nci-cidc-api-modules 1.2.29__py3-none-any.whl → 1.2.45__py3-none-any.whl

cidc_api/shared/gcloud_client.py

@@ -1,13 +1,15 @@
 """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 asyncio
 import base64
 import datetime
 import hashlib
 import io
 import json
 import os
+import re
 import warnings
 from collections import namedtuple
 from concurrent.futures import Future
@@ -25,6 +27,8 @@ from typing import (
 )
 
 import googleapiclient.discovery
+from gcloud.aio.storage import Storage
+from pandas.core.frame import DataFrame
 import pandas as pd
 import requests
 from cidc_schemas.prism.constants import ASSAY_TO_FILEPATH
@@ -56,6 +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,
@@ -361,15 +366,34 @@ def get_intake_bucket_name(user_email: str) -> str:
     return bucket_name
 
 
-def create_intake_bucket(user_email: str) -> storage.Bucket:
+def get_trial_intake_bucket_name(trial_id: str) -> str:
     """
-    Create a new data intake bucket for this user, or get the existing one.
+    Return a sanitized GCS bucket name for a given trial_id.
+
+    Produces:  <GOOGLE_INTAKE_BUCKET>-<sanitized_trial_id>
+    where the trial_id segment is lowercased and restricted to [a-z0-9-].
+    """
+    # Replace non-allowed bucket chars with "-"
+    sanitized_id = re.sub(r"[^a-z0-9-]", "-", trial_id.lower())
+    # Collapse repeated "-" and trim from both ends
+    sanitized_id = re.sub(r"-+", "-", sanitized_id).strip("-")
+
+    return f"{GOOGLE_INTAKE_BUCKET}-{sanitized_id}"
+
+
+def create_intake_bucket(user_email: str, trial_id: str = None) -> storage.Bucket:
+    """
+    Create (or retrieve) the appropriate data intake bucket.
+    If a trial_id is provided, a trial-specific bucket is used;
+    otherwise a user-specific intake bucket is used.
+
     Grant the user GCS object admin permissions on the bucket, or refresh those
     permissions if they've already been granted.
     Created with uniform bucket-level IAM access, so expiring permission.
     """
     storage_client = _get_storage_client()
-    bucket_name = get_intake_bucket_name(user_email)
+    # Get trial-specific bucket name if trial_id is given, otherwise a user-specific bucket name.
+    bucket_name = get_trial_intake_bucket_name(trial_id) if trial_id else get_intake_bucket_name(user_email)
     bucket = storage_client.bucket(bucket_name)
 
     if not bucket.exists():
@@ -423,25 +447,50 @@ def upload_xlsx_to_intake_bucket(user_email: str, trial_id: str, upload_type: st
     return f"https://console.cloud.google.com/storage/browser/_details/{bucket_name}/{blob_name}"
 
 
-def gcs_xlsx_or_csv_file_to_pandas_dataframe(bucket_name: str, blob_name: str):
-    """Reads an XLSX or CSV file from Google Cloud Storage into a Pandas DataFrame."""
-    temp_file = get_file_bytes_from_gcs(bucket_name, blob_name)
-
-    # TODO: specify sheet in xlsx file and/or accept tsv and xls files
-    if blob_name[-3:] == "csv":
-        return strip_whitespaces(pd.read_csv(temp_file))
-    elif blob_name[-4:] == "xlsx":
-        return strip_whitespaces(pd.read_excel(temp_file))
+def prepare_dataframe(extension, bytes) -> DataFrame:
+    if extension == "csv":
+        return strip_whitespaces(pd.read_csv(bytes, dtype=str, keep_default_na=False))
+    elif extension == "xlsx":
+        return strip_whitespaces(pd.read_excel(bytes, dtype=str, keep_default_na=False))
     else:
         raise Exception("Can only read csv or xlsx files")
 
 
+def gcs_xlsx_or_csv_file_to_pandas_dataframe(bucket_name: str, blob_name: str) -> DataFrame:
+    """Reads an XLSX or CSV file from Google Cloud Storage into a Pandas DataFrame."""
+    contents = get_file_bytes_from_gcs(bucket_name, blob_name)
+    extension = blob_name.split(".")[-1]
+    return prepare_dataframe(extension, contents)
+
+
 def get_file_bytes_from_gcs(bucket_name: str, blob_name: str) -> io.BytesIO:
     """Reads a file from Google Cloud Storage and returns it as BytesIO."""
     sheet_data = storage.Client().bucket(bucket_name).blob(blob_name).download_as_bytes()
     return io.BytesIO(sheet_data)
 
