nci-cidc-api-modules 1.2.36__py3-none-any.whl → 1.2.39__py3-none-any.whl

cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.39"

cidc_api/models/models.py

@@ -3478,6 +3478,7 @@ class IngestionJobs(CommonColumns):
     batch_id = Column(String, nullable=True)
     submission_id = Column(String, nullable=True)
     intake_path = Column(String, nullable=True)
+    uploader_email = Column(String, nullable=True)
 
     @staticmethod
     @with_default_session
@@ -3493,6 +3494,7 @@ class IngestionJobs(CommonColumns):
         submission_id: str = None,
         intake_path: str = None,
         start_date: datetime = None,
+        uploader_email: str = None,
         session: Session = None,
     ):
         new_job = IngestionJobs(
@@ -3507,6 +3509,7 @@ class IngestionJobs(CommonColumns):
             submission_id=submission_id,
             intake_path=intake_path,
             start_date=start_date,
+            uploader_email=uploader_email,
         )
         new_job.insert(session=session)
         return new_job

cidc_api/telemetry.py

@@ -0,0 +1,101 @@
+# standard modules
+from functools import wraps
+
+# external modules
+from opentelemetry import trace
+from opentelemetry.sdk.resources import Resource
+from opentelemetry.sdk.trace import TracerProvider
+from opentelemetry.sdk.trace.export import BatchSpanProcessor
+
+# local modules
+from .config.settings import ENV, TESTING
+
+# pylint: disable=import-outside-toplevel
+
+
+def instrument_flask(app):
+    from opentelemetry.instrumentation.flask import FlaskInstrumentor
+    from opentelemetry.propagate import set_global_textmap
+    from opentelemetry.propagators.cloud_trace_propagator import CloudTraceFormatPropagator
+
+    FlaskInstrumentor().instrument_app(app)
+
+    # use the X-Cloud-Trace-Context header
+    set_global_textmap(CloudTraceFormatPropagator())
+
+
+def instrument_requests():
+    from opentelemetry.instrumentation.requests import RequestsInstrumentor
+
+    def _request_hook(span, request_obj):
+        span.update_name(f"requests {request_obj.method}")
+
+    RequestsInstrumentor().instrument(request_hook=_request_hook)
+
+
+def instrument_sqlachemy(engine):
+    from opentelemetry.instrumentation.sqlalchemy import SQLAlchemyInstrumentor
+
+    SQLAlchemyInstrumentor().instrument(engine=engine)
+
+
+resource = Resource(attributes={"service.name": f"CIDC-{ENV}"})
+provider = TracerProvider(resource=resource)
+
+
+if ENV == "dev" and not TESTING:
+    from opentelemetry.exporter.otlp.proto.grpc.trace_exporter import OTLPSpanExporter
+
+    COLLECTOR_ENDPOINT = "127.0.0.1"
+    COLLECTOR_GRPC_PORT = 6004
+
+    # send spans to local exporter
+    # 1. download latest version from https://github.com/open-telemetry/opentelemetry-collector-releases/releases (otelcol-contrib_0.140.1_darwin_arm64)
+    # 2. start exporter from otel folder with `./otelcol-contrib --config=config.yaml`
+    # 3. download and start Jeager (all-in-one image)  - https://www.jaegertracing.io/download/
+    exporter = OTLPSpanExporter(endpoint=f"http://{COLLECTOR_ENDPOINT}:{COLLECTOR_GRPC_PORT}", insecure=True)
+    processor = BatchSpanProcessor(exporter)
+    provider.add_span_processor(processor)
+
+if ENV == "dev-int":
+    from opentelemetry.exporter.cloud_trace import CloudTraceSpanExporter
+
+    # send span to Cloud Trace service - https://console.cloud.google.com/traces/explorer
+    exporter = CloudTraceSpanExporter()
+    processor = BatchSpanProcessor(exporter)
+    provider.add_span_processor(processor)
+
+
+# NOTE: we don't run telemetry in upper tiers; no span processor is noop
+
+trace.set_tracer_provider(provider)
+tracer = trace.get_tracer(__name__)
+
+
+def trace_(*args):
+    def decorator_factory(func):
+
+        @wraps(func)
+        def wrapper(*args_, **kwargs_):
+            func_name = f"{func.__module__.split(".")[-1]}.{func.__name__}"
+
+            with tracer.start_as_current_span(func_name) as span:
+                for arg in args:
+                    value = kwargs_.get(arg)
+
+                    # track id of argument if exists
+                    if hasattr(value, "id"):
+                        value = getattr(value, "id")
+
+                    span.set_attributes({arg: value})
+
+                result = func(*args_, **kwargs_)
+
+                if isinstance(result, (str, int, float, bool)):
+                    span.set_attribute("result", result)
+
+            return result
+
+        return wrapper
+
+    return decorator_factory

