nci-cidc-api-modules 1.0.33__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

@@ -1121,7 +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)

{nci_cidc_api_modules-1.0.33.dist-info → nci_cidc_api_modules-1.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nci_cidc_api_modules
-Version: 1.0.33
+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
@@ -28,7 +28,7 @@ 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==0.26.38
+Requires-Dist: nci-cidc-schemas==0.27.00
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.0.33.dist-info → nci_cidc_api_modules-1.1.0.dist-info}/RECORD

@@ -6,9 +6,9 @@ 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=r23jzbZx_ZG-7ZDdwv3dLic_Wl-m1W5gnqeJjX_ocMg,126260
+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
@@ -19,8 +19,8 @@ cidc_api/shared/emails.py,sha256=TXKrga3A8rvaUKIH68ASmjkg9qMdFCWDf5HHxPvro5M,489
 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-1.0.33.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.0.33.dist-info/METADATA,sha256=T7DUYF57gM5y5mAfal_QVWDqwv3EAbHOqOZ-spj_3Tg,40807
-nci_cidc_api_modules-1.0.33.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nci_cidc_api_modules-1.0.33.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.0.33.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,,