Minor fixes to get tests to pass

galaxyproject · Nov 3, 2023 · 5651d4b · 5651d4b
1 parent fad423a
commit 5651d4b
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Showing 2 changed files with 10 additions and 8 deletions.
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
@@ -1121,7 +1121,7 @@ def do_inputs(inputs, values, prefix, step, other_values=None):
             else:
                 module = step.module
                 step_dict["label"] = module.name
-                step_dict["inputs"] = do_inputs(module.get_runtime_inputs(), step.state.inputs, "", step)
+                step_dict["inputs"] = do_inputs(module.get_runtime_inputs(step), step.state.inputs, "", step)
             step_dicts.append(step_dict)
         return {
             "name": workflow.name,

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
@@ -8,6 +8,7 @@
 import os
 import os.path
 import re
+import urllib.parse
 from typing import (
     Any,
     Dict,
@@ -2691,16 +2692,17 @@ def raw_to_galaxy(trans, as_dict_value):
 
     object_class = as_dict_value["class"]
     if object_class == "File":
-        relative_to = "/"  # TODO
-        from galaxy.tool_util.cwl.util import abs_path
-
-        path = abs_path(as_dict_value.get("location"), relative_to)
-
-        name = os.path.basename(path)
+        # TODO: relative_to = "/"
+        location = as_dict_value.get("location")
+        name = (
+            as_dict_value.get("identifier")
+            or as_dict_value.get("basename")
+            or os.path.basename(urllib.parse.urlparse(location).path)
+        )
         extension = as_dict_value.get("format") or "data"
         dataset = Dataset()
         source = DatasetSource()
-        source.source_uri = path
+        source.source_uri = location
         # TODO: validate this...
         source.transform = as_dict_value.get("transform")
         dataset.sources.append(source)