nci-cidc-api-modules 1.2.35__tar.gz → 1.2.36__tar.gz

{nci_cidc_api_modules-1.2.35/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.36}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.35
+Version: 1.2.36
 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
@@ -33,6 +33,14 @@ Requires-Dist: requests>=2.32.5
 Requires-Dist: sqlalchemy>=2.0.44
 Requires-Dist: sqlalchemy-mixins~=2.0.5
 Requires-Dist: werkzeug>=3.1.4
+Requires-Dist: opentelemetry-api>=1.38.0
+Requires-Dist: opentelemetry-exporter-otlp-proto-grpc>=1.38.0
+Requires-Dist: opentelemetry-sdk>=1.38.0
+Requires-Dist: opentelemetry-instrumentation-flask>=0.59b0
+Requires-Dist: opentelemetry-instrumentation-requests>=0.59b0
+Requires-Dist: opentelemetry-instrumentation-sqlalchemy>=0.59b0
+Requires-Dist: opentelemetry-exporter-gcp-trace>=1.11.0
+Requires-Dist: opentelemetry-propagator-gcp>=1.11.0
 Requires-Dist: nci-cidc-schemas==0.28.10
 Dynamic: description
 Dynamic: description-content-type

{nci_cidc_api_modules-1.2.35 → nci_cidc_api_modules-1.2.36}/cidc_api/models/models.py

@@ -35,7 +35,8 @@ __all__ = [
     "ADMIN_FILE_CATEGORIES",
     "FINAL_JOB_STATUS",
     "INGESTION_JOB_STATUSES",
-    "INGESTION_JOB_COLORS",
+    "ASSAY_JOB_COLORS",
+    "CLINICAL_JOB_COLORS",
 ]
 
 import hashlib
@@ -3436,7 +3437,7 @@ INGESTION_JOB_STATUSES = [
 ]
 
 # Business decision to pass hex codes from the backend though that should be done by the front end...
-INGESTION_JOB_COLORS = {
+CLINICAL_JOB_COLORS = {
     "DRAFT": "",
     "INITIAL SUBMISSION": "#ACCAD7",
     "VALIDATION REVIEW": "#DABE90",
@@ -3444,6 +3445,13 @@ INGESTION_JOB_COLORS = {
     "INGESTION": "#8FCEC7",
     "PUBLISHED": "#90D9E6",
 }
+ASSAY_JOB_COLORS = {
+    "INITIAL SUBMISSION": "#43807E",
+    "VALIDATION REVIEW": "#906F3F",
+    "REVISION SUBMISSION": "#95358A",
+    "INGESTION": "#542C88",
+    "PUBLISHED": "#1C81A0",
+}
 # TODO If have "CANCELLED" concept or other final status, add here
 FINAL_JOB_STATUS = ["PUBLISHED"]
 TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER = "Data Category"

{nci_cidc_api_modules-1.2.35 → nci_cidc_api_modules-1.2.36}/cidc_api/shared/assay_handling.py

@@ -53,7 +53,7 @@ def prepare_assay_job(trial_id: str, assay_type: str, batch_id: str) -> tuple[st
 
     # Create or retrieve intake bucket corresponding to the trial
     intake_bucket = gcloud_client.create_intake_bucket(get_current_user().email, trial_id=trial_id)
-    gcs_path = f"{intake_bucket.name}/{trial_id}/{assay_type}"
+    gcs_path = f"{intake_bucket.name}/{assay_type}/{submission_id}"
 
     return submission_id, job_status, error_status, start_date, version, gcs_path
 

{nci_cidc_api_modules-1.2.35 → nci_cidc_api_modules-1.2.36}/cidc_api/shared/auth.py

@@ -1,16 +1,14 @@
 from functools import wraps
 from typing import List
 
-from packaging import version
-
 from flask import g, request, current_app as app, Flask
+from packaging import version
 from werkzeug.exceptions import Unauthorized, BadRequest, PreconditionFailed
 
-from ..models import Users, UserSchema
-
 from ..config.logging import get_logger
-
+from ..models import Users, UserSchema
 from ..shared.jose import decode_id_token
+from ..telemetry import trace_
 
 logger = get_logger(__name__)
 
@@ -144,6 +142,7 @@ def get_current_user() -> Users:
 _user_schema = UserSchema()
 
 
+@trace_()
 def authenticate() -> Users:
     id_token = _extract_token()
     token_payload = decode_id_token(id_token)
@@ -172,6 +171,7 @@ def _extract_token() -> str:
 
 
 ### Authorization logic ###
+@trace_()
 def authorize(user: Users, allowed_roles: List[str], resource: str, method: str) -> bool:
     """Check if the current user is authorized to act on the current request's resource.
     Raises Unauthorized

{nci_cidc_api_modules-1.2.35 → nci_cidc_api_modules-1.2.36}/cidc_api/shared/file_handling.py

@@ -10,10 +10,12 @@ from ..config.settings import GOOGLE_CLINICAL_DATA_BUCKET
 from ..models import PreprocessedFiles, TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER
 from ..shared.auth import get_current_user
 from ..shared.gcloud_client import upload_file_to_gcs, move_gcs_file
+from ..telemetry import trace_
 
 logger = get_logger(__name__)
 
 
+@trace_()
 def set_current_file(
     file: FileStorage, file_category: str, gcs_folder: str, session: Session, uploader_email: str, job_id: int = None
 ) -> PreprocessedFiles:
@@ -26,6 +28,7 @@ def set_current_file(
     return latest_file
 
 
+@trace_()
 def create_file(
     file: FileStorage,
     gcs_folder: str,

{nci_cidc_api_modules-1.2.35 → nci_cidc_api_modules-1.2.36}/cidc_api/shared/gcloud_client.py

@@ -1,6 +1,6 @@
 """Utilities for interacting with the Google Cloud Platform APIs."""
 
