nci-cidc-api-modules 1.2.11__py3-none-any.whl → 1.2.13__py3-none-any.whl

cidc_api/config/settings.py

@@ -108,5 +108,9 @@ else:
     IS_EMAIL_ON = environ.get("IS_EMAIL_ON")
 
 
+# notification emails
+CIDC_CLINICAL_DATA_EMAIL = environ.get("CIDC_CLINICAL_DATA_EMAIL")
+CIDC_ADMIN_EMAIL = environ.get("CIDC_ADMIN_EMAIL")
+
 # Accumulate all constants defined in this file in a single dictionary
 SETTINGS = {k: v for k, v in globals().items() if k.isupper()}

cidc_api/shared/emails.py

@@ -1,11 +1,12 @@
 """Template functions for CIDC email bodies."""
 
 import html
+import pathlib
 from functools import wraps
 from typing import List
 
 from . import gcloud_client
-from ..config.settings import ENV
+from ..config.settings import ENV, ALLOWED_CLIENT_URL, CIDC_CLINICAL_DATA_EMAIL, CIDC_ADMIN_EMAIL
 
 # emails this list for
 # - new user registration,
@@ -44,7 +45,7 @@ def confirm_account_approval(user) -> dict:
     html_content = f"""
     <p>Hello {user.first_n},</p>
     <p>
-        Your CIMAC-CIDC Portal account has been approved! 
+        Your CIMAC-CIDC Portal account has been approved!
         To begin browsing and downloading data, visit https://cidc.nci.nih.gov.
     </p>
     <p>
@@ -150,3 +151,32 @@ def notify_mailing_list(subject: str, html_content: str) -> dict:
         "html_content": html_content,
     }
     return email
+
+
+with open(pathlib.Path(__file__).parent.joinpath("email_layout.html"), encoding="utf-8") as file:
+    EMAIL_LAYOUT = file.read()
+
+
+@sendable
+def new_validation_review(job: dict) -> dict:
+    # these two emails are set only in prod env file
+    if CIDC_CLINICAL_DATA_EMAIL and CIDC_ADMIN_EMAIL:
+        to_emails = [CIDC_CLINICAL_DATA_EMAIL, CIDC_ADMIN_EMAIL]
+    else:
+        to_emails = CIDC_MAILING_LIST
+
+    subject = f"Trial {job.trial_id} ({job.version}) Ready for Validation Review"
+    html_heading = "Clinical Data Upload Notification"
+    job_url = f"{ALLOWED_CLIENT_URL}/upload-clinical-data/{job.id}"
+
+    html_content = f"""
+        <b>Ready for Validation Review:</b><br>
+        <b><a class="blue-link" href={job_url}>Trial {job.trial_id} version {job.version} (Job ID {job.id})</a></b>
+        Please follow the link to access the trial's clinical data submission page.
+    """
+
+    return {
+        "to_emails": to_emails,
+        "subject": subject,
+        "html_content": EMAIL_LAYOUT.replace("$HEADING", html_heading).replace("$CONTENT", html_content),
+    }

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
 

{nci_cidc_api_modules-1.2.11.dist-info → nci_cidc_api_modules-1.2.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.11
+Version: 1.2.13
 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-1.2.11.dist-info → nci_cidc_api_modules-1.2.13.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=v8PmdR_MSmizuV1VaEX24QR0XHzIZ4jn69r6PwxAxV8,4512
+cidc_api/config/settings.py,sha256=ttOGvk_6zVMn4dtxIZ2-0w3wF2fpAUVfGpVZbKJ2b6s,4653
 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
@@ -12,13 +12,13 @@ cidc_api/models/files/details.py,sha256=sZkGM7iEV4-J6IDQCdiMV6KBDLbPxCOqUMaU3aY9
 cidc_api/models/files/facets.py,sha256=RZoe0FadRGJw8_-jzJQkc4dIVSuaYlunNrsopb2dYho,33325
 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/emails.py,sha256=8kNFEaSnKpY-GX_iE59QUhSp3c4_uzy3SpHYt2QjuqI,6121
+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-1.2.11.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.11.dist-info/METADATA,sha256=LtfTSAzY5wOMrSIrLC3fhLmfbTiLgiBftULBMS_2ftw,39539
-nci_cidc_api_modules-1.2.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.2.11.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.2.11.dist-info/RECORD,,
+nci_cidc_api_modules-1.2.13.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.13.dist-info/METADATA,sha256=gRTTJ2KEYN1B9Ac0rim5nAPVRsQtw5NWr0E9KJhSIc0,39539
+nci_cidc_api_modules-1.2.13.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.2.13.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.2.13.dist-info/RECORD,,