nci-cidc-api-modules 1.2.44__py3-none-any.whl → 1.2.46__py3-none-any.whl

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)

cidc_api/__init__.py

@@ -1 +1 @@
-__version__ = "1.2.44"
+__version__ = "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 = " || "
 

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.dist-info → nci_cidc_api_modules-1.2.46.dist-info}/METADATA

@@ -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.dist-info → nci_cidc_api_modules-1.2.46.dist-info}/RECORD

@@ -1,10 +1,11 @@
-cidc_api/__init__.py,sha256=tZ6_k-1uqq2cr3SCnYO9N-chw-LhbafQ_arSm_DOlLs,23
+boot.py,sha256=oS_16OgU34iDxyFNpJl5rb5KbfbsCXroUCNLwVPxPNg,416
+cidc_api/__init__.py,sha256=s7kBVARFz8lSmh7ulygN5xbxPrps18XAib1Arlvg6cw,23
 cidc_api/telemetry.py,sha256=LuZWkG8CKCn23O41RTNxEOQwMmfpp-fQ6zSInZhVJg8,3333
 cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,148
 cidc_api/config/db.py,sha256=mEz8ugjvRNGylCqDYHaaMqaZfDh7sbd76BowmfBvq5c,2428
 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=ttOGvk_6zVMn4dtxIZ2-0w3wF2fpAUVfGpVZbKJ2b6s,4653
+cidc_api/config/settings.py,sha256=loern8cejUrOJJAog4z0iW9EQaa0nlN0rFrFOdZ-cLE,4483
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
 cidc_api/models/data.py,sha256=TyVXk5jJO1NN05CLqejLf5BPp6yLSNNxPmFOgXUnA1M,1313
 cidc_api/models/migrations.py,sha256=UlS5How3J4ryaRuZT6F5VQtAKikkl0LTv9MgMO_ltiQ,11161
@@ -154,12 +155,12 @@ cidc_api/shared/auth.py,sha256=EIP9AKokLNrI79Fkpv3P7WdzaddJIsuGGICc1W494X0,9110
 cidc_api/shared/email_layout.html,sha256=pBoTNw3ACHH-ncZFaNvcy5bXMqPwizR78usb0uCYtIc,7670
 cidc_api/shared/emails.py,sha256=8kNFEaSnKpY-GX_iE59QUhSp3c4_uzy3SpHYt2QjuqI,6121
 cidc_api/shared/file_handling.py,sha256=ObsLvBrkwHo6Nv48GvFXDKElNNl4inGpxv--001H_xc,5843
-cidc_api/shared/gcloud_client.py,sha256=lZuSmFjJizJ3R_rbKvNs3ddv9igy8MEYKcXv6toTIF0,39625
+cidc_api/shared/gcloud_client.py,sha256=0B13MRF_CUMbzaKtKVDd9fxErNdNGBpxfkknQ5deu7w,39972
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
 cidc_api/shared/utils.py,sha256=-gLnzxCR9E6h0plt2xrNisUG5_Y6GhhVwz3DgDIzpvs,367
-nci_cidc_api_modules-1.2.44.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.44.dist-info/METADATA,sha256=JU98ds9ZfGUDOaKnvb9FSYoWKbgWJNZWvj9TmDYT5eY,40270
-nci_cidc_api_modules-1.2.44.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.2.44.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.2.44.dist-info/RECORD,,
+nci_cidc_api_modules-1.2.46.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.46.dist-info/METADATA,sha256=hj9CUaG-zb8IeE3TShNDdQJRghQ86nlfZdFZq27Fra8,40270
+nci_cidc_api_modules-1.2.46.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.2.46.dist-info/top_level.txt,sha256=BSJqF6ura8-bWCKZvarvQEKvidMM05lH0bLQsNOrI0o,14
+nci_cidc_api_modules-1.2.46.dist-info/RECORD,,

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

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