Merge pull request galaxyproject#19162 from mvdbeek/optimize_converte…

…r_order [24.1] Prefer auto-decompressed datatype when picking conversion target
bgruening · Nov 20, 2024 · f382305 · f382305
2 parents da31407 + 974d7e5
commit f382305
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Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
@@ -881,7 +881,16 @@ def find_conversion_destination_for_dataset_by_extensions(
         if datatype and datatype.matches_any(accepted_datatypes):
             return True, None, None
 
-        for convert_ext in self.get_converters_by_datatype(ext):
+        converter_extensions = self.get_converters_by_datatype(ext)
+        uncompressed_instance = getattr(datatype, "uncompressed_datatype_instance", None)
+        if uncompressed_instance and uncompressed_instance.file_ext in converter_extensions:
+            # sort uncompressed instance ahead of other possible conversions
+            converter_extensions = [
+                uncompressed_instance.file_ext,
+                *(ext for ext in converter_extensions if ext != uncompressed_instance.file_ext),
+            ]
+
+        for convert_ext in converter_extensions:
             convert_ext_datatype = self.get_datatype_by_extension(convert_ext)
             if convert_ext_datatype is None:
                 self.log.warning(

diff --git a/test/functional/tools/implicit_conversion_format_input.xml b/test/functional/tools/implicit_conversion_format_input.xml
@@ -3,7 +3,7 @@
     cut -f 1 '$input1' > '$output1'
   </command>
   <inputs>
-    <param type="data" format="fasta" name="input1" label="Input 1" />
+    <param type="data" format="txt" name="input1" label="Input 1" />
   </inputs>
   <outputs>
     <data name="output1" format="input" />