Merge branch 'main' into mshadbolt/docs-and-error-handling

mohschema.py

@@ -359,9 +359,9 @@ def validate_immunotherapies(self, map_json):
 
 
     def validate_radiations(self, map_json):
-        index = self.validation_schema["radiations"]["extra_args"]["index"]
-        if index > 0:
-            self.fail("Only one radiation is allowed per treatment")
+        # index = self.validation_schema["radiations"]["extra_args"]["index"]
+        # if index > 0:
+        #     self.fail("Only one radiation is allowed per treatment")
 
         for prop in map_json:
             match prop:
@@ -373,9 +373,9 @@ def validate_radiations(self, map_json):
 
     def validate_surgeries(self, map_json):
         specimen_ids = self.validation_schema["primary_diagnoses"]["extra_args"]["specimen_ids"]
-        index = self.validation_schema["surgeries"]["extra_args"]["index"]
-        if index > 0:
-            self.fail("Only one surgery is allowed per treatment")
+        # index = self.validation_schema["surgeries"]["extra_args"]["index"]
+        # if index > 0:
+        #     self.fail("Only one surgery is allowed per treatment")
 
         if "submitter_specimen_id" not in map_json:
             if "surgery_site" not in map_json or map_json["surgery_site"] is None:

test_data_ingest.py

@@ -114,9 +114,8 @@ def test_validation(packets, schema):
     # DONOR_5 > PD_5 > TR_10: treatment type Immunotherapy should have one or more immunotherapies submitted
 
     print(schema.validation_errors)
-    assert len(schema.validation_errors) == 3
-    # should be the following 3 errors:
-    # DONOR_5 > PD_5 > TR_5 > Radiation 1: Only one radiation is allowed per treatment
+    assert len(schema.validation_errors) == 2
+    # should be the following 2 errors:
     # DONOR_6 > PD_6 > TR_9 > Surgery 0: submitter_specimen_id SPECIMEN_43 does not correspond to one of the available specimen_ids ['SPECIMEN_3']
     # Duplicated IDs: in schema followups, FOLLOW_UP_4 occurs 2 times
 

validate_coverage.py

@@ -205,6 +205,8 @@ def validate_coverage(map_json, verbose=False):
         mappings.VERBOSE = True
 
     # read the schema and generate a scaffold
+    if "openapi_url" not in map_json:
+        return {"message": "No openapi_url schema available"}
     schema = MoHSchema(map_json["openapi_url"])
     if schema.json_schema is None:
         sys.exit(f"Did not find an openapi schema at {map_json['openapi_url']}; please check the 'openapi_url' in the map json file.")
@@ -223,7 +225,8 @@ def validate_coverage(map_json, verbose=False):
     # print(json.dumps(schema.validation_results, indent=4))
     return {
         "errors": schema.validation_errors,
-        "warnings": schema.validation_warnings
+        "warnings": schema.validation_warnings,
+        "statistics": schema.statistics
     }
 
 def main(args):