nci-cidc-api-modules 1.1.10__py3-none-any.whl → 1.1.12__py3-none-any.whl

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__)
@@ -1120,13 +1121,15 @@ class TrialMetadata(CommonColumns):
     _metadata_idx = Index("metadata_idx", metadata_json, postgresql_using="gin")
 
     @staticmethod
-    def validate_metadata_json(metadata_json: dict) -> dict:
-        # Prior to running trial_metadata_validator.iter_error_messages on the metadata_json,
-        # strip out unnecessary manifest data for the validation so that existing manifest data
-        # that no longer conform to the post-CSMS-integration schema can be kept.
+    def validate_metadata_json(metadata_json: dict, strip_metadata=True) -> dict:
+        # Prior to running trial_metadata_validator.iter_error_messages on the metadata_json, if
+        # strip_metadata=True, will strip out unnecessary manifest data for the validation so that
+        # existing manifest data that no longer conform to the post-CSMS-integration schema can be kept.
         # See more details in the strip_metadata_for_validation function docs.
-        metadata_to_validate = json_validation.strip_metadata_for_validation(
-            metadata_json
+        metadata_to_validate = (
+            json_validation.strip_metadata_for_validation(metadata_json)
+            if strip_metadata
+            else metadata_json
         )
         errs = trial_metadata_validator.iter_error_messages(metadata_to_validate)
         messages = list(f"'metadata_json': {err}" for err in errs)
@@ -2184,7 +2187,7 @@ 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 +3298,41 @@ 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.dist-info → nci_cidc_api_modules-1.1.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.10
+Version: 1.1.12
 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.dist-info → nci_cidc_api_modules-1.1.12.dist-info}/RECORD

@@ -8,7 +8,7 @@ cidc_api/csms/auth.py,sha256=25Yma2Kz3KLENAPSeBYacFuSZXng-EDgmgInKBsRyP0,3191
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
 cidc_api/models/csms_api.py,sha256=_uB9ZoxCFxKO8ZDTxCjS0CpeQg14EdlkEqnwyAFyYFQ,31377
 cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
-cidc_api/models/models.py,sha256=71QpE6ZdLcnarzTrbckJFkCQ4cNN7WD_X-EsUXt_R-Y,127642
+cidc_api/models/models.py,sha256=xoTl1b92EzwOby5Dct6AgtN9l3wEUB1NdhhrSEHwMR4,129248
 cidc_api/models/schemas.py,sha256=7tDYtmULuzTt2kg7RorWhte06ffalgpQKrFiDRGcPEQ,2711
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
 cidc_api/models/files/details.py,sha256=h6R0p_hi-ukHsO7HV-3Wukccp0zRLJ1Oie_JNA_7Pl0,62274
@@ -19,8 +19,8 @@ cidc_api/shared/emails.py,sha256=FXW9UfI2bCus350SQuL7ZQYq1Vg-vGXaGWmRfA6z2nM,440
 cidc_api/shared/gcloud_client.py,sha256=7dDs0crLMJKdIp4IDSfrZBMB3h-zvWNieB81azoeLO4,33746
 cidc_api/shared/jose.py,sha256=QO30uIhbYDwzPEWWJXz0PfyV7E1AZHReEZJUVT70UJY,1844
 cidc_api/shared/rest_utils.py,sha256=LMfBpvJRjkfQjCzVXuhTTe4Foz4wlvaKg6QntyR-Hkc,6648
-nci_cidc_api_modules-1.1.10.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.1.10.dist-info/METADATA,sha256=WG80O_AKzmoKtYB-85vOLgy6pwduCKhngjKfaBs2S5I,41284
-nci_cidc_api_modules-1.1.10.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-nci_cidc_api_modules-1.1.10.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.1.10.dist-info/RECORD,,
+nci_cidc_api_modules-1.1.12.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.1.12.dist-info/METADATA,sha256=d000X8YPVI4KWjmw1ty9vXrcb1C-C-qUUHheW8_3d2U,41284
+nci_cidc_api_modules-1.1.12.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+nci_cidc_api_modules-1.1.12.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.1.12.dist-info/RECORD,,