nci-cidc-api-modules 1.1.39__py3-none-any.whl → 1.1.40__py3-none-any.whl

cidc_api/config/db.py

@@ -45,7 +45,34 @@ def get_sqlalchemy_database_uri(testing: bool = False) -> str:
         # Connect to the test database
         db_uri = environ.get("TEST_POSTGRES_URI", "fake-conn-string")
     elif not db_uri:
-        db_uri = f"postgresql+pg8000://{environ.get('CLOUD_SQL_DB_USER')}:xxx@/{environ.get('CLOUD_SQL_DB_NAME')}"
+        # TODO: figure out why IAM authentication causes an issue with the huge filter query
+        # db_uri = f"postgresql+pg8000://{environ.get('CLOUD_SQL_DB_USER')}:xxx@/{environ.get('CLOUD_SQL_DB_NAME')}"
+
+        secrets = get_secrets_manager(testing)
+
+        # If POSTGRES_URI env variable is not set,
+        # we're connecting to a Cloud SQL instance.
+
+        config: dict = {
+            "drivername": "postgresql",
+            "username": environ.get("CLOUD_SQL_DB_USER"),
+            "password": secrets.get(environ.get("CLOUD_SQL_DB_PASS_ID")),
+            "database": environ.get("CLOUD_SQL_DB_NAME"),
+        }
+
+        if environ.get("CLOUD_SQL_INSTANCE_NAME"):
+            socket_dir = environ.get("CLOUD_SQL_SOCKET_DIR", "/cloudsql/")
+
+            # If CLOUD_SQL_INSTANCE_NAME is defined, we're connecting
+            # via a unix socket from inside App Engine.
+            config["query"] = {"host": f'{socket_dir}{environ.get("CLOUD_SQL_INSTANCE_NAME")}'}
+        else:
+            raise RuntimeError(
+                "Either POSTGRES_URI or CLOUD_SQL_INSTANCE_NAME must be defined to connect " + "to a database."
+            )
+
+        db_uri = str(URL.create(**config).render_as_string(hide_password=False))
+
     assert db_uri
 
     return db_uri
@@ -53,7 +80,9 @@ def get_sqlalchemy_database_uri(testing: bool = False) -> str:
 
 # Use SQLALCHEMY_ENGINE_OPTIONS to connect to the cloud but use uri for local db
 def cloud_connector(testing: bool = False):
-    if not testing and not environ.get("POSTGRES_URI"):
-        return {"creator": getconn}
-    else:
-        return {}
+    return {}
+    # TODO: figure out IAM authentication
+    # if not testing and not environ.get("POSTGRES_URI"):
+    #    return {"creator": getconn}
+    # else:
+    #    return {}

cidc_api/models/models.py

@@ -3463,13 +3463,15 @@ class IngestionJobs(CommonColumns):
     @with_default_session
     def atomic_set_job_as_pending(cls, job_id: int, session: Session) -> Boolean:
         # Preventing rare race condition where multiple people try and submit a job for validation
-        return bool(
+        result = bool(
             session.execute(
                 update(IngestionJobs)
                 .where(and_(IngestionJobs.id == job_id, IngestionJobs.pending == False))
                 .values(pending=True)
             ).rowcount
         )
+        session.commit()
+        return result
 
     @classmethod
     @with_default_session

{nci_cidc_api_modules-1.1.39.dist-info → nci_cidc_api_modules-1.1.40.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.39
+Version: 1.1.40
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license
@@ -29,7 +29,7 @@ Requires-Dist: requests==2.32.4
 Requires-Dist: jinja2==3.1.6
 Requires-Dist: certifi==2024.7.4
 Requires-Dist: cloud-sql-python-connector[pg8000]==1.18.3
-Requires-Dist: nci-cidc-schemas==0.27.27
+Requires-Dist: nci-cidc-schemas==0.27.28
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.1.39.dist-info → nci_cidc_api_modules-1.1.40.dist-info}/RECORD

@@ -1,11 +1,11 @@
 cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,148
-cidc_api/config/db.py,sha256=XEPRwjPj6rnCgcOM1p0qKb54tNo5708dDQcY6_wbs0U,1682
+cidc_api/config/db.py,sha256=kbCemCDYv_zyczw-V7H2JvLCa_XeEcvXkzvF28FxADw,2862
 cidc_api/config/logging.py,sha256=abhVYtn8lfhIt0tyV2WHFgSmp_s2eeJh7kodB6LH4J0,1149
 cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,1481
 cidc_api/config/settings.py,sha256=NsJbqW6Vqcz2f79xcAbk4th5tHne_I-RPCbKq_3hpz0,4427
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
 cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
-cidc_api/models/models.py,sha256=--EqlKE70vu-0MRvIMBJbp1rrU-kBlKtkHvZD-eGkVA,142895
+cidc_api/models/models.py,sha256=eRZrUcQYIe_V5hMwD3ONc175vPQpUTe_KPcmGdYexJc,142944
 cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
 cidc_api/models/files/details.py,sha256=sZkGM7iEV4-J6IDQCdiMV6KBDLbPxCOqUMaU3aY9rX8,65153
@@ -17,8 +17,8 @@ cidc_api/shared/file_handling.py,sha256=l4wiRkVJLL7QbCoODsLx-uki6Km8QoMmUlRVnUV9
 cidc_api/shared/gcloud_client.py,sha256=cNtzCRsD_StBQRAzWJ8BimW-ecEGOqywvlM7kip8CrE,36681
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
-nci_cidc_api_modules-1.1.39.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.1.39.dist-info/METADATA,sha256=6OU-ZN-TmCrbxAwF162kbfvsUCaeqsgHcPWGNZG0UGQ,39967
-nci_cidc_api_modules-1.1.39.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.1.39.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.1.39.dist-info/RECORD,,
+nci_cidc_api_modules-1.1.40.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.1.40.dist-info/METADATA,sha256=IZwg1tt0j0d6j8ve8d3yYrfck4Hnp_GKo2By-9bb0vM,39967
+nci_cidc_api_modules-1.1.40.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.1.40.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.1.40.dist-info/RECORD,,