{nci_cidc_api_modules-1.2.36.dist-info → nci_cidc_api_modules-1.2.39.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.36
+Version: 1.2.39
 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
@@ -8,34 +8,34 @@ Requires-Python: >=3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: certifi>=2025.11.12
-Requires-Dist: cloud-sql-python-connector[pg8000]>=1.18.5
+Requires-Dist: cloud-sql-python-connector[pg8000]>=1.19.0
 Requires-Dist: flask>=3.1.2
 Requires-Dist: flask-migrate>=4.1.0
 Requires-Dist: flask-sqlalchemy>=3.1.1
 Requires-Dist: flask-talisman>=0.7.0
-Requires-Dist: google-auth==2.43.0
+Requires-Dist: google-auth==2.45.0
 Requires-Dist: google-api-python-client>=2.187.0
-Requires-Dist: google-cloud-bigquery>=3.38.0
-Requires-Dist: google-cloud-pubsub>=2.33.0
-Requires-Dist: google-cloud-secret-manager>=2.25.0
-Requires-Dist: google-cloud-storage>=3.6.0
+Requires-Dist: google-cloud-bigquery>=3.39.0
+Requires-Dist: google-cloud-pubsub>=2.34.0
+Requires-Dist: google-cloud-secret-manager>=2.26.0
+Requires-Dist: google-cloud-storage>=3.7.0
 Requires-Dist: jinja2>=3.1.6
-Requires-Dist: joserfc>=1.5.0
-Requires-Dist: marshmallow>=4.1.0
+Requires-Dist: joserfc>=1.6.0
+Requires-Dist: marshmallow>=4.1.2
 Requires-Dist: marshmallow-sqlalchemy>=1.4.2
-Requires-Dist: numpy>=2.3.5
+Requires-Dist: numpy>=2.4.0
 Requires-Dist: packaging>=25.0
 Requires-Dist: pandas>=2.3.3
 Requires-Dist: pyarrow>=22.0.0
 Requires-Dist: pydantic~=2.12.5
 Requires-Dist: python-dotenv>=1.2.1
 Requires-Dist: requests>=2.32.5
-Requires-Dist: sqlalchemy>=2.0.44
+Requires-Dist: sqlalchemy>=2.0.45
 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-api>=1.39.1
+Requires-Dist: opentelemetry-exporter-otlp-proto-grpc>=1.39.1
+Requires-Dist: opentelemetry-sdk>=1.39.1
 Requires-Dist: opentelemetry-instrumentation-flask>=0.59b0
 Requires-Dist: opentelemetry-instrumentation-requests>=0.59b0
 Requires-Dist: opentelemetry-instrumentation-sqlalchemy>=0.59b0

{nci_cidc_api_modules-1.2.36.dist-info → nci_cidc_api_modules-1.2.39.dist-info}/RECORD

@@ -1,3 +1,5 @@
+cidc_api/__init__.py,sha256=-YGSx2TBmytNvZuuZBF4IMYrZU5cQnr5VfDEpKUnxb0,23
+cidc_api/telemetry.py,sha256=LuZWkG8CKCn23O41RTNxEOQwMmfpp-fQ6zSInZhVJg8,3333
 cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,148
 cidc_api/config/db.py,sha256=CRgpyw7uVP9v7CTAa7_1dcXURqrfjRcLNjGgZC7iPQE,1627
 cidc_api/config/logging.py,sha256=abhVYtn8lfhIt0tyV2WHFgSmp_s2eeJh7kodB6LH4J0,1149
@@ -6,7 +8,7 @@ cidc_api/config/settings.py,sha256=ttOGvk_6zVMn4dtxIZ2-0w3wF2fpAUVfGpVZbKJ2b6s,4
 cidc_api/models/__init__.py,sha256=cTyK0Z1ttLo9itwZVRFr-d6aX-zX633YhqipqPgoGfE,115
 cidc_api/models/data.py,sha256=uLkgAJ6tCtsi3bOGt8I9esYrZqgbsTYM1rGfL2gx5sY,837
 cidc_api/models/migrations.py,sha256=UlS5How3J4ryaRuZT6F5VQtAKikkl0LTv9MgMO_ltiQ,11161
-cidc_api/models/models.py,sha256=QLVxftl9vEgHEPA5au0lh2usTTsh5lI8vWjuS2Twxdk,152921
+cidc_api/models/models.py,sha256=p0_8AgWaQ_6PW8BrMLm-7sil5NReXZfgYuWLLYfNH9A,153051
 cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
 cidc_api/models/types.py,sha256=nq_PvzDz67HzceOI_ve9AxReExAZ-XFE7T3G2bbpqJ4,29667
 cidc_api/models/db/base_orm.py,sha256=EV78qFBcOR7spK_PhjbkpsGcmcP33AQItX61SidDa_8,813
@@ -103,8 +105,8 @@ cidc_api/shared/gcloud_client.py,sha256=fDNgRpU7jAeDtYfY-Zz09KE-__jHo6v0J7fI3eLg
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
 cidc_api/shared/utils.py,sha256=Po14K_7cvMKI9zJVzS0YDP1IqDBQS5Mvs6UMvS0RT4g,328
-nci_cidc_api_modules-1.2.36.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.36.dist-info/METADATA,sha256=94lsTOKAtCJgZoANklikdDqfp-R7UQoU2qCOobI2sHI,40229
-nci_cidc_api_modules-1.2.36.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.2.36.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.2.36.dist-info/RECORD,,
+nci_cidc_api_modules-1.2.39.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.39.dist-info/METADATA,sha256=C_EZkWucWYx5taqgp0jwNwcQc41WNM9aM2_G6V9uFws,40229
+nci_cidc_api_modules-1.2.39.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.2.39.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.2.39.dist-info/RECORD,,