nci-cidc-api-modules 1.2.9__py3-none-any.whl → 1.2.16__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 = " || "
 
@@ -107,5 +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/models/models.py

@@ -26,10 +26,12 @@ __all__ = [
     "FileValidationErrors",
     "IngestionJobs",
     "JobFileCategories",
+    "CategoryDataElements",
     "ValidationConfigs",
     "TRIAL_APPENDIX_A",
     "TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER",
     "REQUEST_LETTER",
+    "DETAILED_VALIDATION",
     "ADMIN_FILE_CATEGORIES",
     "FINAL_JOB_STATUS",
     "INGESTION_JOB_STATUSES",
@@ -130,7 +132,6 @@ from ..config.settings import (
     MAX_PAGINATION_PAGE_SIZE,
     TESTING,
     INACTIVE_USER_DAYS,
-    GOOGLE_CLINICAL_DATA_BUCKET,
 )
 from ..shared import emails
 from ..shared.gcloud_client import (
@@ -144,7 +145,6 @@ from ..shared.gcloud_client import (
     revoke_intake_access,
     revoke_lister_access,
     revoke_bigquery_access,
-    gcs_xlsx_or_csv_file_to_pandas_dataframe,
 )
 
 os.environ["TZ"] = "UTC"
@@ -3449,30 +3449,9 @@ class IngestionJobs(CommonColumns):
 
     @with_default_session
     def transition_status(self, status: str, session: Session):
-        # create required categories after opening job for submission
-        if self.status == "DRAFT" and status == "INITIAL SUBMISSION":
-            for category in self.derive_required_categories_from_appendix_a():
-                JobFileCategories.create(category=category, job_id=self.id, type="required")
         self.status = status
         self.update(session=session)
 
-    def derive_required_categories_from_appendix_a(self) -> List:
-        appendix_a = PreprocessedFiles.get_files_by_category_and_status(TRIAL_APPENDIX_A, "current", job_id=self.id)[0]
-        df = gcs_xlsx_or_csv_file_to_pandas_dataframe(GOOGLE_CLINICAL_DATA_BUCKET, appendix_a.object_url)
-        categories = []
-        headers_ended = False
-        for _index, row in df.iterrows():
-            cell = str(row.iloc[0])
-            if headers_ended:
-                if cell != "nan" and cell not in categories:
-                    categories.append(cell)
-            elif cell.lower() == TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER.lower():
-                headers_ended = True
-        if "data_dictionary" not in categories:
-            # Ensure Data_Dictionary is always a required file category
-            categories.append("data_dictionary")
-        return categories
-
     @classmethod
     @with_default_session
     def atomic_set_job_as_pending(cls, job_id: int, session: Session) -> Boolean:
@@ -3552,6 +3531,7 @@ class JobFileCategories(CommonColumns):
     category = Column(String)
     job_id = Column(Integer)
     type = Column(Enum("required", "optional", name="type"))
+    is_custom = Column(Boolean, default=False, server_default="false")
 
     @staticmethod
     @with_default_session
@@ -3559,12 +3539,14 @@ class JobFileCategories(CommonColumns):
         category: str,
         job_id: int,
         type: str,
+        is_custom: bool = False,
         session: Session = None,
     ):
         new_category = JobFileCategories(
             category=category,
             job_id=job_id,
             type=type,
+            is_custom=is_custom,
         )
         new_category.insert(session=session)
         return new_category
@@ -3576,6 +3558,28 @@ class JobFileCategories(CommonColumns):
         return [c.category for c in categories]
 
 
+class CategoryDataElements(CommonColumns):
+    __tablename__ = "category_data_elements"
+    __table_args__ = (
+        ForeignKeyConstraint(
+            ["category_id"],
+            ["job_file_categories.id"],
+            ondelete="CASCADE",
+        ),
+        Index(
+            "idx_elements_category_id" "category_id",
+            "name",
+            unique=True,
+        ),
+    )
+
+    category_id = Column(Integer, nullable=False)
+    name = Column(String, nullable=False)
+    is_custom = Column(Boolean, nullable=False, default=False, server_default="false")
+    element_type = Column(String, nullable=False)
+    cardinality = Column(String, nullable=True)
+
+
 class FileValidationErrors(CommonColumns):
     __tablename__ = "file_validation_errors"
     __table_args__ = (

