Merge pull request #1228 from blankenberg/wf_extrac_15.10

[15.10] Fixes for dataset 'cleanup'/association linking when extracting workflows from a history.
galaxyproject · Dec 8, 2015 · 2be1707 · 2be1707
2 parents 94b0499 + 8334593
commit 2be1707
Showing 1 changed file with 14 additions and 8 deletions.
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
@@ -14,7 +14,8 @@
 from galaxy.tools import ToolOutputCollectionPart
 from galaxy.tools.parameters.grouping import (
     Conditional,
-    Repeat
+    Repeat,
+    Section
 )
 from .steps import (
     attach_ordered_steps,
@@ -340,10 +341,11 @@ def cleanup( prefix, inputs, values ):
                     if k.startswith( key ):
                         del root_values[k]
             elif isinstance( input, Repeat ):
-                group_values = values[key]
-                for i, rep_values in enumerate( group_values ):
-                    rep_index = rep_values['__index__']
-                    cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
+                if key in values:
+                    group_values = values[key]
+                    for i, rep_values in enumerate( group_values ):
+                        rep_index = rep_values['__index__']
+                        cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
             elif isinstance( input, Conditional ):
                 # Scrub dynamic resource related parameters from workflows,
                 # they cause problems and the workflow probably should include
@@ -352,9 +354,13 @@ def cleanup( prefix, inputs, values ):
                     if input.name in values:
                         del values[input.name]
                     return
-                group_values = values[input.name]
-                current_case = group_values['__current_case__']
-                cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
+                if input.name in values:
+                    group_values = values[input.name]
+                    current_case = group_values['__current_case__']
+                    cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
+            elif isinstance( input, Section ):
+                if input.name in values:
+                    cleanup( "%s%s|" % ( prefix, key ), input.inputs, values[input.name] )
     cleanup( "", inputs, values )
     return associations