Logic is wrong, everything must fail

ga4gh/htsget/compliance/file_validator.py

@@ -57,6 +57,7 @@ def identify_file(self, fp, source) -> (str, str):
             file_payload, responses = methods.fetch_url(fp).json()
             file_type = responses[0]["htsget"]["format"] # First response code is from htsget endpoint itself
 
+            # htsfile needs a file
             with tempfile.NamedTemporaryFile(delete=True) as temp_file:
                 temp_file.write(file_payload.encode())
                 temp_file.flush()
@@ -74,6 +75,11 @@ def identify_file(self, fp, source) -> (str, str):
             ext = c.EXTENSION_BCF
         else:
             ext = ".unknown_file_format"
+
+        # Append encryption file extension to file type if encrypted
+        if encryption_scheme is not None:
+            if encryption_scheme == c.ENCRYPTION_SCHEME_CRYPT4GH:
+                ext = ext + c.EXTENSION_C4GH
 
         return (ext, encryption_scheme)
 
@@ -86,6 +92,10 @@ def validate(self):
 
         if string_returned != string_expected:
             result = FileValidator.FAILURE
+        if string_expected is None:
+            result = FileValidator.FAILURE
+        if string_returned is None:
+            result = FileValidator.FAILURE
 
         return result
 

ga4gh/htsget/compliance/test_case.py

@@ -62,7 +62,7 @@ def execute_test(self):
             self.validate_response_code(responses)
             # Validate the htsget response schema, not the payload of the individual URLs
             self.validate_response_schema(htsget_response)
-            # FIXME: Consolidate fileparts logic with methods.fetch_url() since it aggregates as well, anyway
+            # Check against samtools (and crypt4gh) with local files fetched on the filesystem
             self.validate_file_contents(htsget_response, params=params)
             report_case.set_status_success()