nci-cidc-api-modules 1.1.10__tar.gz → 1.1.11__tar.gz

{nci_cidc_api_modules-1.1.10/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.10
+Version: 1.1.11
 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-1.1.10 → nci_cidc_api_modules-1.1.11}/cidc_api/models/models.py

@@ -24,9 +24,9 @@ __all__ = [
     "with_default_session",
 ]
 
-import re
 import hashlib
 import os
+import re
 from collections import defaultdict
 from datetime import datetime, timedelta
 from enum import Enum as EnumBaseClass
@@ -46,8 +46,10 @@ from typing import (
 )
 
 import pandas as pd
+from cidc_schemas import prism, unprism, json_validation
 from flask import current_app as app
 from google.cloud.storage import Blob
+from jsonschema.exceptions import ValidationError
 from sqlalchemy import (
     and_,
     Column,
@@ -76,11 +78,15 @@ from sqlalchemy import (
     Table,
     MetaData,
 )
+from sqlalchemy.dialects.postgresql import JSONB, UUID
+from sqlalchemy.engine import ResultProxy
+from sqlalchemy.exc import IntegrityError
+from sqlalchemy.ext.hybrid import hybrid_property
 from sqlalchemy.orm import relationship, validates
 from sqlalchemy.orm.attributes import flag_modified
 from sqlalchemy.orm.exc import NoResultFound
-from sqlalchemy.orm.session import Session
 from sqlalchemy.orm.query import Query
+from sqlalchemy.orm.session import Session
 from sqlalchemy.sql import (
     # This is unfortunate but other code in this file relies on sqlalchemy.and_, or_, etc
     # instead of the sqlalchemy.sql versions we are importing here.  The solution is to
@@ -91,12 +97,7 @@ from sqlalchemy.sql import (
     text,
 )
 from sqlalchemy.sql.functions import coalesce
-from sqlalchemy.exc import IntegrityError
-from sqlalchemy.ext.hybrid import hybrid_property
-from sqlalchemy.dialects.postgresql import JSONB, UUID
-from sqlalchemy.engine import ResultProxy
-
-from cidc_schemas import prism, unprism, json_validation
+from werkzeug.exceptions import BadRequest
 
 from .files import (
     build_trial_facets,
@@ -107,8 +108,8 @@ from .files import (
     FilePurpose,
     FACET_NAME_DELIM,
 )
-
 from ..config.db import BaseModel
+from ..config.logging import get_logger
 from ..config.settings import (
     PAGINATION_PAGE_SIZE,
     MAX_PAGINATION_PAGE_SIZE,
@@ -121,13 +122,13 @@ from ..shared.gcloud_client import (
     grant_lister_access,
     grant_download_access,
     publish_artifact_upload,
+    publish_patient_sample_update,
     refresh_intake_access,
     revoke_download_access,
     revoke_intake_access,
     revoke_lister_access,
     revoke_bigquery_access,
 )
-from ..config.logging import get_logger
 
 os.environ["TZ"] = "UTC"
 logger = get_logger(__name__)
@@ -2184,7 +2185,7 @@ class UploadJobs(CommonColumns):
         job.insert(session=session, commit=commit)
 
         if send_email:
-            trial = TrialMetadata.find_by_trial_id(trial_id)
+            trial = TrialMetadata.find_by_trial_id(trial_id, session=session)
             job.alert_upload_success(trial)
 
         return job
@@ -3295,3 +3296,41 @@ def result_proxy_to_models(
 ) -> List[BaseModel]:
     """Materialize a sqlalchemy `result_proxy` iterable as a list of `model` instances"""
     return [model(**dict(row_proxy)) for row_proxy in result_proxy.all()]
+
+
+@with_default_session
+def upload_manifest_json(
+    uploader_email: str,
+    trial_id: str,
+    template_type: str,
+    md_patch: dict,
+    session: Session,
+):
+    """
+    Ingest manifest data from JSON.
+
+    * Tries to load existing trial metadata blob (if fails, merge request fails; nothing saved).
+    * Merges the request JSON into the trial metadata (if fails, merge request fails; nothing saved).
+    * The merge request JSON is saved to `UploadJobs`.
+    * The updated trial metadata object is updated in the `TrialMetadata` table.
+    """
+    try:
+        TrialMetadata.patch_manifest(trial_id, md_patch, session=session, commit=False)
+    except ValidationError as e:
+        raise BadRequest(json_validation.format_validation_error(e)) from e
+    except ValidationMultiError as e:
+        raise BadRequest({"errors": e.args[0]}) from e
+
+    manifest_upload = UploadJobs.create(
+        upload_type=template_type,
+        uploader_email=uploader_email,
+        metadata=md_patch,
+        gcs_xlsx_uri="",  # not saving xlsx so we won't have phi-ish stuff in it
+        gcs_file_map=None,
+        session=session,
+        send_email=True,
+        status=UploadJobStatus.MERGE_COMPLETED.value,
+    )
+    # Publish that a manifest upload has been received
+    publish_patient_sample_update(manifest_upload.id)
+    return manifest_upload.id

{nci_cidc_api_modules-1.1.10 → nci_cidc_api_modules-1.1.11/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.10
+Version: 1.1.11
 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