 
+async def async_gcs_files_to_pandas_dataframes(bucket_name: str, blob_names: List[str]) -> List[DataFrame]:
+    """Async reads a XLSX or CSV files from Google Cloud Storage into a list of Pandas DataFrames."""
+
+    all_contents = await asyncio.gather(
+        *[async_get_file_bytes_from_gcs(bucket_name, blob_name) for blob_name in blob_names]
+    )
+    dataframes = []
+
+    for blob_name, contents in zip(blob_names, all_contents):
+        extension = blob_name.split(".")[-1]
+        dataframes.append(prepare_dataframe(extension, contents))
+    return dataframes
+
+
+async def async_get_file_bytes_from_gcs(bucket_name: str, blob_name: str) -> io.BytesIO:
+    """Async reads a file from Google Cloud Storage and returns it as BytesIO."""
+
+    async with Storage() as client:
+        sheet_data = await client.download(bucket_name, blob_name)
+    return io.BytesIO(sheet_data)
+
+
 def _execute_multiblob_acl_change(
     user_email_list: List[str],
     blob_list: List[storage.Blob],
@@ -614,6 +663,7 @@ 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)}
@@ -886,6 +936,7 @@ def get_signed_url(
     bucket_name: str = GOOGLE_ACL_DATA_BUCKET,
     method: str = "GET",
     expiry_mins: int = 30,
+    use_short_filename: bool = False,
 ) -> str:
     """
     Generate a signed URL for `object_name` to give a client temporary access.
@@ -900,7 +951,11 @@ def get_signed_url(
 
     # Generate the signed URL, allowing a client to use `method` for `expiry_mins` minutes
     expiration = datetime.timedelta(minutes=expiry_mins)
-    full_filename = object_name.replace("/", "_").replace('"', "_").replace(" ", "_")
+    if use_short_filename:
+        filename = os.path.basename(object_name)
+    else:
+        # full filename with path included
+        filename = object_name.replace("/", "_").replace('"', "_").replace(" ", "_")
     other_kwargs = {}
     if os.environ.get("DEV_GOOGLE_STORAGE", None):
         other_kwargs["api_access_endpoint"] = (os.environ.get("DEV_GOOGLE_STORAGE") or "") + (
@@ -910,7 +965,7 @@ def get_signed_url(
         version="v2",
         expiration=expiration,
         method=method,
-        response_disposition=f'attachment; filename="{full_filename}"',
+        response_disposition=f'attachment; filename="{filename}"',
         **other_kwargs,
     )
     logger.info(f"generated signed URL for {object_name}: {url}")
@@ -920,7 +975,8 @@ 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")
 
@@ -994,6 +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.

cidc_api/shared/utils.py

@@ -1,11 +1,20 @@
-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)
+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)
+    df.replace("", None, inplace=True)
 
     return df

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-1.2.29.dist-info → nci_cidc_api_modules-1.2.45.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.29
+Version: 1.2.45
 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
@@ -8,30 +8,41 @@ 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: google-auth==2.43.0
-Requires-Dist: google-api-python-client>=2.185.0
-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: flask-talisman>=0.7.0
+Requires-Dist: gcloud-aio-storage~=9.6.1
+Requires-Dist: google-auth==2.45.0
+Requires-Dist: google-api-python-client>=2.187.0
+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: 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~=2.12.4
+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>=3.1.3
-Requires-Dist: nci-cidc-schemas==0.28.10
+Requires-Dist: werkzeug>=3.1.4
+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
+Requires-Dist: opentelemetry-exporter-gcp-trace>=1.11.0
+Requires-Dist: opentelemetry-propagator-gcp>=1.11.0
+Requires-Dist: nci-cidc-schemas==0.28.11
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

