Improve initial value injection, adjust former run form

galaxyproject · Aug 12, 2016 · e614a6e · e614a6e
1 parent 87038d2
commit e614a6e
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Showing 2 changed files with 14 additions and 28 deletions.
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
@@ -21,7 +21,7 @@
 from galaxy.tools.parameters.wrapped import make_dict_copy
 from galaxy.tools import DefaultToolState
 from galaxy.tools import ToolInputsNotReadyException
-from galaxy.util import odict, listify
+from galaxy.util import odict
 from galaxy.util.bunch import Bunch
 from galaxy.web.framework import formbuilder
 from tool_shed.util import common_util
@@ -1152,28 +1152,24 @@ def _handle_post_job_actions( self, step, job, replacement_dict ):
 
     def add_dummy_datasets( self, connections=None, steps=None ):
         if connections:
-            # Store onnections by input name
+            # Store connections by input name
             input_connections_by_name = dict( ( conn.input_name, conn ) for conn in connections )
         else:
             input_connections_by_name = {}
 
-        # Any connected input needs to have value RuntimeValue (these
-        # are not persisted so we need to do it every time)
+        # Any input needs to have value RuntimeValue or obtain the value from connected steps
         def callback( input, prefixed_name, context, **kwargs ):
             if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ):
-                if self.trans.workflow_building_mode is workflow_building_modes.USE_HISTORY:
-                    if connections is None or prefixed_name in input_connections_by_name:
-                        if steps:
-                            connection = input_connections_by_name[ prefixed_name ]
-                            output_step = next( output_step for output_step in steps if connection.output_step_id == output_step.id )
-                            if output_step.type.startswith( 'data' ):
-                                output_inputs = output_step.module.get_runtime_inputs( connections=connections )
-                                output_value = output_inputs[ 'input' ].get_initial_value( self.trans, context )
-                                if isinstance( input, DataToolParameter ):
-                                    for v in listify( output_value ):
-                                        if isinstance( v, self.trans.app.model.HistoryDatasetCollectionAssociation ):
-                                            return v.to_hda_representative()
-                                return output_value
+                if connections is not None and steps is not None and self.trans.workflow_building_mode is workflow_building_modes.USE_HISTORY:
+                    if prefixed_name in input_connections_by_name:
+                        connection = input_connections_by_name[ prefixed_name ]
+                        output_step = next( output_step for output_step in steps if connection.output_step_id == output_step.id )
+                        if output_step.type.startswith( 'data' ):
+                            output_inputs = output_step.module.get_runtime_inputs( connections=connections )
+                            output_value = output_inputs[ 'input' ].get_initial_value( self.trans, context )
+                            if isinstance( input, DataToolParameter ) and isinstance( output_value, self.trans.app.model.HistoryDatasetCollectionAssociation ):
+                                return output_value.to_hda_representative()
+                            return output_value
                         return RuntimeValue()
                     else:
                         return input.get_initial_value( self.trans, context )

diff --git a/templates/webapps/galaxy/workflow/run.mako b/templates/webapps/galaxy/workflow/run.mako
@@ -699,17 +699,7 @@ import base64
                   % endif
           </div>
           <div class="toolFormBody">
-              <%
-              # Filter possible inputs to data types that are valid for subsequent steps
-              type_filter = []
-              for oc in step.output_connections:
-                  for ic in oc.input_step.module.get_data_inputs():
-                      if 'extensions' in ic and ic['name'] == oc.input_name:
-                          type_filter += ic['extensions']
-              if not type_filter:
-                  type_filter = ['data']
-              %>
-              ${do_inputs( module.get_runtime_inputs(filter_set=type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
+              ${do_inputs( module.get_runtime_inputs( connections=step.output_connections ), step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
           </div>
       </div>
     %endif