(merge dev)

.gitignore

@@ -83,6 +83,9 @@ tool-data/shared/ucsc/ucsc_build_sites.txt
 tool-data/*.loc
 tool-data/genome/*
 tool-data/*.sample
+tool-data/testtoolshed.g2.bx.psu.edu/
+tool-data/toolshed.g2.bx.psu.edu/
+
 
 # Test output
 test-data-cache
@@ -121,4 +124,3 @@ doc/build
 .DS_Store
 *.rej
 *~
-

CONTRIBUTORS.md

@@ -32,6 +32,7 @@ The following individuals have contributed code to Galaxy:
 * Ira Cooke <iracooke@gmail.com>
 * Nate Coraor <nate@bx.psu.edu>
 * Michael Cotterell <mepcotterell@gmail.com>
+* Michael R. Crusoe <crusoe@ucdavis.edu>
 * Gianmauro Cuccuru <gmauro@crs4.it>
 * Frederik Delaere <frederik.delaere@gmail.com>
 * Olivia Doppelt <olivia.doppelt@pasteur.fr>

client/galaxy/scripts/galaxy-app-base.js

@@ -137,6 +137,10 @@ GalaxyApp.prototype._initLogger = function _initLogger( loggerOptions ){
         } catch( storageErr ){}
     }
     self.logger = new metricsLogger.MetricsLogger( loggerOptions );
+    self.emit = {};
+    [ 'log', 'debug', 'info', 'warn', 'error', 'metric' ].map(function( i ) {
+        self.emit[ i ] = function( data ) { self.logger.emit( i, arguments[ 0 ], Array.prototype.slice.call( arguments, 1 ) ) };
+    });
 
     if( self.config.debug ){
         // add this logger to mvc's loggable mixin so that all models can use the logger

client/galaxy/scripts/libs/jquery/select2.js

@@ -2980,13 +2980,12 @@ the specific language governing permissions and limitations under the Apache Lic
 
             // keep track of the search's value before it gets cleared
             this.nextSearchTerm = this.opts.nextSearchTerm(data, this.search.val());
-
-            this.clearSearch();
-            this.updateResults();
-
+            this.moveHighlight(1);
             if (this.select || !this.opts.closeOnSelect) this.postprocessResults(data, false, this.opts.closeOnSelect===true);
 
             if (this.opts.closeOnSelect) {
+                this.clearSearch()
+                this.updateResults()
                 this.close();
                 this.search.width(10);
             } else {

client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js

@@ -393,8 +393,8 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
         strategy = strategy || this.strategy;
         split = this._splitByFilters();
         paired = paired.concat( this[ strategy ].call( this, {
-                listA : split[0],
-                listB : split[1]
+            listA : split[0],
+            listB : split[1]
         }));
         return paired;
     },
@@ -506,8 +506,8 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
         var fwdName = fwd.name,
             revName = rev.name,
             lcs = this._naiveStartingAndEndingLCS(
-                fwdName.replace( this.filters[0], '' ),
-                revName.replace( this.filters[1], '' )
+                fwdName.replace( new RegExp( this.filters[0] ), '' ),
+                revName.replace( new RegExp( this.filters[1] ), '' )
             );
         if( removeExtensions ){
             var lastDotIndex = lcs.lastIndexOf( '.' );

client/galaxy/scripts/mvc/form/form-parameters.js

@@ -71,7 +71,7 @@ define(['utils/utils',
                 }
 
                 // log
-                console.debug('tools-form::_addRow() : Auto matched field type (' + input_def.type + ').');
+                Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').');
             }
 
             // set field value

client/galaxy/scripts/mvc/form/form-repeat.js

@@ -67,7 +67,7 @@ var View = Backbone.View.extend({
     add: function(options) {
         // repeat block already exists
         if (!options.id || this.list[options.id]) {
-            console.debug('form-repeat::add - Duplicate repeat block id.');
+            Galaxy.emit.debug('form-repeat::add()', 'Duplicate repeat block id.');
             return;
         }
 
