Merge pull request #4271 from mvdbeek/job_rerun_changed_parameters

Keep tool parameters when rerunning a job

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

@@ -66,14 +66,23 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view
             // build request url
             var build_url = '';
             var build_data = {};
+            var job_id = '';
+            // When re-running a job the job_id is found in the new_options object.
+            // When re-running a job and requesting a new tool_version,
+            // the job_id is in the options object.
             if ( new_options.job_id ) {
-                build_url = Galaxy.root + 'api/jobs/' + new_options.job_id + '/build_for_rerun';
+                job_id = new_options.job_id;
+            } else if (options.job_id) {
+                job_id = options.job_id;
+            }
+            if ( job_id ) {
+                build_url = Galaxy.root + 'api/jobs/' + job_id + '/build_for_rerun';
             } else {
                 build_url = Galaxy.root + 'api/tools/' + options.id + '/build';
                 build_data = $.extend( {}, Galaxy.params );
                 build_data[ 'tool_id' ] && ( delete build_data[ 'tool_id' ] );
-                options.version && ( build_data[ 'tool_version' ] = options.version );
             }
+            options.version && ( build_data[ 'tool_version' ] = options.version );
 
             // get initial model
             Utils.get({

lib/galaxy/tools/__init__.py

@@ -1795,7 +1795,7 @@ class Tool( object, Dictifiable ):
         if job:
             try:
                 job_params = job.get_param_values( self.app, ignore_errors=True )
-                tool_warnings = self.check_and_update_param_values( job_params, request_context, update_values=False )
+                tool_warnings = self.check_and_update_param_values( job_params, request_context, update_values=True )
                 self._map_source_to_history( request_context, self.inputs, job_params )
                 tool_message = self._compare_tool_version( job )
                 params_to_incoming( kwd, self.inputs, job_params, self.app )

lib/galaxy/tools/toolbox/base.py

@@ -415,10 +415,11 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
             tool_ids = [tool_id]
         for tool_id in tool_ids:
             if tool_id in self._tools_by_id and not get_all_versions:
-                if tool_version and tool_version in self._tool_versions_by_id[ tool_id ]:
-                    return self._tool_versions_by_id[ tool_id ][ tool_version ]
                 # tool_id exactly matches an available tool by id (which is 'old' tool_id or guid)
-                return self._tools_by_id[ tool_id ]
+                if not tool_version:
+                    return self._tools_by_id[ tool_id ]
+                elif tool_version in self._tool_versions_by_id[ tool_id ]:
+                    return self._tool_versions_by_id[ tool_id ][ tool_version ]
             elif exact:
                 # We're looking for an exact match, so we skip lineage and
                 # versionless mapping, though we may want to check duplicate

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -204,7 +204,7 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ):
         job = self.__get_job(trans, id)
         if not job:
             raise exceptions.ObjectNotFound("Could not access job with id '%s'" % id)
-        tool = self.app.toolbox.get_tool( job.tool_id, job.tool_version )
+        tool = self.app.toolbox.get_tool( job.tool_id, kwd.get('tool_version') or job.tool_version )
         if tool is None:
             raise exceptions.ObjectNotFound( "Requested tool not found" )
         if not tool.is_workflow_compatible: