Fix sniff_compressed_dynamic_datatypes_default config option not prop…

…agating to upload tool.

Resolving the default when unspecified in the XML before writing out datatype confs fixes this. This makes this option always explicit in the datatypes conf that is shared with the upload tool.

lib/galaxy/datatypes/registry.py

@@ -140,6 +140,11 @@ def __import_module(full_path, datatype_module, datatype_class_name):
                 type_extension = elem.get('type_extension', None)
                 auto_compressed_types = galaxy.util.listify(elem.get('auto_compressed_types', ''))
                 sniff_compressed_types = galaxy.util.string_as_bool_or_none(elem.get("sniff_compressed_types", "None"))
+                if sniff_compressed_types is None:
+                    sniff_compressed_types = getattr(self.config, "sniff_compressed_dynamic_datatypes_default", True)
+                    # Make sure this is set in the elems we write out so the config option is passed ot the upload
+                    # tool which does not have a config object.
+                    elem.set("sniff_compressed_types", str(sniff_compressed_types))
                 mimetype = elem.get('mimetype', None)
                 display_in_upload = galaxy.util.string_as_bool(elem.get('display_in_upload', False))
                 # If make_subclass is True, it does not necessarily imply that we are subclassing a datatype that is contained
@@ -321,9 +326,6 @@ def __import_module(full_path, datatype_module, datatype_class_name):
                                     else:
                                         raise Exception("Unknown auto compression type [%s]" % auto_compressed_type)
                                     attributes["file_ext"] = compressed_extension
-                                    if sniff_compressed_types is None:
-                                        sniff_compressed_types = getattr(self.config, "sniff_compressed_dynamic_datatypes_default", True)
-
                                     attributes["uncompressed_datatype_instance"] = datatype_instance
                                     compressed_datatype_class = type(auto_compressed_type_name, (datatype_class, dynamic_parent, ), attributes)
                                     if edam_format: