nci-cidc-api-modules 1.1.37__py3-none-any.whl → 1.1.38__py3-none-any.whl

cidc_api/models/models.py

@@ -357,6 +357,7 @@ class CIDCRole(EnumBaseClass):
     NCI_BIOBANK_USER = "nci-biobank-user"
     NETWORK_VIEWER = "network-viewer"
     PACT_USER = "pact-user"
+    CLINICAL_TRIAL_USER = "clinical-trial-user"
 
 
 ROLES = [role.value for role in CIDCRole]
@@ -3215,7 +3216,7 @@ def upload_manifest_json(
     * The updated trial metadata object is updated in the `TrialMetadata` table.
     """
     try:
-        TrialMetadata.patch_manifest(trial_id, md_patch, session=session, commit=False)
+        TrialMetadata.patch_manifest(trial_id, md_patch, session=session, commit=True)
     except ValidationError as e:
         raise BadRequest(json_validation.format_validation_error(e)) from e
     except ValidationMultiError as e:

cidc_api/shared/file_handling.py

@@ -54,3 +54,37 @@ def format_common_preprocessed_file_response(file: PreprocessedFiles):
         "uploader_email": file.uploader_email,
         "date": file._created.isoformat(),
     }
+
+
+# TODO Below functions approve_pending_file and delete_pending_files were copied from deleted clinical_data.py
+# Consider re-implementing with pending files in clinical data file uploads, or remove
+# def approve_pending_file(pending_file: FileStorage):
+#     original_filename = pending_file.file_name
+#     pending_gcs_path = pending_file.object_url
+#     try:
+#         new_gcs_path = gcloud_client.move_gcs_file(
+#             GOOGLE_CLINICAL_DATA_BUCKET, pending_gcs_path, f"{MASTER_APPENDIX_A}/"
+#         )
+#     except Exception as e:
+#         logger.error(str(e))
+#         raise InternalServerError(str(e))
+#     # Move any 'current' file(s) to 'archived' status
+#     latest_version = PreprocessedFiles.archive_current_files(MASTER_APPENDIX_A)
+#     # Insert new "approved" DB record
+#     PreprocessedFiles.create(
+#         file_name=original_filename,
+#         object_url=new_gcs_path,
+#         file_category=MASTER_APPENDIX_A,
+#         uploader_email=get_current_user().email,
+#         status="current",
+#         version=latest_version + 1,
+#     )
+#     # Delete pending record
+#     pending_file.delete()
+#     return new_gcs_path
+#
+#
+# def delete_pending_files(pending_folder: str, file_category: str):
+#     """Deletes specified pending file(s) from GCS and associated db record(s)."""
+#     gcloud_client.delete_items_from_folder(GOOGLE_CLINICAL_DATA_BUCKET, pending_folder)
+#     PreprocessedFiles.delete_pending_files_by_category(file_category)

{nci_cidc_api_modules-1.1.37.dist-info → nci_cidc_api_modules-1.1.38.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.37
+Version: 1.1.38
 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

{nci_cidc_api_modules-1.1.37.dist-info → nci_cidc_api_modules-1.1.38.dist-info}/RECORD

@@ -5,7 +5,7 @@ cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,14
 cidc_api/config/settings.py,sha256=mA-4r7oB60uFepYtl5abbPigjwX8aBz__qCJXdcWWbs,4272
 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=u2SA3R0xaVgdoU8nnnl2dptt_hMtkdgQcmZhdEQbLv4,141631
+cidc_api/models/models.py,sha256=D4GmcQSLKGBi0k3-w3TZk7J46zKR80JViN2_vTBZ1ZQ,141678
 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
@@ -13,12 +13,12 @@ cidc_api/models/files/facets.py,sha256=WqjfqtYJgY2tBnZ598Yc0eJdQUo2slFNLyTDaqPx_
 cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cidc_api/shared/auth.py,sha256=PHqmVGkqDjbmUofytVFwD_9ssgUomESl3fFtFHPwZYQ,9062
 cidc_api/shared/emails.py,sha256=HQIixEUsR8yyu7Iv8S81RjtvEQeGuzQHzBfGsWIfP7k,4961
-cidc_api/shared/file_handling.py,sha256=z9Fza4PNTQ2U2VgMEiwx-Xpsp1AKgJuBugEl8loglec,2334
+cidc_api/shared/file_handling.py,sha256=lbdY4XH-otpNjWDY1g6EQoVWtEYM_9j95OlQXeeFkhE,3808
 cidc_api/shared/gcloud_client.py,sha256=tgi6Ja31EUQcJueAIYHc3VyrMchoMZCdui1eruakCLg,36351
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
-nci_cidc_api_modules-1.1.37.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.1.37.dist-info/METADATA,sha256=lkOyyerechLmU60nEzlIxONbexRRnvVbB1T1qApjjtM,41284
-nci_cidc_api_modules-1.1.37.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.1.37.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.1.37.dist-info/RECORD,,
+nci_cidc_api_modules-1.1.38.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.1.38.dist-info/METADATA,sha256=Vlhx5ZliL-b3-3Umhqm1q22BztzUG-mc2dTIyyHzZ24,41284
+nci_cidc_api_modules-1.1.38.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.1.38.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.1.38.dist-info/RECORD,,