nci-cidc-api-modules 1.1.41__tar.gz → 1.2.1__tar.gz

{nci_cidc_api_modules-1.1.41/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.1}/PKG-INFO

@@ -1,35 +1,35 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.41
+Version: 1.2.1
 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
-Requires-Python: >=3.9
+Requires-Python: >=3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: werkzeug==3.0.6
-Requires-Dist: flask==3.0.3
-Requires-Dist: flask-migrate==3.1.0
-Requires-Dist: flask-sqlalchemy==3.1.1
-Requires-Dist: sqlalchemy==2.0.41
-Requires-Dist: marshmallow==3.19.0
-Requires-Dist: marshmallow-sqlalchemy==1.4.2
-Requires-Dist: google-cloud-storage==2.18.0
-Requires-Dist: google-cloud-secret-manager==2.20.1
-Requires-Dist: google-cloud-pubsub==2.22.0
-Requires-Dist: google-cloud-bigquery==3.18.0
-Requires-Dist: google-api-python-client==2.64.0
-Requires-Dist: google-auth==2.32.0
-Requires-Dist: packaging>=20.0.0
-Requires-Dist: pyarrow==14.0.1
-Requires-Dist: numpy<2,>=1.16.5
-Requires-Dist: pandas==1.5.3
-Requires-Dist: python-dotenv==0.10.3
-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==0.27.28
+Requires-Dist: werkzeug>=3.1.3
+Requires-Dist: flask>=3.1.2
+Requires-Dist: flask-migrate>=4.1.0
+Requires-Dist: flask-sqlalchemy>=3.1.1
+Requires-Dist: sqlalchemy>=2.0.43
+Requires-Dist: marshmallow>=4.0.0
+Requires-Dist: marshmallow-sqlalchemy>=1.4.2
+Requires-Dist: google-cloud-storage>=3.3.0
+Requires-Dist: google-cloud-secret-manager>=2.24.0
+Requires-Dist: google-cloud-pubsub>=2.31.1
+Requires-Dist: google-cloud-bigquery>=3.36.0
+Requires-Dist: google-api-python-client>=2.179.0
+Requires-Dist: google-auth>=2.40.3
+Requires-Dist: packaging>=25.0
+Requires-Dist: pyarrow>=21.0.0
+Requires-Dist: numpy>=2.3.2
+Requires-Dist: pandas>=2.3.1
+Requires-Dist: python-dotenv>=1.1.1
+Requires-Dist: requests>=2.32.5
+Requires-Dist: jinja2>=3.1.6
+Requires-Dist: certifi>=2025.8.3
+Requires-Dist: cloud-sql-python-connector[pg8000]>=1.18.4
+Requires-Dist: nci-cidc-schemas==0.28.2
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
@@ -62,7 +62,7 @@ The next generation of the CIDC API, reworked to use Google Cloud-managed servic
 
 ## Install Python dependencies
 
-Python versions tested include 3.9 and 3.10. The current App Engine is using version 3.9 (see [app.prod.yaml](./app.prod.yaml)). You can use https://github.com/pyenv/pyenv to manage your python versions. Homebrew will also work, but you will have to be specific when you install packages with pip outside of virtual environments. On that note, it is recommended that you install your python dependencies in an isolated environment. For example,
+Use Python version 3.13
 
 ```bash
 # make a virtual environment in the current direcory called "venv"

{nci_cidc_api_modules-1.1.41 → nci_cidc_api_modules-1.2.1}/README.md

@@ -21,7 +21,7 @@ The next generation of the CIDC API, reworked to use Google Cloud-managed servic
 
 ## Install Python dependencies
 
-Python versions tested include 3.9 and 3.10. The current App Engine is using version 3.9 (see [app.prod.yaml](./app.prod.yaml)). You can use https://github.com/pyenv/pyenv to manage your python versions. Homebrew will also work, but you will have to be specific when you install packages with pip outside of virtual environments. On that note, it is recommended that you install your python dependencies in an isolated environment. For example,
+Use Python version 3.13
 
 ```bash
 # make a virtual environment in the current direcory called "venv"

{nci_cidc_api_modules-1.1.41 → nci_cidc_api_modules-1.2.1}/cidc_api/models/models.py