@@ -123,7 +123,7 @@ var View = Backbone.View.extend({
     del: function(id) {
         // could not find element
         if (!this.list[id]) {
-            console.debug('form-repeat::del - Invalid repeat block id.');
+            Galaxy.emit.debug('form-repeat::del()', 'Invalid repeat block id.');
             return;
         }
 

client/galaxy/scripts/mvc/form/form-select-content.js

@@ -237,7 +237,7 @@ var View = Backbone.View.extend({
                         }
                     }
                 } catch (err) {
-                    console.debug('tools-select-content::value() - Skipped.');
+                    Galaxy.emit.debug('tools-select-content::value()', 'Skipped.');
                 }
             } else {
                 for (var i in this.list) {

client/galaxy/scripts/mvc/form/form-view.js

@@ -23,7 +23,7 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
             this.options = Utils.merge(options, this.optionsDefault);
 
             // log options
-            console.debug(this.options);
+            Galaxy.emit.debug('form-view::initialize()', 'Ready to build form.', this.options);
 
             // link galaxy modal or create one
             var galaxy = parent.Galaxy;
@@ -69,7 +69,7 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
                             }
                             field.update(new_options);
                             field.trigger('change');
-                            console.debug('Updating options for ' + input_id);
+                            Galaxy.emit.debug('form-view::update()', 'Updating options for ' + input_id);
                         }
                     }
                 }
@@ -231,7 +231,7 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
             }
 
             // log
-            console.debug('tools-form-base::initialize() - Completed.');
+            Galaxy.emit.debug('form-view::initialize()', 'Completed');
         }
     });
 });

client/galaxy/scripts/mvc/grid/grid-template.js

@@ -213,7 +213,7 @@ return {
                         } else {
                             label_class = 'use-outbound';
                         }
-                        tmpl += '<a class="label ' + label_class + '" href="' + link + '" onclick="return false;">' + value + '</a>';
+                        tmpl += '<a class="menubutton-label ' + label_class + '" href="' + link + '" onclick="return false;">' + value + '</a>';
                         if (options.operations.length != 0) {
                             tmpl += '</div>';
                         }

client/galaxy/scripts/mvc/library/library-folderrow-view.js

@@ -37,7 +37,7 @@ var FolderRowView = Backbone.View.extend({
       } else{
         template = this.templateRowFolder();
       }
-    } else if (folder_item.get('type') === 'file' || folder_item.get('model_class') === 'LibraryDataset'){
+    } else if (folder_item.get('type') === 'file' || folder_item.get('model_class') === 'LibraryDatasetDatasetAssociation'){
       this.options.type = 'file';
       if (folder_item.get('deleted')){
         template = this.templateRowDeletedFile();

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

@@ -33,7 +33,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
             this.$el.hide();
             this.deferred.execute(function(){
                 Backbone.View.prototype.remove.call(self);
-                console.debug('tools-form-base::remove() - Destroy view.');
+                Galaxy.emit.debug('tools-form-base::remove()', 'Destroy view.');
             });
         },
 
@@ -102,8 +102,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
                         message     : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + '.',
                         persistent  : false
                     });
-                    console.debug('tools-form::initialize() - Initial tool model ready.');
-                    console.debug(new_model);
+                    Galaxy.emit.debug('tools-form-base::initialize()', 'Initial tool model ready.', new_model);
                     process.resolve();
 
                 },
@@ -127,8 +126,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
                             }
                         });
                     }
-                    console.debug('tools-form::initialize() - Initial tool model request failed.');
-                    console.debug(response);
+                    Galaxy.emit.debug('tools-form::initialize()', 'Initial tool model request failed.', response);
                     process.reject();
                 }
             });
@@ -157,8 +155,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
             form.wait(true);
 
             // log tool state
-            console.debug('tools-form-base::_updateModel() - Sending current state (see below).');
-            console.debug(current_state);
+            Galaxy.emit.debug('tools-form-base::_updateModel()', 'Sending current state.', current_state);
 
             // post job
             Utils.request({
@@ -169,13 +166,11 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
                     self.form.update(new_model['tool_model'] || new_model);
                     self.options.update && self.options.update(new_model);
                     form.wait(false);
-                    console.debug('tools-form-base::_updateModel() - Received new model (see below).');
-                    console.debug(new_model);
+                    Galaxy.emit.debug('tools-form-base::_updateModel()', 'Received new model.', new_model);
                     process.resolve();
                 },
                 error   : function(response) {
-                    console.debug('tools-form-base::_updateModel() - Refresh request failed.');
-                    console.debug(response);
+                    Galaxy.emit.debug('tools-form-base::_updateModel()', 'Refresh request failed.', response);
                     process.reject();
                 }
             });

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

@@ -13,7 +13,7 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
             // link with node representation in workflow module
             this.node = options.node;
             if (!this.node) {
-                console.debug('FAILED - tools-form-workflow:initialize() - Node not found in workflow.');
+                Galaxy.emit.debug('tools-form-workflow::initialize()', 'Node not found in workflow.');
                 return;
             }
 

client/galaxy/scripts/mvc/tools/tools-jobs.js

@@ -19,13 +19,13 @@ return {
 
         // validate job definition
         if (!this._validation(form, job_def)) {
-            console.debug('tools-jobs::submit - Submission canceled. Validation failed.');
+            Galaxy.emit.debug('tools-jobs::submit()', 'Submission canceled. Validation failed.');
             callback && callback();
             return;
         }
 
         // debug
-        console.debug(job_def);
+        Galaxy.emit.debug('tools-jobs::submit()', 'Validation complete.', job_def);
 
         // post job
         Utils.request({
@@ -40,7 +40,7 @@ return {
             },
             error   : function(response) {
                 callback && callback();
-                console.debug(response);
+                Galaxy.emit.debug('tools-jobs::submit', 'Submission failed.', response);
                 if (response && response.err_data) {
                     var error_messages = form.data.matchResponse(response.err_data);
                     for (var input_id in error_messages) {
@@ -84,7 +84,7 @@ return {
 
             // check if objects where properly identified
             if (!input_id || !input_def || !input_field) {
-                console.debug('tools-jobs::_validation - Retrieving input objects failed.');
+                Galaxy.emit.debug('tools-jobs::_validation()', 'Retrieving input objects failed.');
                 continue;
             }
 

client/galaxy/scripts/mvc/ui/ui-select-default.js

@@ -29,8 +29,20 @@ var View = Backbone.View.extend({
 
         // link elements
         this.$select = this.$el.find('.select');
-        this.$icon = this.$el.find('.icon');
-        this.$button = this.$el.find('.button');
+        this.$icon_dropdown = this.$el.find('.icon-dropdown');
+
+        // allow regular multi-select field to be resized
+        var minHeight = null;
+        this.$('.icon-resize').on('mousedown', function(event) {
+            var currentY = event.pageY;
+            var currentHeight = self.$select.height();
+            minHeight = minHeight || currentHeight;
+            $('#dd-helper').show().on('mousemove', function(event) {
+                self.$select.height(Math.max(currentHeight + (event.pageY - currentY), minHeight));
+            }).on('mouseup mouseleave', function() {
+                $('#dd-helper').hide().off();
+            });
+        });
 
         // multiple select fields have an additional button and other custom properties
         if (this.options.multiple) {
@@ -47,11 +59,11 @@ var View = Backbone.View.extend({
                     }
                 });
                 this.$el.prepend(this.all_button.$el);
+            } else {
+                this.$el.addClass('ui-select-multiple');
             }
-            // customize style and content
-            this.$el.addClass('ui-select-multiple');
             this.$select.prop('multiple', true);
-            this.$button.remove();
+            this.$icon_dropdown.remove();
         }
 
         // update initial options
@@ -142,15 +154,15 @@ var View = Backbone.View.extend({
     /** Show a spinner indicating that the select options are currently loaded
     */
     wait: function() {
-        this.$icon.removeClass();
-        this.$icon.addClass('fa fa-spinner fa-spin');
+        this.$icon_dropdown.removeClass();
+        this.$icon_dropdown.addClass('icon-dropdown fa fa-spinner fa-spin');
     },
 
     /** Hide spinner indicating that the request has been completed
     */
     unwait: function() {
-        this.$icon.removeClass();
-        this.$icon.addClass('fa fa-caret-down');
+        this.$icon_dropdown.removeClass();
+        this.$icon_dropdown.addClass('icon-dropdown fa fa-caret-down');
     },
 
     /** Returns true if the field is disabled
@@ -205,7 +217,7 @@ var View = Backbone.View.extend({
         // update to searchable field (in this case select2)
         if (this.options.searchable) {
             this.$select.select2('destroy');
-            this.$select.select2();
+            this.$select.select2({ closeOnSelect: !this.options.multiple });
             this.$( '.select2-container .select2-search input' ).off( 'blur' );
         }
 
@@ -267,8 +279,9 @@ var View = Backbone.View.extend({
     _template: function(options) {
         return  '<div id="' + options.id + '" class="' + options.cls + '">' +
                     '<select id="' + options.id + '_select" class="select"/>' +
-                    '<div class="button">' +
-                        '<i class="icon"/>' +
+                    '<div class="icon-dropdown"/>' +
+                    '<div class="icon-resize">' +
+                         '<i class="fa fa-angle-double-right fa-rotate-45"/>' +
                     '</div>' +
                 '</div>';
     }

client/galaxy/scripts/mvc/upload/upload-button.js

@@ -76,11 +76,9 @@ var View = Backbone.View.extend({
     _template: function() {
         return  '<div class="upload-button">' +
                     '<div class="progress">' +
-                        '<div class="progress-bar"></div>' +
-                    '</div>' +
-                    '<div id="label" class="label">' +
+                        '<div class="progress-bar"/>' +
                         '<a class="panel-header-button" href="javascript:void(0)">' +
-                            '<span class="fa fa-upload"></span>' +
+                            '<span class="fa fa-upload"/>' +
                         '</a>' +
                     '</div>' +
                 '</div>';

client/galaxy/scripts/utils/deferred.js

@@ -23,13 +23,13 @@ return Backbone.Model.extend({
         var process = $.Deferred();
         process.promise().always(function() {
             delete self.active[ id ];
-            has_deferred && console.debug( 'Deferred::execute() - ' + this.state() + ' ' + id );
+            has_deferred && Galaxy.emit.debug( 'deferred::execute()', this.state().charAt(0).toUpperCase() + this.state().slice(1) + ' ' + id );
         });
 
         // deferred queue
         $.when( this.last ).always(function() {
             if ( self.active[ id ] ) {
-                has_deferred && console.debug( 'Deferred::execute() - running ' + id );
+                has_deferred && Galaxy.emit.debug( 'deferred::execute()', 'Running ' + id );
                 callback( process );
                 !has_deferred && process.resolve();
             } else {
@@ -42,7 +42,7 @@ return Backbone.Model.extend({
     /** Resets the promise queue. All currently queued but unexecuted callbacks/promises will be rejected.
     */
     reset: function() {
-        console.debug('Deferred::execute() - reset');
+        Galaxy.emit.debug('deferred::execute()', 'Reset');
         for ( var i in this.active ) {
             this.active[ i ] = false;
         }

client/galaxy/scripts/utils/uploadbox.js

@@ -97,8 +97,7 @@
         }, false);
 
