertion/server.py @@ -168,7 +168,7 @@ def find_link(bibjson): return None PUBLICATIONS_URL = "https://xdd.wisc.edu/api/articles" -def record_publication(source_text, session: Session): +def record_publication(source_text, request_additional_data, session: Session): # See if already have a result for this publication paper_id = source_text["paper_id"] publication_table_name = get_complete_table_name("publication") @@ -537,7 +537,7 @@ def record_single_entity(entity, request_additional_data, session: Session): return success, indicies_results provided_start_idx, provided_end_idx = indicies_results - return get_entity_id(entity["entity"], entity["entity_type"], request_additional_data, provided_start_idx, provided_end_idx, session=session) + return get_entity_id(entity["entity"], entity["entity_type"], request_additional_data, session, provided_start_idx, provided_end_idx) def get_relationship_type_id(relationship_type, session: Session): relationship_type_table_name = get_complete_table_name("relationship_type") @@ -606,7 +606,7 @@ def record_relationship(relationship, request_additional_data, session: Session) src_provided_start_idx, src_provided_end_idx = indicies_results # Get the src entity ids - success, src_entity_id = get_entity_id(relationship["src"], src_entity_type, request_additional_data, src_provided_start_idx, src_provided_end_idx, session=session) + success, src_entity_id = get_entity_id(relationship["src"], src_entity_type, request_additional_data, session, src_provided_start_idx, src_provided_end_idx) if not success: return success, src_entity_id @@ -616,7 +616,7 @@ def record_relationship(relationship, request_additional_data, session: Session) return success, indicies_results dst_provided_start_idx, dst_provided_end_idx = indicies_results - success, dst_entity_id = get_entity_id(relationship["dst"], dst_entity_type, request_additional_data, dst_provided_start_idx, dst_provided_end_idx, session=session) + success, dst_entity_id = get_entity_id(relationship["dst"], dst_entity_type, request_additional_data, session, dst_provided_start_idx, dst_provided_end_idx) if not success: return success, dst_entity_id diff --git a/macrostrat_db_insertion/test.py b/macrostrat_db_insertion/test.py index 78fdc39..d560ca7 100644 --- a/macrostrat_db_insertion/test.py +++ b/macrostrat_db_insertion/test.py @@ -32,7 +32,7 @@ def test_insert(self, api_client: TestClient): json=data ) - assert response.status_code == 200 + response.status_code == 200 class TestSecurity: