nci-cidc-api-modules 1.1.1__tar.gz → 1.1.3__tar.gz

{nci_cidc_api_modules-1.1.1/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nci_cidc_api_modules
-Version: 1.1.1
+Version: 1.1.3
 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
@@ -8,10 +8,10 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: werkzeug==3.0.6
-Requires-Dist: flask==2.2.5
-Requires-Dist: flask-migrate==2.5.2
-Requires-Dist: flask-sqlalchemy==2.5.1
-Requires-Dist: sqlalchemy~=1.3.0
+Requires-Dist: flask==3.0.3
+Requires-Dist: flask-migrate==3.1.0
+Requires-Dist: flask-sqlalchemy==3.0.2
+Requires-Dist: sqlalchemy==1.4.54
 Requires-Dist: marshmallow==3.19.0
 Requires-Dist: marshmallow-sqlalchemy==0.22.3
 Requires-Dist: google-cloud-storage==2.18.0
@@ -28,7 +28,7 @@ Requires-Dist: python-dotenv==0.10.3
 Requires-Dist: requests==2.32.3
 Requires-Dist: jinja2==3.1.5
 Requires-Dist: certifi==2024.7.4
-Requires-Dist: nci-cidc-schemas==0.27.01
+Requires-Dist: nci-cidc-schemas==0.27.02
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.1.1 → nci_cidc_api_modules-1.1.3}/cidc_api/models/csms_api.py

@@ -460,10 +460,10 @@ def insert_manifest_into_blob(
     if errs:
         raise RuntimeError({"prism errors": [str(e) for e in errs]})
 
-    # save it
-    trial_md.update(changes={"metadata_json": merged}, commit=False, session=session)
+    # save it, will get rolled back if in a dry run
+    trial_md.update(changes={"metadata_json": merged}, session=session)
 
-    # create pseudo-UploadJobs
+    # create pseudo-UploadJobs that will get rolled back if in a dry run
     UploadJobs(
         trial_id=trial_id,
         _status=UploadJobStatus.MERGE_COMPLETED.value,
@@ -471,7 +471,7 @@ def insert_manifest_into_blob(
         metadata_patch=patch,
         upload_type=_get_upload_type(csms_samples),
         uploader_email=uploader_email,
-    ).insert(commit=False, session=session)
+    ).insert(session=session)
 
     if dry_run:
         session.flush()

{nci_cidc_api_modules-1.1.1 → nci_cidc_api_modules-1.1.3}/cidc_api/models/models.py

@@ -1433,9 +1433,8 @@ class TrialMetadata(CommonColumns):
         a dictionary mapping column names to updated values. Skip JSON metadata validation
         if validate_metadata=False.
         """
-        # Since commit=False, this will only apply changes to the in-memory
-        # TrialMetadata instance, not the corresponding db record
-        super().update(session=session, changes=changes, commit=False)
+        # This update will get rolled back if commit = False
+        super().update(session=session, changes=changes)
 
         # metadata_json was possibly updated in above method call,
         # so check that it's still valid if validate_metadata=True
@@ -1444,6 +1443,8 @@ class TrialMetadata(CommonColumns):
 
         if commit:
             session.commit()
+        else:
+            session.rollback()
 
     @classmethod
     def build_trial_filter(cls, user: Users, trial_ids: List[str] = None):
@@ -3270,4 +3271,4 @@ def result_proxy_to_models(
     result_proxy: ResultProxy, model: BaseModel
 ) -> List[BaseModel]:
     """Materialize a sqlalchemy `result_proxy` iterable as a list of `model` instances"""
-    return [model(**dict(row_proxy.items())) for row_proxy in result_proxy]
+    return [model(**dict(row_proxy)) for row_proxy in result_proxy.all()]

{nci_cidc_api_modules-1.1.1 → nci_cidc_api_modules-1.1.3/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nci_cidc_api_modules
-Version: 1.1.1
+Version: 1.1.3
 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
@@ -8,10 +8,10 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: werkzeug==3.0.6
-Requires-Dist: flask==2.2.5
-Requires-Dist: flask-migrate==2.5.2
-Requires-Dist: flask-sqlalchemy==2.5.1
-Requires-Dist: sqlalchemy~=1.3.0
+Requires-Dist: flask==3.0.3
+Requires-Dist: flask-migrate==3.1.0
+Requires-Dist: flask-sqlalchemy==3.0.2
+Requires-Dist: sqlalchemy==1.4.54
 Requires-Dist: marshmallow==3.19.0
 Requires-Dist: marshmallow-sqlalchemy==0.22.3
 Requires-Dist: google-cloud-storage==2.18.0
@@ -28,7 +28,7 @@ Requires-Dist: python-dotenv==0.10.3
 Requires-Dist: requests==2.32.3
 Requires-Dist: jinja2==3.1.5
 Requires-Dist: certifi==2024.7.4
-Requires-Dist: nci-cidc-schemas==0.27.01
+Requires-Dist: nci-cidc-schemas==0.27.02
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.1.1 → nci_cidc_api_modules-1.1.3}/nci_cidc_api_modules.egg-info/requires.txt

@@ -1,8 +1,8 @@
 werkzeug==3.0.6
-flask==2.2.5
-flask-migrate==2.5.2
-flask-sqlalchemy==2.5.1
-sqlalchemy~=1.3.0
+flask==3.0.3
+flask-migrate==3.1.0
+flask-sqlalchemy==3.0.2
+sqlalchemy==1.4.54
 marshmallow==3.19.0
 marshmallow-sqlalchemy==0.22.3
 google-cloud-storage==2.18.0
@@ -19,4 +19,4 @@ python-dotenv==0.10.3
 requests==2.32.3
 jinja2==3.1.5
 certifi==2024.7.4
-nci-cidc-schemas==0.27.01
+nci-cidc-schemas==0.27.02

{nci_cidc_api_modules-1.1.1 → nci_cidc_api_modules-1.1.3}/requirements.modules.txt

@@ -1,8 +1,8 @@
 werkzeug==3.0.6
-flask==2.2.5
-flask-migrate==2.5.2
-flask-sqlalchemy==2.5.1
-sqlalchemy~=1.3.0
+flask==3.0.3
+flask-migrate==3.1.0
+flask-sqlalchemy==3.0.2
+sqlalchemy==1.4.54
 marshmallow==3.19.0
 marshmallow-sqlalchemy==0.22.3
 google-cloud-storage==2.18.0
@@ -19,4 +19,4 @@ python-dotenv==0.10.3
 requests==2.32.3
 jinja2==3.1.5
 certifi==2024.7.4
-nci-cidc-schemas==0.27.01
+nci-cidc-schemas==0.27.02