Merge pull request #12685 from bernt-matthias/topic/illumina-sniffer

lib/galaxy/datatypes/sequence.py

@@ -860,6 +860,11 @@ class FastqSolexa(Fastq):
                 return False
         return True
 
+    def sniff_prefix(self, file_prefix: FilePrefix):
+        # we expicitely do not want to have this sniffed. so we keep this here
+        # such that it can not be enabled in datatypes_conf
+        raise NotImplementedError
+
 
 class FastqIllumina(Fastq):
     """Class representing a FASTQ sequence ( the Illumina 1.3+ variant )
@@ -880,6 +885,11 @@ class FastqIllumina(Fastq):
                 return False
         return True
 
+    def sniff_prefix(self, file_prefix: FilePrefix):
+        # we expicitely do not want to have this sniffed. so we keep this here
+        # such that it can not be enabled in datatypes_conf
+        raise NotImplementedError
+
 
 class FastqCSSanger(Fastq):
     """Class representing a Color Space FASTQ sequence ( e.g a SOLiD variant )

lib/galaxy/datatypes/upload_util.py

@@ -80,9 +80,13 @@ def handle_upload(
     if requested_ext != 'auto':
         datatype = registry.get_datatype_by_extension(requested_ext)
         # Enable sniffer "validate mode" (prevents certain sniffers from disabling themselves)
-        if check_content and hasattr(datatype, 'sniff') and not datatype.sniff(path):
-            stdout = ("Warning: The file 'Type' was set to '{ext}' but the file does not appear to be of that"
-                      " type".format(ext=requested_ext))
+        if check_content and hasattr(datatype, 'sniff'):
+            try:
+                is_of_datatype = datatype.sniff(path)
+            except Exception:
+                is_of_datatype = False
+            if not is_of_datatype:
+                stdout = f"Warning: The file 'Type' was set to '{requested_ext}' but the file does not appear to be of that type"
 
     # Handle unsniffable binaries
     if is_binary and ext == 'binary':