nci-cidc-api-modules 1.1.2__py3-none-any.whl → 1.1.3__py3-none-any.whl

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()

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-1.1.2.dist-info → nci_cidc_api_modules-1.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nci_cidc_api_modules
-Version: 1.1.2
+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

{nci_cidc_api_modules-1.1.2.dist-info → nci_cidc_api_modules-1.1.3.dist-info}/RECORD

@@ -6,9 +6,9 @@ cidc_api/config/settings.py,sha256=2VHOVWdN4yUCNYMob2gaWgH2-1_4sbuo46JEIVT_PCY,4
 cidc_api/csms/__init__.py,sha256=eJkY6rWNOAUBmSd4G1_U6h7i472druKEtBdVmgFZVPg,20
 cidc_api/csms/auth.py,sha256=25Yma2Kz3KLENAPSeBYacFuSZXng-EDgmgInKBsRyP0,3191
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
-cidc_api/models/csms_api.py,sha256=U_JP6Z41G4hi48yNn9MAd70IYfBcm3AF3wHa31NdA78,31578
+cidc_api/models/csms_api.py,sha256=k8QAE-uU6b8PvkFx_dBG-i224J-bUhM4KGwqZSq6Ua8,31630
 cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
-cidc_api/models/models.py,sha256=ykt0aG8jMjDdHYw3iPnU3laOaOZloHLf3ep6BeYM2cI,126732
+cidc_api/models/models.py,sha256=kszT6ApBOIDsRJRHiYQvWo8283Jox_x0nPuetXBeK74,126680
 cidc_api/models/schemas.py,sha256=7tDYtmULuzTt2kg7RorWhte06ffalgpQKrFiDRGcPEQ,2711
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
 cidc_api/models/files/details.py,sha256=h6R0p_hi-ukHsO7HV-3Wukccp0zRLJ1Oie_JNA_7Pl0,62274
@@ -19,8 +19,8 @@ cidc_api/shared/emails.py,sha256=TXKrga3A8rvaUKIH68ASmjkg9qMdFCWDf5HHxPvro5M,489
 cidc_api/shared/gcloud_client.py,sha256=7dDs0crLMJKdIp4IDSfrZBMB3h-zvWNieB81azoeLO4,33746
 cidc_api/shared/jose.py,sha256=QO30uIhbYDwzPEWWJXz0PfyV7E1AZHReEZJUVT70UJY,1844
 cidc_api/shared/rest_utils.py,sha256=LMfBpvJRjkfQjCzVXuhTTe4Foz4wlvaKg6QntyR-Hkc,6648
-nci_cidc_api_modules-1.1.2.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.1.2.dist-info/METADATA,sha256=Hma7qYjTas8rMWIIK1qCakAvR33LjGsj4ibv31CbgeI,40806
-nci_cidc_api_modules-1.1.2.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nci_cidc_api_modules-1.1.2.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.1.2.dist-info/RECORD,,
+nci_cidc_api_modules-1.1.3.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.1.3.dist-info/METADATA,sha256=sePEUJbt_M0zOTBdkhMA5wAAs8D9masRfulJDmlVJzg,40807
+nci_cidc_api_modules-1.1.3.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+nci_cidc_api_modules-1.1.3.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.1.3.dist-info/RECORD,,

{nci_cidc_api_modules-1.1.2.dist-info → nci_cidc_api_modules-1.1.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any