@@ -1345,14 +1345,14 @@ class TrialMetadata(CommonColumns):
                     if not trial.file_bundle[assay]:
                         del trial.file_bundle[assay]
             # Check if trial is ready for submission
-            setattr(trial, "ready_for_submission", trial.ready_for_submission())
+            setattr(trial, "ready_for_submission", trial.determine_ready_for_submission())
 
             trials.append(trial)
 
         return trials
 
     @with_default_session
-    def ready_for_submission(self, session: Session) -> Boolean:
+    def determine_ready_for_submission(self, session: Session) -> Boolean:
         open_job = IngestionJobs.get_open_job_by_trial(self.trial_id)
         if not open_job:
             return False
@@ -3571,3 +3571,11 @@ class FileValidationErrors(CommonColumns):
         new_error = FileValidationErrors(file_id=file_id, job_id=job_id, error_message=error_message, location=location)
         new_error.insert(session=session)
         return new_error
+
+    @classmethod
+    @with_default_session
+    def delete_by_file_ids(cls, file_ids: list[int], session: Session = None):
+        """Delete all validation errors for the given list of file_ids."""
+        if file_ids:
+            session.query(cls).filter(cls.file_id.in_(file_ids)).delete(synchronize_session=False)
+            session.commit()

{nci_cidc_api_modules-1.1.41 → nci_cidc_api_modules-1.2.1/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,35 +1,35 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.41
+Version: 1.2.1
 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
-Requires-Python: >=3.9
+Requires-Python: >=3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: werkzeug==3.0.6
-Requires-Dist: flask==3.0.3
-Requires-Dist: flask-migrate==3.1.0
-Requires-Dist: flask-sqlalchemy==3.1.1
-Requires-Dist: sqlalchemy==2.0.41
-Requires-Dist: marshmallow==3.19.0
-Requires-Dist: marshmallow-sqlalchemy==1.4.2
-Requires-Dist: google-cloud-storage==2.18.0
-Requires-Dist: google-cloud-secret-manager==2.20.1
-Requires-Dist: google-cloud-pubsub==2.22.0
-Requires-Dist: google-cloud-bigquery==3.18.0
-Requires-Dist: google-api-python-client==2.64.0
-Requires-Dist: google-auth==2.32.0
-Requires-Dist: packaging>=20.0.0
-Requires-Dist: pyarrow==14.0.1
-Requires-Dist: numpy<2,>=1.16.5
-Requires-Dist: pandas==1.5.3
-Requires-Dist: python-dotenv==0.10.3
-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==0.27.28
+Requires-Dist: werkzeug>=3.1.3
+Requires-Dist: flask>=3.1.2
+Requires-Dist: flask-migrate>=4.1.0
+Requires-Dist: flask-sqlalchemy>=3.1.1
+Requires-Dist: sqlalchemy>=2.0.43
+Requires-Dist: marshmallow>=4.0.0
+Requires-Dist: marshmallow-sqlalchemy>=1.4.2
+Requires-Dist: google-cloud-storage>=3.3.0
+Requires-Dist: google-cloud-secret-manager>=2.24.0
+Requires-Dist: google-cloud-pubsub>=2.31.1
+Requires-Dist: google-cloud-bigquery>=3.36.0
+Requires-Dist: google-api-python-client>=2.179.0
+Requires-Dist: google-auth>=2.40.3
+Requires-Dist: packaging>=25.0
+Requires-Dist: pyarrow>=21.0.0
+Requires-Dist: numpy>=2.3.2
+Requires-Dist: pandas>=2.3.1
+Requires-Dist: python-dotenv>=1.1.1
+Requires-Dist: requests>=2.32.5
+Requires-Dist: jinja2>=3.1.6
+Requires-Dist: certifi>=2025.8.3
+Requires-Dist: cloud-sql-python-connector[pg8000]>=1.18.4
+Requires-Dist: nci-cidc-schemas==0.28.2
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
@@ -62,7 +62,7 @@ The next generation of the CIDC API, reworked to use Google Cloud-managed servic
 
