nci-cidc-api-modules 1.2.44__tar.gz → 1.2.46__tar.gz

{nci_cidc_api_modules-1.2.44/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.46}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.44
+Version: 1.2.46
 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-1.2.46/boot.py

@@ -0,0 +1,14 @@
+from os import mkdir, path
+import shutil
+
+TEMPLATES_DIR = path.join("/tmp", "templates")
+
+
+# set up the directories for holding generated templates
+def set_up_templates_directories():
+    if path.exists(TEMPLATES_DIR):
+        shutil.rmtree(TEMPLATES_DIR)
+    mkdir(TEMPLATES_DIR)
+    for family in ["assays", "manifests", "analyses"]:
+        family_dir = path.join(TEMPLATES_DIR, family)
+        mkdir(family_dir)

nci_cidc_api_modules-1.2.46/cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.46"

{nci_cidc_api_modules-1.2.44 → nci_cidc_api_modules-1.2.46}/cidc_api/config/settings.py

@@ -5,11 +5,11 @@ Any 'UPPER_CASE' variables will be exported as a key-value pair
 in the `SETTINGS` dictionary defined at the bottom of this file.
 """
 
-import shutil
-from os import environ, path, mkdir
+from os import environ, path
 
 from dotenv import load_dotenv
 
+from boot import TEMPLATES_DIR as templates_dir
 from .db import get_sqlalchemy_database_uri, cloud_connector
 from .secrets import get_secrets_manager
 
@@ -36,14 +36,7 @@ PAGINATION_PAGE_SIZE = 25
 MAX_PAGINATION_PAGE_SIZE = 200
 INACTIVE_USER_DAYS = 60
 MAX_THREADPOOL_WORKERS = 32
-TEMPLATES_DIR = path.join("/tmp", "templates")
-# Also, set up the directories for holding generated templates
-if path.exists(TEMPLATES_DIR):
-    shutil.rmtree(TEMPLATES_DIR)
-mkdir(TEMPLATES_DIR)
-for family in ["assays", "manifests", "analyses"]:
-    family_dir = path.join(TEMPLATES_DIR, family)
-    mkdir(family_dir)
+TEMPLATES_DIR = templates_dir
 
 ### Configure prism encrypt ###
 if not TESTING:
@@ -84,6 +77,7 @@ 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_ASSAY_METADATA_VALIDATION_TOPIC = environ["GOOGLE_ASSAY_METADATA_VALIDATION_TOPIC"]
 GOOGLE_AND_OPERATOR = " && "
 GOOGLE_OR_OPERATOR = " || "
 

{nci_cidc_api_modules-1.2.44 → nci_cidc_api_modules-1.2.46}/cidc_api/shared/gcloud_client.py

@@ -60,6 +60,7 @@ from ..config.settings import (
     GOOGLE_GRANT_DOWNLOAD_PERMISSIONS_TOPIC,
     GOOGLE_HL_CLINICAL_VALIDATION_TOPIC,
     GOOGLE_DL_CLINICAL_VALIDATION_TOPIC,
+    GOOGLE_ASSAY_METADATA_VALIDATION_TOPIC,
     TESTING,
     ENV,
     IS_EMAIL_ON,
@@ -1049,6 +1050,12 @@ def publish_detailed_validation(job_id: int) -> None:
     _report = _encode_and_publish(str(job_id), GOOGLE_DL_CLINICAL_VALIDATION_TOPIC)
 
 
+def publish_assay_metadata_validation(job_id: int) -> None:
+    """Publish to the assay_metadata_validation topic that a job's assay metadata file is ready to be validated."""
+    # Start validation asynchronously
+    _report = _encode_and_publish(str(job_id), GOOGLE_ASSAY_METADATA_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.

{nci_cidc_api_modules-1.2.44 → nci_cidc_api_modules-1.2.46/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.44
+Version: 1.2.46
 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-1.2.44 → nci_cidc_api_modules-1.2.46}/nci_cidc_api_modules.egg-info/SOURCES.txt

@@ -1,6 +1,7 @@
 LICENSE
 MANIFEST.in
 README.md
+boot.py
 pyproject.toml
 requirements.modules.txt
 setup.py

{nci_cidc_api_modules-1.2.44 → nci_cidc_api_modules-1.2.46}/nci_cidc_api_modules.egg-info/top_level.txt

@@ -1 +1,2 @@
+boot
 cidc_api

{nci_cidc_api_modules-1.2.44 → nci_cidc_api_modules-1.2.46}/setup.py

@@ -23,7 +23,7 @@ setup(
     name="nci_cidc_api_modules",
     description="SQLAlchemy data models and configuration tools used in the NCI CIDC API",
     python_requires=">=3.13",
-    py_modules=["cidc_api.telemetry"],
+    py_modules=["cidc_api.telemetry", "boot"],
     install_requires=requirements,
     license="MIT license",
     include_package_data=True,

{nci_cidc_api_modules-1.2.44 → nci_cidc_api_modules-1.2.46}/tests/test_api.py

@@ -415,6 +415,7 @@ def test_endpoint_urls(cidc_api):
     """
     expected_endpoints = {
         "/",
+        "/_ah/warmup",
         "/downloadable_files/",
         "/downloadable_files/filelist",
         "/downloadable_files/compressed_batch",

nci_cidc_api_modules-1.2.44/cidc_api/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.2.44"