nci-cidc-api-modules 1.2.10__py3-none-any.whl → 1.2.12__py3-none-any.whl

cidc_api/config/settings.py

@@ -83,6 +83,7 @@ GOOGLE_EMAILS_TOPIC = environ["GOOGLE_EMAILS_TOPIC"]
 GOOGLE_ARTIFACT_UPLOAD_TOPIC = environ["GOOGLE_ARTIFACT_UPLOAD_TOPIC"]
 GOOGLE_GRANT_DOWNLOAD_PERMISSIONS_TOPIC = environ["GOOGLE_GRANT_DOWNLOAD_PERMISSIONS_TOPIC"]
 GOOGLE_HL_CLINICAL_VALIDATION_TOPIC = environ["GOOGLE_HL_CLINICAL_VALIDATION_TOPIC"]
+GOOGLE_DL_CLINICAL_VALIDATION_TOPIC = environ["GOOGLE_DL_CLINICAL_VALIDATION_TOPIC"]
 GOOGLE_AND_OPERATOR = " && "
 GOOGLE_OR_OPERATOR = " || "
 

cidc_api/shared/file_handling.py

@@ -8,22 +8,31 @@ from ..config.settings import GOOGLE_CLINICAL_DATA_BUCKET
 from ..models import PreprocessedFiles
 from ..shared.auth import get_current_user
 from ..shared.gcloud_client import upload_file_to_gcs, move_gcs_file
+from sqlalchemy.orm.session import Session
 
 logger = get_logger(__name__)
 
 
-def set_current_file(file: FileStorage, file_category: str, gcs_folder: str, job_id: int = None) -> PreprocessedFiles:
+def set_current_file(
+    file: FileStorage, file_category: str, gcs_folder: str, session: Session, uploader_email: str, job_id: int = None
+) -> PreprocessedFiles:
     """
     Archives any existing 'current' files for the given category and job,
     then uploads the new file as the latest 'current' version.
     """
-    latest_version = PreprocessedFiles.archive_current_files(file_category, job_id=job_id)
-    latest_file = create_file(file, gcs_folder, file_category, job_id, latest_version + 1)
+    latest_version = PreprocessedFiles.archive_current_files(file_category, job_id=job_id, session=session)
+    latest_file = create_file(file, gcs_folder, file_category, session, uploader_email, job_id, latest_version + 1)
     return latest_file
 
 
 def create_file(
-    file: FileStorage, gcs_folder: str, file_category: str, job_id: int = None, version: int = None
+    file: FileStorage,
+    gcs_folder: str,
+    file_category: str,
+    session: Session,
+    uploader_email: str,
+    job_id: int = None,
+    version: int = None,
 ) -> PreprocessedFiles:
     """Upload file to GCS and create corresponding metadata record in the database."""
     status = "pending" if gcs_folder.endswith("pending/") else "current"
@@ -36,10 +45,11 @@ def create_file(
         file_name=file.filename,
         object_url=gcs_file_path,
         file_category=file_category,
-        uploader_email=get_current_user().email,
+        uploader_email=uploader_email,
         status=status,
         job_id=job_id,
         version=version,
+        session=session,
     )
     return file
 

cidc_api/shared/gcloud_client.py

@@ -55,6 +55,7 @@ from ..config.settings import (
     GOOGLE_ARTIFACT_UPLOAD_TOPIC,
     GOOGLE_GRANT_DOWNLOAD_PERMISSIONS_TOPIC,
     GOOGLE_HL_CLINICAL_VALIDATION_TOPIC,
+    GOOGLE_DL_CLINICAL_VALIDATION_TOPIC,
     TESTING,
     ENV,
     IS_EMAIL_ON,

{nci_cidc_api_modules-1.2.10.dist-info → nci_cidc_api_modules-1.2.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.10
+Version: 1.2.12
 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-1.2.10.dist-info → nci_cidc_api_modules-1.2.12.dist-info}/RECORD

@@ -2,7 +2,7 @@ cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,1
 cidc_api/config/db.py,sha256=eFCkJDeykRIJZ25kePVjRNrZcrcKTc1s2K0yErr46LI,1683
 cidc_api/config/logging.py,sha256=abhVYtn8lfhIt0tyV2WHFgSmp_s2eeJh7kodB6LH4J0,1149
 cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,1481
-cidc_api/config/settings.py,sha256=NsJbqW6Vqcz2f79xcAbk4th5tHne_I-RPCbKq_3hpz0,4427
+cidc_api/config/settings.py,sha256=v8PmdR_MSmizuV1VaEX24QR0XHzIZ4jn69r6PwxAxV8,4512
 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=b7HWj8uOD_xdv7p3WkrhRODauLCVGvSLQsSbJGUmr9Q,146956
@@ -13,12 +13,12 @@ cidc_api/models/files/facets.py,sha256=RZoe0FadRGJw8_-jzJQkc4dIVSuaYlunNrsopb2dY
 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=l4wiRkVJLL7QbCoODsLx-uki6Km8QoMmUlRVnUV9vkk,3894
-cidc_api/shared/gcloud_client.py,sha256=AGF4OHvZtgvDe6_YL4gZUajBJL9nY6tjVBVkXGBEIIw,37169
+cidc_api/shared/file_handling.py,sha256=4xkekdrzxWsfmfBtWpylyDMT98ICjQwx1meqqh1FAis,4103
+cidc_api/shared/gcloud_client.py,sha256=BaoYv-lWWLwdZvyRjCWCyAyZMXtqlT8IPJpw9XDODCY,37210
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
-nci_cidc_api_modules-1.2.10.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.10.dist-info/METADATA,sha256=j8DWxMQLIegbilW9COrSACclr3jFDMX2YYJcLkrGLEg,39539
-nci_cidc_api_modules-1.2.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.2.10.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.2.10.dist-info/RECORD,,
+nci_cidc_api_modules-1.2.12.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.12.dist-info/METADATA,sha256=cYaS5WnYnxEjX8tg7GNIwanF5Gy0nUCwV4DiGeCfBq4,39539
+nci_cidc_api_modules-1.2.12.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.2.12.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.2.12.dist-info/RECORD,,