Add resume option for job dependencies

client/galaxy/scripts/mvc/tools/tools-form-base.js

@@ -295,6 +295,20 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
                 });
             }
 
+            // add remap button
+            if (this.options.job_id && this.options.job_remap) {
+                options.inputs['rerun_remap_job_id'] = {
+                    label       : 'Resume dependencies from this job',
+                    name        : 'rerun_remap_job_id',
+                    type        : 'select',
+                    display     : 'radio',
+                    ignore      : '__ignore__',
+                    value       : '__ignore__',
+                    options     : [['Yes', this.options.job_id], ['No', '__ignore__']],
+                    help        : 'The previous run of this tool failed and other tools were waiting for it to finish successfully, use this option to resume those tools using the outputs of this tool run.'
+                }
+            }
+
             // create tool form section
             this.section = new ToolSection.View(self, {
                 inputs : options.inputs

lib/galaxy/tools/__init__.py

@@ -1215,7 +1215,8 @@ class Tool( object, Dictifiable ):
         if 'rerun_remap_job_id' in incoming:
             try:
                 rerun_remap_job_id = trans.app.security.decode_id( incoming[ 'rerun_remap_job_id' ] )
-            except Exception:
+            except Exception, exception:
+                log.error( str( exception ) )
                 message = 'Failure executing tool (attempting to rerun invalid job).'
                 return 'message.mako', dict( status='error', message=message, refresh_frames=[] )
 
@@ -2296,6 +2297,7 @@ class Tool( object, Dictifiable ):
                 params_to_incoming( kwd, self.inputs, job_params, trans.app, to_html=False )
             except Exception, exception:
                 trans.response.status = 500
+                log.error( str( exception ) )
                 return { 'error': str( exception ) }
 
         # create parameter object
@@ -2555,7 +2557,8 @@ class Tool( object, Dictifiable ):
             'versions'      : tool_versions,
             'requirements'  : tool_requirements,
             'errors'        : state_errors,
-            'state_inputs'  : state_inputs
+            'state_inputs'  : state_inputs,
+            'job_remap'     : self._get_job_remap(job)
         })
 
         # check for errors
@@ -2565,6 +2568,18 @@ class Tool( object, Dictifiable ):
         # return enriched tool model
         return tool_model
 
+    def _get_job_remap ( self, job):
+        if job:
+            if job.state == job.states.ERROR:
+                return True
+                try:
+                    if [ hda.dependent_jobs for hda in [ jtod.dataset for jtod in job.output_datasets ] if hda.dependent_jobs ]:
+                        return True
+                except Exception, exception:
+                    log.error( str( exception ) )
+                    pass
+        return False
+
     def _map_source_to_history(self, trans, tool_inputs, params):
         # Need to remap dataset parameters. Job parameters point to original
         # dataset used; parameter should be the analygous dataset in the

static/scripts/mvc/tools/tools-form-base.js

@@ -295,6 +295,20 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
                 });
             }
 
+            // add remap button
+            if (this.options.job_id && this.options.job_remap) {
+                options.inputs['rerun_remap_job_id'] = {
+                    label       : 'Resume dependencies from this job',
+                    name        : 'rerun_remap_job_id',
+                    type        : 'select',
+                    display     : 'radio',
+                    ignore      : '__ignore__',
+                    value       : '__ignore__',
+                    options     : [['Yes', this.options.job_id], ['No', '__ignore__']],
+                    help        : 'The previous run of this tool failed and other tools were waiting for it to finish successfully, use this option to resume those tools using the outputs of this tool run.'
+                }
+            }
+
             // create tool form section
             this.section = new ToolSection.View(self, {
                 inputs : options.inputs