nci-cidc-api-modules 1.1.14__tar.gz → 1.1.16__tar.gz

{nci_cidc_api_modules-1.1.14/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.1.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.14
+Version: 1.1.16
 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
@@ -26,7 +26,7 @@ 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: jinja2==3.1.5
+Requires-Dist: jinja2==3.1.6
 Requires-Dist: certifi==2024.7.4
 Requires-Dist: nci-cidc-schemas==0.27.09
 Dynamic: description

{nci_cidc_api_modules-1.1.14 → nci_cidc_api_modules-1.1.16}/cidc_api/shared/emails.py

@@ -1,14 +1,11 @@
 """Template functions for CIDC email bodies."""
 
 import html
-import base64
 from functools import wraps
-from typing import Dict, Union
-
-from cidc_schemas.prism import generate_analysis_configs_from_upload_patch
+from typing import List
 
 from . import gcloud_client
-from ..config.settings import ENV, GOOGLE_ACL_DATA_BUCKET
+from ..config.settings import ENV
 
 # emails this list for
 # - new user registration,
@@ -87,14 +84,12 @@ def new_user_registration(email: str) -> dict:
 @sendable
 def new_upload_alert(upload, full_metadata) -> dict:
     """Alert the CIDC administrators that an upload succeeded."""
-    pipeline_configs: Dict[str, Union[bytes, str]] = generate_analysis_configs_from_upload_patch(
-        full_metadata,
-        upload.metadata_patch,
-        upload.upload_type,
-        GOOGLE_ACL_DATA_BUCKET,
-    )
+    possible_manifest_info = ""
+    if upload.metadata_patch and "shipments" in upload.metadata_patch and upload.metadata_patch["shipments"]:
+        manifest_id = upload.metadata_patch["shipments"][0].get("manifest_id")
+        possible_manifest_info = f" manifest {manifest_id}"
 
-    subject = f"[UPLOAD SUCCESS]({ENV}) {upload.upload_type} uploaded to {upload.trial_id}"
+    subject = f"[UPLOAD SUCCESS]({ENV}) {upload.upload_type}{possible_manifest_info} uploaded to {upload.trial_id}"
 
     html_content = f"""
     <ul>
@@ -137,3 +132,21 @@ def intake_metadata(user, trial_id: str, assay_type: str, description: str, xlsx
     }
 
     return email
+
+
+def notify_manifest_errors(subject_message: str, errors: List[str], send_email=True) -> dict:
+    """Alert the CIDC administrators of errors in an attempted upload."""
+    subject = f"[UPLOAD FAILURE]({ENV}) {subject_message}"
+    html_content = f"<ul>{''.join(f'<li>{error}</li>' for error in errors)}</ul>"
+    return notify_mailing_list(subject, html_content, send_email=send_email)
+
+
+@sendable
+def notify_mailing_list(subject: str, html_content: str) -> dict:
+    """Generic notification to the CIDC administrators based on info passed."""
+    email = {
+        "to_emails": CIDC_MAILING_LIST,
+        "subject": subject,
+        "html_content": html_content,
+    }
+    return email

{nci_cidc_api_modules-1.1.14 → nci_cidc_api_modules-1.1.16/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.14
+Version: 1.1.16
 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
@@ -26,7 +26,7 @@ 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: jinja2==3.1.5
+Requires-Dist: jinja2==3.1.6
 Requires-Dist: certifi==2024.7.4
 Requires-Dist: nci-cidc-schemas==0.27.09
 Dynamic: description

{nci_cidc_api_modules-1.1.14 → nci_cidc_api_modules-1.1.16}/nci_cidc_api_modules.egg-info/requires.txt

@@ -17,6 +17,6 @@ numpy<2,>=1.16.5
 pandas==1.5.3
 python-dotenv==0.10.3
 requests==2.32.3
-jinja2==3.1.5
+jinja2==3.1.6
 certifi==2024.7.4
 nci-cidc-schemas==0.27.09

nci_cidc_api_modules-1.1.16/pyproject.toml

@@ -0,0 +1,10 @@
+[tool.black]
+exclude = "migrations"
+target-version = ["py39"]
+line-length = 120
+
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+# configure a webdriver for testing Dash dashboards
+# addopts = "--webdriver Chrome --headless"

{nci_cidc_api_modules-1.1.14 → nci_cidc_api_modules-1.1.16}/requirements.modules.txt

@@ -17,6 +17,6 @@ numpy>=1.16.5,<2
 pandas==1.5.3
 python-dotenv==0.10.3
 requests==2.32.3
-jinja2==3.1.5
+jinja2==3.1.6
 certifi==2024.7.4
 nci-cidc-schemas==0.27.09

nci_cidc_api_modules-1.1.14/pyproject.toml

@@ -1,71 +0,0 @@
-[tool.black]
-exclude = "migrations"
-target-version = ["py39"]
-line-length = 120
-
-
-[tool.pytest.ini_options]
-minversion = "6.0"
-# configure a webdriver for testing Dash dashboards
-# addopts = "--webdriver Chrome --headless"
-
-[tool.poetry]
-name = "cidc-api-gae"
-version = "1.0.2"
-description = ""
-authors = []
-readme = "README.md"
-
-[tool.poetry.dependencies]
-python = ">3.9.0,<3.9.1 || >3.9.1,<3.10"
-flask-cors = "5.0.0"
-flask-cachecontrol = "0.3.0"
-six = "1.13.0"
-joserfc = "1.0.0"
-psycopg2-binary = ">=2,<3"
-packaging = ">=20.0.0"
-protobuf = "3.20.3"
-gunicorn = "^22.0.0"
-gevent = "23.9.1"
-psycogreen = "1.0.2"
-webargs = "6.0.0"
-dash = "2.15.0"
-markupsafe = "2.1.5"
-pyarrow="14.0.1"
-certifi="2024.7.4"
-
-[tool.poetry.group.dev.dependencies]
-pytest = ">=8.0.1,<8.1.0"
-black = "24.3.0"
-pre-commit = "2.9.2"
-ipython = "8.13.0"
-flask-shell-ipython = "0.5.1"
-webdriver-manager = "^4.0.1"
-percy = "2.0.2"
-selenium = "3.141.0"
-bs4 = "0.0.1"
-
-
-[tool.poetry.group.modules.dependencies]
-werkzeug = "3.0.6"
-flask = "2.2.5"
-flask-migrate = "2.5.2"
-flask-sqlalchemy = "2.5.1"
-sqlalchemy = ">=1.3.0,<1.4.0"
-marshmallow = "3.19.0"
-marshmallow-sqlalchemy = "0.22.3"
-google-cloud-storage = "2.18.0"
-google-cloud-secret-manager = "2.20.1"
-google-cloud-pubsub = "2.22.0"
-google-cloud-bigquery = "3.18.0"
-google-api-python-client = "2.64.0"
-pandas = "1.5.3"
-python-dotenv = "0.10.3"
-requests = "2.32.3"
-jinja2 = "3.1.5"
-nci-cidc-schemas = "0.26.36"
-
-# keep the existing build step
-# [build-system]
-# requires = ["poetry-core"]
-# build-backend = "poetry.core.masonry.api"