cidc_api/shared/email_layout.html

@@ -0,0 +1,258 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+  <title>Manifest Status Notification</title>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <meta http-equiv="Content-Type" content="text/html charset=UTF-8" />
+  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+  <style type="text/css">
+    /* CLIENT-SPECIFIC STYLES */
+    body,
+    table,
+    td,
+    a {
+      -webkit-text-size-adjust: 100%;
+      -ms-text-size-adjust: 100%;
+    }
+
+    /* Prevent WebKit and Windows mobile changing default text sizes */
+    table,
+    td {
+      mso-table-lspace: 0pt;
+      mso-table-rspace: 0pt;
+    }
+
+    /* Remove spacing between tables in Outlook 2007 and up */
+    img {
+      -ms-interpolation-mode: bicubic;
+    }
+
+    /* Allow smoother rendering of resized image in Internet Explorer */
+
+    /* RESET STYLES */
+    img {
+      border: 0;
+      height: auto;
+      line-height: 100%;
+      outline: none;
+      text-decoration: none;
+    }
+
+    table {
+      border-collapse: collapse !important;
+    }
+
+    body {
+      height: 100% !important;
+      margin: 0 !important;
+      padding: 0 !important;
+      width: 100% !important;
+    }
+
+    /* iOS BLUE LINKS */
+    a[x-apple-data-detectors] {
+      color: inherit !important;
+      text-decoration: none !important;
+      font-size: inherit !important;
+      font-family: inherit !important;
+      font-weight: inherit !important;
+      line-height: inherit !important;
+    }
+
+    /* MOBILE STYLES */
+    @media screen and (max-width: 525px) {
+
+      /* ALLOWS FOR FLUID TABLES */
+      .wrapper {
+        width: 100% !important;
+        max-width: 100% !important;
+      }
+
+      /* ADJUSTS LAYOUT OF LOGO IMAGE */
+      .logo img {
+        margin: 0 auto !important;
+      }
+
+      /* USE THESE CLASSES TO HIDE CONTENT ON MOBILE */
+      .mobile-hide {
+        display: none !important;
+      }
+
+      .img-max {
+        max-width: 100% !important;
+        width: 100% !important;
+        height: auto !important;
+      }
+
+      /* FULL-WIDTH TABLES */
+      .responsive-table {
+        width: 100% !important;
+      }
+
+      /* UTILITY CLASSES FOR ADJUSTING PADDING ON MOBILE */
+      .padding {
+        padding: 10px 5% 15px 5% !important;
+      }
+
+      .padding-meta {
+        padding: 30px 5% 0px 5% !important;
+        text-align: center;
+      }
+
+      .padding-copy {
+        padding: 10px 5% 10px 5% !important;
+        text-align: center;
+      }
+
+      .no-padding {
+        padding: 0 !important;
+      }
+
+      .section-padding {
+        padding: 50px 15px 50px 15px !important;
+      }
+
+      /* ADJUST BUTTONS ON MOBILE */
+      .mobile-button-container {
+        margin: 0 auto;
+        width: 100% !important;
+      }
+
+      .mobile-button {
+        padding: 15px !important;
+        border: 0 !important;
+        font-size: 16px !important;
+        display: block !important;
+      }
+
+    }
+
+    /* ANDROID CENTER FIX */
+    div[style*="margin: 16px 0;"] {
+      margin: 0 !important;
+    }
+
+    a {
+      color: white;
+      text-decoration: underline;
+    }
+
+    .blue-link {
+      color: #1B6B82;
+    }
+  </style>
+</head>
+
+<body style="margin: 0 !important; padding: 0 !important; background-color:#F5F5F5;">
+
+  <!-- ONE COLUMN SECTION -->
+  <table bgcolor="#F5F5F5" border="0" cellpadding="0" cellspacing="0" width="100%">
+
+    <tr>
+      <td align="center" style="padding: 60px 16px 16px; margin-top: -32px;" class="section-padding">
+        <!--[if (gte mso 9)|(IE)]>
+            <table align="center" border="0" cellspacing="0" cellpadding="0" width="500">
+            <tr>
+            <td align="center" valign="top" width="500">
+            <![endif]-->
+        <table bgcolor="#ffffff" border="0" cellpadding="0" cellspacing="0" width="100%" style="max-width: 520px;"
