nci-cidc-api-modules 1.0.29__py3-none-any.whl → 1.1.0__py3-none-any.whl

cidc_api/models/csms_api.py

@@ -456,7 +456,6 @@ def insert_manifest_into_blob(
 
     logger.info("Patch for %s manifest %s:\n%s", trial_id, manifest_id, patch)
     # merge and validate the data
-    # the existence of the correct cohort and collection_event names are checked here
     merged, errs = merge_clinical_trial_metadata(patch, trial_md.metadata_json)
     if errs:
         raise RuntimeError({"prism errors": [str(e) for e in errs]})

cidc_api/models/models.py

@@ -272,6 +272,13 @@ class CommonColumns(BaseModel):  # type: ignore
                 asc(sort_attribute) if sort_direction == "asc" else desc(sort_attribute)
             )
             query = query.order_by(field_with_dir)
+            if sort_field != "id":
+                # When sorting, need to guarantee unique order for offset/limit pagination to produce
+                # consistent results. Adding secondary "id" sort field to ensure unique order.
+                secondary_field_with_dir = (
+                    asc("id") if sort_direction == "asc" else desc("id")
+                )
+                query = query.order_by(secondary_field_with_dir)
 
         # Apply filter function
         query = filter_(query)
@@ -1114,7 +1121,14 @@ class TrialMetadata(CommonColumns):
 
     @staticmethod
     def validate_metadata_json(metadata_json: dict) -> dict:
-        errs = trial_metadata_validator.iter_error_messages(metadata_json)
+        # 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.
+        # See more details in the strip_metadata_for_validation function docs.
+        metadata_to_validate = json_validation.strip_metadata_for_validation(
+            metadata_json
+        )
+        errs = trial_metadata_validator.iter_error_messages(metadata_to_validate)
         messages = list(f"'metadata_json': {err}" for err in errs)
         if messages:
             raise ValidationMultiError(messages)

cidc_api/shared/emails.py

@@ -19,7 +19,7 @@ from ..config.settings import ENV, GOOGLE_ACL_DATA_BUCKET
 # - errors from CSMS in update_cidc_from_csms,
 # - errors from kicking off permissions in grant_download_permissions, and
 # - errors from implementing permissions in worker > permissions_worker
-CIDC_MAILING_LIST = "essex-alert@cimac-network.org"
+CIDC_MAILING_LIST = ["essex-alert@cimac-network.org", "mustafa.kucukkal@nih.gov"]
 
 
 def sendable(email_template):
@@ -76,7 +76,7 @@ def new_user_registration(email: str) -> dict:
     )
 
     email = {
-        "to_emails": [CIDC_MAILING_LIST],
+        "to_emails": CIDC_MAILING_LIST,
         "subject": subject,
         "html_content": html_content,
     }
@@ -110,7 +110,7 @@ def new_upload_alert(upload, full_metadata) -> dict:
     """
 
     email = {
-        "to_emails": [CIDC_MAILING_LIST],
+        "to_emails": CIDC_MAILING_LIST,
         "subject": subject,
         "html_content": html_content,
     }
@@ -152,7 +152,7 @@ def intake_metadata(
     """
 
     email = {
-        "to_emails": [CIDC_MAILING_LIST],
+        "to_emails": CIDC_MAILING_LIST,
         "subject": subject,
         "html_content": html_content,
     }

{nci_cidc_api_modules-1.0.29.dist-info → nci_cidc_api_modules-1.1.0.dist-info}/METADATA