nci_cidc_api_modules-1.2.45.dist-info/RECORD

@@ -0,0 +1,165 @@
+cidc_api/__init__.py,sha256=TdZZy40X_55kxtHKjwbGqPrDr5qQe_uUz_Fvup_EuNI,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=Zql6Gxb5MNBW-rxcDNIPUqPiYHnD9nxd2-ievHaEYcI,4744
+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
+cidc_api/models/models.py,sha256=DTt0eFkFVVxVn23Aqr6TA8CQ7qb2hdqQ0xVJ3RakBBw,153684
+cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
+cidc_api/models/types.py,sha256=WVOTEH61FH5aGVwRbEcfNOce8NLjiEnl1ixtPWav2OA,30058
+cidc_api/models/db/stage1/__init__.py,sha256=zsxOSoogzL_xZ8B5OwcwLXvAmm6g2GYx1Zf6LLw8dq8,1917
+cidc_api/models/db/stage1/additional_treatment_orm.py,sha256=GCMzsYZl_B-7-TWYDBUXbt_Gri6YDv8XkYRheDLh3pc,926
+cidc_api/models/db/stage1/adverse_event_orm.py,sha256=32Kjpg6fvByp4gEVy6K28MlgMWQryG6GPh3un1F8x64,1914
+cidc_api/models/db/stage1/base_orm.py,sha256=izKizTf2W1fCK2CRUeyuErJbOaxNp6d299n4gqKWHDQ,246
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+cidc_api/models/db/stage1/gvhd_diagnosis_chronic_orm.py,sha256=seH3WO9IzQmau47N7zjJOa6OCSYi9_25WE5jOvxl6q8,1552
+cidc_api/models/db/stage1/gvhd_organ_acute_orm.py,sha256=knzkKz2qkRU0R6HjdtfClOuRpGEYEsLxbhqYUmOAjSg,838
+cidc_api/models/db/stage1/gvhd_organ_chronic_orm.py,sha256=mkhS1jFgCt_2NRXZfoqHWZh1ShkzLoPLR9W8ac_wzGs,862
+cidc_api/models/db/stage1/medical_history_orm.py,sha256=nyNOG_odEvPWqgu2DmiHT3K-FBB1ltI536iiNwCF0wA,1282
+cidc_api/models/db/stage1/other_malignancy_orm.py,sha256=wfoSCPUIzfw4anDi6FeqyhTzYrwTNlpDRCvL608zmXM,1303
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+cidc_api/models/db/stage1/radiotherapy_dose_orm.py,sha256=dLp_ENJAq-_f6MAspaGK-6R6ngHceFKpsrjoBM8yviI,1500
+cidc_api/models/db/stage1/response_by_system_orm.py,sha256=pOQSE5g-EFUApgEDOXwxyQCmvoC6M9atSfBDsF9f3KI,1524
+cidc_api/models/db/stage1/response_orm.py,sha256=P9a0ZVq_hJ3dipRgJTFcdjuWi9ueyGd0oQYHRiACNpc,1163
+cidc_api/models/db/stage1/specimen_orm.py,sha256=m1cq5SfkUETk6dk4s3uYLyXohpZgE8iU1Rzh0xVRTmw,1354
+cidc_api/models/db/stage1/stem_cell_transplant_orm.py,sha256=CqOAo-Pnj11XqR9a0CeaIGyLn5Ar42Hl_10tqEllnO0,1097
+cidc_api/models/db/stage1/surgery_orm.py,sha256=DCggc6xbjGhm-G93bueY5u43t896aBPTvRFTk3Gq8ys,1018
+cidc_api/models/db/stage1/therapy_agent_dose_orm.py,sha256=y8vaJazcoJ5mb0dmGXiAN8dQPP6yyDGpAOs_wDlH3SY,1306
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+cidc_api/models/db/stage1/trial_orm.py,sha256=bS2zIngkv8ruXdXskinSwz8H1EeAgs9aHnteUWqaplE,1266
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cidc_api/models/db/base_orm.py

@@ -1,25 +0,0 @@
-from typing import Self
-
-from sqlalchemy_mixins import SerializeMixin, ReprMixin
-
-from cidc_api.config.db import db
-
-
-class BaseORM(db.Model, ReprMixin, SerializeMixin):
-    __abstract__ = True
-    __repr__ = ReprMixin.__repr__
-
-    def merge(self, d: dict) -> Self:
-        """Merge keys and values from dict d into this model, overwriting as necessary."""
-        for key, value in d.items():
-            setattr(self, key, value)
-        return self
-
-    def clone(self) -> "BaseORM":
-        """Clones a SQLAlchemy ORM object, excluding primary keys."""
-        mapper = self.__mapper__
-        new_instance = self.__class__()
-        for column in mapper.columns:
-            if not column.primary_key:
-                setattr(new_instance, column.key, getattr(self, column.key))
-        return new_instance