-# pylint: disable=logging-fstring-interpolation,too-many-lines
+# pylint: disable=logging-fstring-interpolation,too-many-lines, broad-exception-raised
 
 import base64
 import datetime
@@ -634,6 +634,7 @@ def _build_trial_upload_prefixes(
     trial_set: Set[str] = set()
     upload_set: Set[str] = set()
     if not trial_id:
+        # import is here becasue of circular import
         from ..models.models import TrialMetadata
 
         trial_set = {str(t.trial_id) for t in session.query(TrialMetadata).add_columns(TrialMetadata.trial_id)}
@@ -940,7 +941,8 @@ def get_signed_url(
 
 def _encode_and_publish(content: str, topic: str) -> Future:
     """Convert `content` to bytes and publish it to `topic`."""
-    pubsub_publisher = pubsub.PublisherClient()
+    publisher_options = pubsub.types.PublisherOptions(enable_open_telemetry_tracing=ENV == "dev-int")
+    pubsub_publisher = pubsub.PublisherClient(publisher_options=publisher_options)
     topic = pubsub_publisher.topic_path(GOOGLE_CLOUD_PROJECT, topic)
     data = bytes(content, "utf-8")
 

nci_cidc_api_modules-1.2.36/cidc_api/shared/utils.py

@@ -0,0 +1,19 @@
+from cidc_api.telemetry import trace_
+
+
+def _stripper(x):
+    if x and isinstance(x, str):
+        return x.strip()
+    else:
+        return x
+
+
+@trace_("sheet")
+def strip_whitespaces(df, sheet=None):
+    if sheet:
+        df = df[sheet]
+
+    df.rename(columns=_stripper, inplace=True)
+    df = df.map(_stripper)
+
+    return df

{nci_cidc_api_modules-1.2.35 → nci_cidc_api_modules-1.2.36/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.35
+Version: 1.2.36
 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
@@ -33,6 +33,14 @@ Requires-Dist: requests>=2.32.5
 Requires-Dist: sqlalchemy>=2.0.44
 Requires-Dist: sqlalchemy-mixins~=2.0.5
 Requires-Dist: werkzeug>=3.1.4
+Requires-Dist: opentelemetry-api>=1.38.0
+Requires-Dist: opentelemetry-exporter-otlp-proto-grpc>=1.38.0
+Requires-Dist: opentelemetry-sdk>=1.38.0
+Requires-Dist: opentelemetry-instrumentation-flask>=0.59b0
+Requires-Dist: opentelemetry-instrumentation-requests>=0.59b0
+Requires-Dist: opentelemetry-instrumentation-sqlalchemy>=0.59b0
+Requires-Dist: opentelemetry-exporter-gcp-trace>=1.11.0
+Requires-Dist: opentelemetry-propagator-gcp>=1.11.0
 Requires-Dist: nci-cidc-schemas==0.28.10
 Dynamic: description
 Dynamic: description-content-type

{nci_cidc_api_modules-1.2.35 → nci_cidc_api_modules-1.2.36}/nci_cidc_api_modules.egg-info/requires.txt

@@ -24,4 +24,12 @@ requests>=2.32.5
 sqlalchemy>=2.0.44
 sqlalchemy-mixins~=2.0.5
 werkzeug>=3.1.4
+opentelemetry-api>=1.38.0
+opentelemetry-exporter-otlp-proto-grpc>=1.38.0
+opentelemetry-sdk>=1.38.0
+opentelemetry-instrumentation-flask>=0.59b0
+opentelemetry-instrumentation-requests>=0.59b0
+opentelemetry-instrumentation-sqlalchemy>=0.59b0
+opentelemetry-exporter-gcp-trace>=1.11.0
+opentelemetry-propagator-gcp>=1.11.0
 nci-cidc-schemas==0.28.10

{nci_cidc_api_modules-1.2.35 → nci_cidc_api_modules-1.2.36}/requirements.modules.txt

@@ -25,5 +25,19 @@ sqlalchemy>=2.0.44
 sqlalchemy-mixins~=2.0.5
 werkzeug>=3.1.4
 
+# open telemetry sdk
+opentelemetry-api >= 1.38.0
+opentelemetry-exporter-otlp-proto-grpc >= 1.38.0
+opentelemetry-sdk >= 1.38.0
+
+# open telemetry instrumentation
+opentelemetry-instrumentation-flask >= 0.59b0
+opentelemetry-instrumentation-requests >= 0.59b0
+opentelemetry-instrumentation-sqlalchemy >= 0.59b0
+
+# open telemetry gcp
+opentelemetry-exporter-gcp-trace >= 1.11.0
+opentelemetry-propagator-gcp >= 1.11.0
+
 # cidc deps
 nci-cidc-schemas==0.28.10

nci_cidc_api_modules-1.2.35/cidc_api/shared/utils.py

@@ -1,11 +0,0 @@
-def strip_whitespaces(df):
-    def stripper(x):
-        if x and isinstance(x, str):
-            return x.strip()
-        else:
-            return x
-
-    df.rename(columns=stripper, inplace=True)
-    df = df.map(stripper)
-
-    return df