+          class="responsive-table">
+          <tr>
+            <td>
+              <table width="100%" border="0" cellspacing="0" cellpadding="0">
+                <tr>
+                  <td>
+                    <table width="100%" border="0" cellspacing="0" cellpadding="0">
+                      <tr>
+                        <td align="center"
+                          style="padding: 32px 0 0 0; font-size: 18px; line-height: 25px; font-family: Helvetica, Arial, sans-serif; color: #3F414F;"
+                          class="padding-copy">
+                          Cancer Immunologic Data Center (CIDC)</td>
+                      </tr>
+                      <tr>
+                        <td align="center"
+                          style="padding: 50px 32px 0 32px; line-height: 42px; font-family: Helvetica, Arial, sans-serif; color: #666666;">
+                          <h1 style="margin:0; mso-line-height-rule:exactly; padding: 0 32px 0 32px">
+                            $HEADING
+                          </h1>
+                        </td>
+                      </tr>
+                      <tr>
+                        <td align="center"
+                          style="padding: 40px 40px 40px 40px; font-size: 16px; line-height: 25px; font-family: Helvetica, Arial, sans-serif; color: #666666;"
+                          class="padding-copy">
+                          $CONTENT
+                        </td>
+                      </tr>
+                    </table>
+                  </td>
+                </tr>
+              </table>
+            </td>
+          </tr>
+        </table>
+        <!--[if (gte mso 9)|(IE)]>
+            </td>
+            </tr>
+            </table>
+            <![endif]-->
+      </td>
+    </tr>
+    <tr>
+      <td align="center" style="padding: 20px 0px;">
+        <!--[if (gte mso 9)|(IE)]>
+            <table align="center" border="0" cellspacing="0" cellpadding="0" width="500">
+            <tr>
+            <td align="center" valign="top" width="500">
+            <![endif]-->
+        <table bgcolor="#1B6B82" width="100%" border="0" cellspacing="0" cellpadding="0" align="center"
+          style="max-width: 520px; " class="responsive-table">
+          <tr>
+            <td align="center"
+              style="padding: 20px 0 0 0; font-size: 18px; line-height: 18px; font-family: Helvetica, Arial, sans-serif; color:#fff; text-align: center">
+              Need help?
+            </td>
+          </tr>
+          <tr>
+            <td align="center"
+              style="padding: 10px 0 20px 0; font-size: 14px; line-height: 18px; font-family: Helvetica, Arial, sans-serif; color:#fff; text-align: center">
+              Send us an email at <a href="mailto:ncicidcadmin@mail.nih.gov">ncicidcadmin@mail.nih.gov</a>
+            </td>
+          </tr>
+        </table>
+        <!--[if (gte mso 9)|(IE)]>
+            </td>
+            </tr>
+            </table>
+            <![endif]-->
+      </td>
+    </tr>
+    <tr>
+      <td align="center" style="padding: 20px 0px;">
+        <!--[if (gte mso 9)|(IE)]>
+              <table align="center" border="0" cellspacing="0" cellpadding="0" width="500">
+              <tr>
+              <td align="center" valign="top" width="500">
+              <![endif]-->
+        <table width="100%" border="0" cellspacing="0" cellpadding="0" align="center" style="max-width: 520px; "
+          class="responsive-table">
+          <tr>
+            <td align="center"
+              style="padding: 10px 0 20px 0; font-size: 14px; line-height: 18px; font-family: Helvetica, Arial, sans-serif; color:#666666;">
+              National Cancer Institute at the National institutes of Health
+            </td>
+          </tr>
+        </table>
+        <!--[if (gte mso 9)|(IE)]>
+              </td>
+              </tr>
+              </table>
+              <![endif]-->
+      </td>
+    </tr>
+  </table>
+</body>
+
+</html>