@@ -1,34 +1,41 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nci_cidc_api_modules
-Version: 1.0.29
+Version: 1.1.0
 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
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: werkzeug ==3.0.6
-Requires-Dist: flask ==2.2.5
-Requires-Dist: flask-migrate ==2.5.2
-Requires-Dist: flask-sqlalchemy ==2.5.1
-Requires-Dist: sqlalchemy ~=1.3.0
-Requires-Dist: marshmallow ==3.19.0
-Requires-Dist: marshmallow-sqlalchemy ==0.22.3
-Requires-Dist: google-cloud-storage ==2.18.0
-Requires-Dist: google-cloud-secret-manager ==2.20.1
-Requires-Dist: google-cloud-pubsub ==2.22.0
-Requires-Dist: google-cloud-bigquery ==3.18.0
-Requires-Dist: google-api-python-client ==2.64.0
-Requires-Dist: google-auth ==2.32.0
-Requires-Dist: packaging >=20.0.0
-Requires-Dist: pyarrow ==14.0.1
-Requires-Dist: numpy <2,>=1.16.5
-Requires-Dist: pandas ==1.5.3
-Requires-Dist: python-dotenv ==0.10.3
-Requires-Dist: requests ==2.32.3
-Requires-Dist: jinja2 ==3.1.4
-Requires-Dist: certifi ==2024.7.4
-Requires-Dist: nci-cidc-schemas ==0.26.38
+Requires-Dist: werkzeug==3.0.6
+Requires-Dist: flask==2.2.5
+Requires-Dist: flask-migrate==2.5.2
+Requires-Dist: flask-sqlalchemy==2.5.1
+Requires-Dist: sqlalchemy~=1.3.0
+Requires-Dist: marshmallow==3.19.0
+Requires-Dist: marshmallow-sqlalchemy==0.22.3
+Requires-Dist: google-cloud-storage==2.18.0
+Requires-Dist: google-cloud-secret-manager==2.20.1
+Requires-Dist: google-cloud-pubsub==2.22.0
+Requires-Dist: google-cloud-bigquery==3.18.0
+Requires-Dist: google-api-python-client==2.64.0
+Requires-Dist: google-auth==2.32.0
+Requires-Dist: packaging>=20.0.0
+Requires-Dist: pyarrow==14.0.1
+Requires-Dist: numpy<2,>=1.16.5
+Requires-Dist: pandas==1.5.3
+Requires-Dist: python-dotenv==0.10.3
+Requires-Dist: requests==2.32.3
+Requires-Dist: jinja2==3.1.5
+Requires-Dist: certifi==2024.7.4
+Requires-Dist: nci-cidc-schemas==0.27.00
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # NCI CIDC API <!-- omit in TOC -->
 

{nci_cidc_api_modules-1.0.29.dist-info → nci_cidc_api_modules-1.1.0.dist-info}/RECORD

@@ -6,21 +6,21 @@ cidc_api/config/settings.py,sha256=2VHOVWdN4yUCNYMob2gaWgH2-1_4sbuo46JEIVT_PCY,4
 cidc_api/csms/__init__.py,sha256=eJkY6rWNOAUBmSd4G1_U6h7i472druKEtBdVmgFZVPg,20
 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=Wp4b53vwOqSlOIaoAYGlI1p8ZfXRXmVJ6MLcsvzq0LA,31664
+cidc_api/models/csms_api.py,sha256=U_JP6Z41G4hi48yNn9MAd70IYfBcm3AF3wHa31NdA78,31578
 cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
-cidc_api/models/models.py,sha256=PHfajlTGXVMHJ4SSqoZwYX8NmtkeL14sq7d4--n1an8,125827
+cidc_api/models/models.py,sha256=ykt0aG8jMjDdHYw3iPnU3laOaOZloHLf3ep6BeYM2cI,126732
 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
 cidc_api/models/files/facets.py,sha256=0owlp-is2QJ7DemcsJ4VdlnN255NkkV1Cimg0VaXHpY,28967
 cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cidc_api/shared/auth.py,sha256=EzMpYAR_gN5x985hgFAXTd24xygyctqZ80Yp05Ph_HQ,9104
-cidc_api/shared/emails.py,sha256=5dyuKlpcg1M4P_RrAt0ss2hiCqb-Y7p2XXR1d9uBXg8,4868
+cidc_api/shared/emails.py,sha256=TXKrga3A8rvaUKIH68ASmjkg9qMdFCWDf5HHxPvro5M,4892
 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-1.0.29.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.0.29.dist-info/METADATA,sha256=rmJORWrqsRApIivfppJ8UwTYz8OsAFPtl2yNTs4wUt8,40673
-nci_cidc_api_modules-1.0.29.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
-nci_cidc_api_modules-1.0.29.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.0.29.dist-info/RECORD,,
+nci_cidc_api_modules-1.1.0.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.1.0.dist-info/METADATA,sha256=eoV-3nV3Dvp-1-IUkjxDou2lX1THb_7McxLDjGMkyFE,40806
+nci_cidc_api_modules-1.1.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nci_cidc_api_modules-1.1.0.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.1.0.dist-info/RECORD,,

{nci_cidc_api_modules-1.0.29.dist-info → nci_cidc_api_modules-1.1.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.5.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any