 ## Install Python dependencies
 
-Python versions tested include 3.9 and 3.10. The current App Engine is using version 3.9 (see [app.prod.yaml](./app.prod.yaml)). You can use https://github.com/pyenv/pyenv to manage your python versions. Homebrew will also work, but you will have to be specific when you install packages with pip outside of virtual environments. On that note, it is recommended that you install your python dependencies in an isolated environment. For example,
+Use Python version 3.13
 
 ```bash
 # make a virtual environment in the current direcory called "venv"

nci_cidc_api_modules-1.2.1/nci_cidc_api_modules.egg-info/requires.txt

@@ -0,0 +1,23 @@
+werkzeug>=3.1.3
+flask>=3.1.2
+flask-migrate>=4.1.0
+flask-sqlalchemy>=3.1.1
+sqlalchemy>=2.0.43
+marshmallow>=4.0.0
+marshmallow-sqlalchemy>=1.4.2
+google-cloud-storage>=3.3.0
+google-cloud-secret-manager>=2.24.0
+google-cloud-pubsub>=2.31.1
+google-cloud-bigquery>=3.36.0
+google-api-python-client>=2.179.0
+google-auth>=2.40.3
+packaging>=25.0
+pyarrow>=21.0.0
+numpy>=2.3.2
+pandas>=2.3.1
+python-dotenv>=1.1.1
+requests>=2.32.5
+jinja2>=3.1.6
+certifi>=2025.8.3
+cloud-sql-python-connector[pg8000]>=1.18.4
+nci-cidc-schemas==0.28.2

nci_cidc_api_modules-1.2.1/requirements.modules.txt

@@ -0,0 +1,23 @@
+werkzeug>=3.1.3
+flask>=3.1.2
+flask-migrate>=4.1.0
+flask-sqlalchemy>=3.1.1
+sqlalchemy>=2.0.43
+marshmallow>=4.0.0
+marshmallow-sqlalchemy>=1.4.2
+google-cloud-storage>=3.3.0
+google-cloud-secret-manager>=2.24.0
+google-cloud-pubsub>=2.31.1
+google-cloud-bigquery>=3.36.0
+google-api-python-client>=2.179.0
+google-auth>=2.40.3
+packaging>=25.0
+pyarrow>=21.0.0
+numpy>=2.3.2
+pandas>=2.3.1
+python-dotenv>=1.1.1
+requests>=2.32.5
+jinja2>=3.1.6
+certifi>=2025.8.3
+cloud-sql-python-connector[pg8000]>=1.18.4
+nci-cidc-schemas==0.28.2

{nci_cidc_api_modules-1.1.41 → nci_cidc_api_modules-1.2.1}/setup.py

@@ -13,7 +13,7 @@ from cidc_api import __version__
 setup(
     name="nci_cidc_api_modules",
     description="SQLAlchemy data models and configuration tools used in the NCI CIDC API",
-    python_requires=">=3.9",
+    python_requires=">=3.13",
     install_requires=requirements,
     license="MIT license",
     packages=[

nci_cidc_api_modules-1.1.41/nci_cidc_api_modules.egg-info/requires.txt

@@ -1,23 +0,0 @@
-werkzeug==3.0.6
-flask==3.0.3
-flask-migrate==3.1.0
-flask-sqlalchemy==3.1.1
-sqlalchemy==2.0.41
-marshmallow==3.19.0
-marshmallow-sqlalchemy==1.4.2
-google-cloud-storage==2.18.0
-google-cloud-secret-manager==2.20.1
-google-cloud-pubsub==2.22.0
-google-cloud-bigquery==3.18.0
-google-api-python-client==2.64.0
-google-auth==2.32.0
-packaging>=20.0.0
-pyarrow==14.0.1
-numpy<2,>=1.16.5
-pandas==1.5.3
-python-dotenv==0.10.3
-requests==2.32.4
-jinja2==3.1.6
-certifi==2024.7.4
-cloud-sql-python-connector[pg8000]==1.18.3
-nci-cidc-schemas==0.27.28

nci_cidc_api_modules-1.1.41/requirements.modules.txt

@@ -1,23 +0,0 @@
-werkzeug==3.0.6
-flask==3.0.3
-flask-migrate==3.1.0
-flask-sqlalchemy==3.1.1
-sqlalchemy==2.0.41
-marshmallow==3.19.0
-marshmallow-sqlalchemy==1.4.2
-google-cloud-storage==2.18.0
-google-cloud-secret-manager==2.20.1
-google-cloud-pubsub==2.22.0
-google-cloud-bigquery==3.18.0
-google-api-python-client==2.64.0
-google-auth==2.32.0
-packaging>=20.0.0
-pyarrow==14.0.1
-numpy>=1.16.5,<2
-pandas==1.5.3
-python-dotenv==0.10.3
-requests==2.32.4
-jinja2==3.1.6
-certifi==2024.7.4
-cloud-sql-python-connector[pg8000]==1.18.3
-nci-cidc-schemas==0.27.28