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
 

cidc_api/shared/gcloud_client.py

@@ -1,6 +1,6 @@
 """Utilities for interacting with the Google Cloud Platform APIs."""
 
-# pylint: disable=logging-fstring-interpolation
+# pylint: disable=logging-fstring-interpolation,too-many-lines
 
 import base64
 import datetime
@@ -37,8 +37,8 @@ from sqlalchemy.orm.session import Session
 from werkzeug.datastructures import FileStorage
 from werkzeug.utils import secure_filename
 
-from cidc_api.config.secrets import get_secrets_manager
 from ..config.logging import get_logger
+from ..config.secrets import get_secrets_manager
 from ..config.settings import (
     DEV_USE_GCS,
     GOOGLE_INTAKE_ROLE,
@@ -55,12 +55,15 @@ 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,
     DEV_CFUNCTIONS_SERVER,
     INACTIVE_USER_DAYS,
 )
+from ..shared.utils import strip_whitespaces
+
 
 os.environ["TZ"] = "UTC"
 logger = get_logger(__name__)
@@ -426,9 +429,9 @@ def gcs_xlsx_or_csv_file_to_pandas_dataframe(bucket_name: str, blob_name: str):
 
     # TODO: specify sheet in xlsx file and/or accept tsv and xls files
     if blob_name[-3:] == "csv":
-        return pd.read_csv(temp_file)
+        return strip_whitespaces(pd.read_csv(temp_file))
     elif blob_name[-4:] == "xlsx":
-        return pd.read_excel(temp_file)
+        return strip_whitespaces(pd.read_excel(temp_file))
     else:
         raise Exception("Can only read csv or xlsx files")
 
@@ -985,6 +988,12 @@ def publish_hl_clinical_validation(job_id: int) -> None:
     _report = _encode_and_publish(str(job_id), GOOGLE_HL_CLINICAL_VALIDATION_TOPIC)
 
 
+def publish_detailed_validation(job_id: int) -> None:
+    """Start detailed validation and create the detailed validation preprocessed file"""
+    # Start validation asynchronously
+    _report = _encode_and_publish(str(job_id), GOOGLE_DL_CLINICAL_VALIDATION_TOPIC)
+
+
 def send_email(to_emails: List[str], subject: str, html_content: str, **kw) -> None:
     """
     Publish an email-to-send to the emails topic.

cidc_api/shared/utils.py

@@ -0,0 +1,8 @@
+def strip_whitespaces(df):
+    def stripper(x):
+        if x and isinstance(x, str):
+            return x.strip()
+        else:
+            return x
+
+    return df.map(stripper)

{nci_cidc_api_modules-1.2.9.dist-info → nci_cidc_api_modules-1.2.16.dist-info}/METADATA

@@ -1,35 +1,35 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.9
+Version: 1.2.16
 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: >=3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: certifi>=2025.8.3
-Requires-Dist: cloud-sql-python-connector[pg8000]>=1.18.4
+Requires-Dist: certifi>=2025.10.5
+Requires-Dist: cloud-sql-python-connector[pg8000]>=1.18.5
 Requires-Dist: flask>=3.1.2
 Requires-Dist: flask-migrate>=4.1.0
 Requires-Dist: flask-sqlalchemy>=3.1.1
-Requires-Dist: google-auth>=2.41.0
-Requires-Dist: google-api-python-client>=2.183.0
+Requires-Dist: google-auth==2.41.1
+Requires-Dist: google-api-python-client>=2.185.0
 Requires-Dist: google-cloud-bigquery>=3.38.0
-Requires-Dist: google-cloud-pubsub>=2.31.1
-Requires-Dist: google-cloud-secret-manager>=2.24.0
-Requires-Dist: google-cloud-storage>=3.4.0
+Requires-Dist: google-cloud-pubsub>=2.32.0
+Requires-Dist: google-cloud-secret-manager>=2.25.0
+Requires-Dist: google-cloud-storage>=3.4.1
 Requires-Dist: jinja2>=3.1.6
-Requires-Dist: marshmallow>=4.0.0
+Requires-Dist: marshmallow>=4.0.1
 Requires-Dist: marshmallow-sqlalchemy>=1.4.2
-Requires-Dist: numpy>=2.3.2
+Requires-Dist: numpy>=2.3.4
 Requires-Dist: packaging>=25.0
 Requires-Dist: pandas>=2.3.3
-Requires-Dist: pyarrow>=21.0.0
-Requires-Dist: python-dotenv>=1.1.1
+Requires-Dist: pyarrow>=22.0.0
+Requires-Dist: python-dotenv>=1.2.1
 Requires-Dist: requests>=2.32.5
-Requires-Dist: sqlalchemy>=2.0.43
+Requires-Dist: sqlalchemy>=2.0.44
 Requires-Dist: werkzeug>=3.1.3
-Requires-Dist: nci-cidc-schemas==0.28.7
+Requires-Dist: nci-cidc-schemas==0.28.8
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.2.9.dist-info → nci_cidc_api_modules-1.2.16.dist-info}/RECORD

@@ -2,23 +2,25 @@ 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
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