nci-cidc-api-modules 1.2.8__py3-none-any.whl → 1.2.10__py3-none-any.whl

cidc_api/models/models.py

@@ -30,6 +30,7 @@ __all__ = [
     "TRIAL_APPENDIX_A",
     "TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER",
     "REQUEST_LETTER",
+    "DETAILED_VALIDATION",
     "ADMIN_FILE_CATEGORIES",
     "FINAL_JOB_STATUS",
     "INGESTION_JOB_STATUSES",
@@ -3247,7 +3248,8 @@ def upload_manifest_json(
 
 TRIAL_APPENDIX_A = "trial_appendix_a"
 REQUEST_LETTER = "request_letter"
-ADMIN_FILE_CATEGORIES = [TRIAL_APPENDIX_A, REQUEST_LETTER]
+DETAILED_VALIDATION = "detailed_validation"
+ADMIN_FILE_CATEGORIES = [TRIAL_APPENDIX_A, REQUEST_LETTER, DETAILED_VALIDATION]
 
 
 class PreprocessedFiles(CommonColumns):
@@ -3419,7 +3421,7 @@ INGESTION_JOB_COLORS = {
 }
 # TODO If have "CANCELLED" concept or other final status, add here
 FINAL_JOB_STATUS = ["PUBLISHED"]
-TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER = "Entity"
+TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER = "Data Category"
 
 
 class IngestionJobs(CommonColumns):
@@ -3465,7 +3467,7 @@ class IngestionJobs(CommonColumns):
             if headers_ended:
                 if cell != "nan" and cell not in categories:
                     categories.append(cell)
-            elif cell == TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER:
+            elif cell.lower() == TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER.lower():
                 headers_ended = True
         if "data_dictionary" not in categories:
             # Ensure Data_Dictionary is always a required file category
@@ -3628,7 +3630,7 @@ class FileValidationErrors(CommonColumns):
 class ValidationConfigs(CommonColumns):
     __tablename__ = "validation_configs"
 
-    data_label = Column(String, nullable=True)
+    data_element = Column(String, nullable=True)
     validation = Column(String, nullable=True)
     scope = Column(String, nullable=True)
     active = Column(Boolean, nullable=False, default=True, server_default="true")

cidc_api/shared/gcloud_client.py

@@ -985,6 +985,12 @@ def publish_hl_clinical_validation(job_id: int) -> None:
     _report = _encode_and_publish(str(job_id), GOOGLE_HL_CLINICAL_VALIDATION_TOPIC)
 
 
+def publish_detailed_validation(job_id: int) -> None:
+    """Start detailed validation and create the detailed validation preprocessed file"""
+    # Start validation asynchronously
+    _report = _encode_and_publish(str(job_id), GOOGLE_DL_CLINICAL_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.

{nci_cidc_api_modules-1.2.8.dist-info → nci_cidc_api_modules-1.2.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.8
+Version: 1.2.10
 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-1.2.8.dist-info → nci_cidc_api_modules-1.2.10.dist-info}/RECORD

@@ -5,7 +5,7 @@ cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,14
 cidc_api/config/settings.py,sha256=NsJbqW6Vqcz2f79xcAbk4th5tHne_I-RPCbKq_3hpz0,4427
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
 cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
-cidc_api/models/models.py,sha256=8hfETKW-FN27aDmntprcj-4T59oB46oK9sdrll5tprs,146839
+cidc_api/models/models.py,sha256=b7HWj8uOD_xdv7p3WkrhRODauLCVGvSLQsSbJGUmr9Q,146956
 cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
 cidc_api/models/files/details.py,sha256=sZkGM7iEV4-J6IDQCdiMV6KBDLbPxCOqUMaU3aY9rX8,65153
@@ -14,11 +14,11 @@ cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cidc_api/shared/auth.py,sha256=PHqmVGkqDjbmUofytVFwD_9ssgUomESl3fFtFHPwZYQ,9062
 cidc_api/shared/emails.py,sha256=HQIixEUsR8yyu7Iv8S81RjtvEQeGuzQHzBfGsWIfP7k,4961
 cidc_api/shared/file_handling.py,sha256=l4wiRkVJLL7QbCoODsLx-uki6Km8QoMmUlRVnUV9vkk,3894
-cidc_api/shared/gcloud_client.py,sha256=ETQ34qKtO7l0svVhiHXxXewiyNjwIMgoeVcqrg-Twtk,36902
+cidc_api/shared/gcloud_client.py,sha256=AGF4OHvZtgvDe6_YL4gZUajBJL9nY6tjVBVkXGBEIIw,37169
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
-nci_cidc_api_modules-1.2.8.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.8.dist-info/METADATA,sha256=AZJg2SGHrtzfm5wNtIBAzSfqRyrJdPGwRtmFKEoWxTY,39538
-nci_cidc_api_modules-1.2.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.2.8.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.2.8.dist-info/RECORD,,
+nci_cidc_api_modules-1.2.10.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.10.dist-info/METADATA,sha256=j8DWxMQLIegbilW9COrSACclr3jFDMX2YYJcLkrGLEg,39539
+nci_cidc_api_modules-1.2.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.2.10.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.2.10.dist-info/RECORD,,