nci-cidc-api-modules 1.1.31__tar.gz → 1.1.33__tar.gz

{nci_cidc_api_modules-1.1.31/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.1.33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.31
+Version: 1.1.33
 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
@@ -25,10 +25,10 @@ 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==2.32.3
+Requires-Dist: requests==2.32.4
 Requires-Dist: jinja2==3.1.6
 Requires-Dist: certifi==2024.7.4
-Requires-Dist: nci-cidc-schemas==0.27.21
+Requires-Dist: nci-cidc-schemas==0.27.24
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.1.31 → nci_cidc_api_modules-1.1.33}/cidc_api/models/models.py

@@ -3229,18 +3229,21 @@ class PreprocessedFiles(CommonColumns):
     @classmethod
     @with_default_session
     def archive_current_files(cls, file_category: str, session: Session = None):
-        """Update any 'current' files in the given category to 'archived'."""
+        """Update any 'current' files in the given category to 'archived'. Returns latest existing version number."""
+        current_version = 0
         current_files = cls.get_files_by_category_and_status(file_category, "current", session=session)
         for file in current_files:
             file.status = "archived"
             file._updated = datetime.now()
+            current_version = file.version if file.version > current_version else current_version
         session.commit()
+        return current_version
 
     @classmethod
     @with_default_session
-    def delete_pending_files_by_category(cls, file_category: str, session: Session = None):
-        """Delete all pending files matching given file_category."""
-        records = cls.get_files_by_category_and_status(file_category, "pending", session=session)
+    def delete_pending_files_by_category(cls, file_category: str, trial_id: str = None, session: Session = None):
+        """Delete all pending files matching given file_category and optional trial_id."""
+        records = cls.get_files_by_category_and_status(file_category, "pending", trial_id=trial_id, session=session)
         for record in records:
             session.delete(record)
         session.commit()
@@ -3248,7 +3251,18 @@ class PreprocessedFiles(CommonColumns):
     @classmethod
     @with_default_session
     def get_files_by_category_and_status(
-        cls, file_category: str, status: str, session: Session = None
+        cls, file_category: str, status: str, trial_id: str = None, session: Session = None
     ) -> list["PreprocessedFiles"]:
-        """Return all files matching given file_category and status."""
-        return session.query(cls).filter_by(file_category=file_category, status=status).all()
+        """Return all files matching given file_category and status, optionally filtered by trial_id."""
+        query = session.query(cls).filter_by(file_category=file_category, status=status)
+        if trial_id:
+            query = query.filter_by(trial_id=trial_id)
+        return query.all()
+
+    @classmethod
+    @with_default_session
+    def get_file_by_category_and_version(
+        cls, file_category: str, version: int, session: Session = None
+    ) -> Optional["PreprocessedFiles"]:
+        """Return the file matching the given category and version number."""
+        return session.query(cls).filter_by(file_category=file_category, version=version).one_or_none()

{nci_cidc_api_modules-1.1.31 → nci_cidc_api_modules-1.1.33/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.31
+Version: 1.1.33
 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
@@ -25,10 +25,10 @@ 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==2.32.3
+Requires-Dist: requests==2.32.4
 Requires-Dist: jinja2==3.1.6
 Requires-Dist: certifi==2024.7.4
-Requires-Dist: nci-cidc-schemas==0.27.21
+Requires-Dist: nci-cidc-schemas==0.27.24
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.1.31 → nci_cidc_api_modules-1.1.33}/nci_cidc_api_modules.egg-info/requires.txt

@@ -16,7 +16,7 @@ pyarrow==14.0.1
 numpy<2,>=1.16.5
 pandas==1.5.3
 python-dotenv==0.10.3
-requests==2.32.3
+requests==2.32.4
 jinja2==3.1.6
 certifi==2024.7.4
-nci-cidc-schemas==0.27.21
+nci-cidc-schemas==0.27.24

{nci_cidc_api_modules-1.1.31 → nci_cidc_api_modules-1.1.33}/requirements.modules.txt

@@ -16,7 +16,7 @@ pyarrow==14.0.1
 numpy>=1.16.5,<2
 pandas==1.5.3
 python-dotenv==0.10.3
-requests==2.32.3
+requests==2.32.4
 jinja2==3.1.6
 certifi==2024.7.4
-nci-cidc-schemas==0.27.21
+nci-cidc-schemas==0.27.24

{nci_cidc_api_modules-1.1.31 → nci_cidc_api_modules-1.1.33}/tests/test_api.py

@@ -410,8 +410,12 @@ def test_endpoint_urls(cidc_api):
     """
     expected_endpoints = {
         "/",
+        "/clinical_data/files/master_appendix_a/current",
         "/clinical_data/files/master_appendix_a/pending",
+        "/clinical_data/files/master_appendix_a/versions",
+        "/clinical_data/files/master_appendix_a/versions/<int:version>",
         "/clinical_data/jobs",
+        "/clinical_data/trials/<string:trial_id>/files/trial_appendix_a/pending",
         "/downloadable_files/",
         "/downloadable_files/filelist",
         "/downloadable_files/compressed_batch",

{nci_cidc_api_modules-1.1.31 → nci_cidc_api_modules-1.1.33}/cidc_api/shared/gcloud_client.py

@@ -237,7 +237,6 @@ def upload_file_to_gcs(file: FileStorage, bucket_name: str, gcs_folder: str) ->
 
 def move_gcs_file(bucket_name: str, existing_path: str, to_folder: str, append_timestamp: bool = True) -> str:
     """Move a file within a GCS bucket to a new folder, optionally appending a timestamp to the filename."""
-    bucket = _get_bucket(bucket_name)
     filename = os.path.basename(existing_path)
     if append_timestamp:
         filename = _append_iso_timestamp_to_filename(filename)
@@ -250,6 +249,7 @@ def move_gcs_file(bucket_name: str, existing_path: str, to_folder: str, append_t
         logger.info(f"Would've moved {existing_path} to {new_gcs_file_path} in {bucket_name}")
         return new_gcs_file_path
 
+    bucket = _get_bucket(bucket_name)
     source_blob = bucket.blob(existing_path)
     if not source_blob.exists():
         raise Exception("Expected file not found in GCS")
@@ -263,10 +263,10 @@ def move_gcs_file(bucket_name: str, existing_path: str, to_folder: str, append_t
 
 def delete_items_from_folder(bucket_name: str, folder: str):
     """Deletes all blobs from the specified folder in the specified bucket."""
-    bucket = _get_bucket(bucket_name)
     if ENV == "dev" and not DEV_USE_GCS:
         logger.info(f"Would've deleted file(s) from {folder} in {bucket_name}")
         return
+    bucket = _get_bucket(bucket_name)
     existing_blobs = bucket.list_blobs(prefix=folder)
     for blob in existing_blobs:
         blob.delete()