         // send request
-        console.debug('uploadbox::uploadpost() - Posting following data:');
-        console.debug(cnf);
+        Galaxy.emit.debug('uploadbox::uploadpost()', 'Posting following data.', cnf);
         xhr.send(form);
     }
 

client/galaxy/style/less/base.less

@@ -211,7 +211,7 @@ body.has-message-box.has-inactivity-box {
     height: @panel_footer_height;
     line-height: @panel_footer_height;
     width: 100%;
-    z-index: 1000; // Above #DD-helper
+    z-index: 1000; // Above #dd-helper
     border-top: solid @layout-border-color 1px;
     background: @navbar-default-bg;
 
@@ -328,7 +328,7 @@ div.unified-panel-body-background {
 }
 
 // Used for dragging panels, popup menus, to deal with capturing clicks in iframes
-#DD-helper {
+#dd-helper {
     background: white;
     opacity: 0;
     z-index: 900; // Bootstrap elements start at 1000
@@ -1230,7 +1230,7 @@ a.action-button {
         text-decoration: none;
     }
 
-    .label, > label {
+    .menubutton-label, > label {
         position: relative;
         display: inline-block;
         border-right: none;
@@ -1243,7 +1243,7 @@ a.action-button {
         text-overflow: ellipsis;
     }
 
-    &.popup .label {
+    &.popup .menubutton-label {
         border-right: solid @btn-default-border 1px;
         padding-right: 6px;
     }

client/galaxy/style/less/ui.less

@@ -19,6 +19,14 @@
   transition: none !important;
 }
 
+.fa-rotate-45 {
+    -webkit-transform: rotate(45deg);
+    -moz-transform: rotate(45deg);
+    -ms-transform: rotate(45deg);
+    -o-transform: rotate(45deg);
+    transform: rotate(45deg);
+}
+
 // default margins
 @ui-margin-vertical: 5px;
 @ui-margin-horizontal: 5px;
@@ -566,10 +574,13 @@
 
 .ui-select {
     position: relative;
-    .button {
+    .icon-dropdown {
         position: absolute;
-        top: 5px;
-        right: 5px;
+        top: 8px;
+        right: 8px;
+    }
+    .icon-resize {
+        display: none;
     }
     select {
         position: relative;
@@ -601,8 +612,22 @@
 }
 
 .ui-select-multiple {
+    .icon-resize {
+        display: block;
+        position: absolute;
+        bottom: 0px;
+        right: 0px;
+        width: 20px;
+        height: 20px;
+        cursor: row-resize;
+        i {
+            position: absolute;
+            right: 3px;
+            bottom: 2px;
+        }
+    }
     select {
-        height: 80px !important;
+        height: 80px;
         .box-shadow(inset 0 1px 1px rgba(0,0,0,.075));
     }
 }

client/galaxy/style/less/upload.less

@@ -8,6 +8,7 @@
     border-radius: @border-radius-base;
     .progress {
         height: 21px;
+        margin: 0px;
     }
     .progress-bar-danger {
         background: @state-danger-bg;
@@ -25,13 +26,12 @@
         -o-transition: none;
         transition: none;
     }
-    .label {
+    .panel-header-button {
         position: absolute;
-        top: 2px;
-        width: inherit;
-        text-align: center;
-        line-height: 19px;
+        top: 4px;
+        right: 8px;
         font-size: 1.2em;
+        padding: 0px;
     }
 }
 

lib/galaxy/dependencies/__init__.py

@@ -3,6 +3,7 @@ Determine what optional dependencies are needed.
 """
 import pkg_resources
 
+from sys import version_info
 from os.path import dirname, join
 from xml.etree import ElementTree
 
@@ -25,8 +26,9 @@ class ConditionalDependencies( object ):
             "job_config_file",
             join( dirname( self.config_file ), 'job_conf.xml' ) )
         try:
-            for plugin in ElementTree.parse( job_conf_xml ).findall( './plugins/plugin[@load]' ):
-                self.job_runners.append( plugin.attrib['load'] )
+            for plugin in ElementTree.parse( job_conf_xml ).find( 'plugins' ).findall( 'plugin' ):
+                if 'load' in plugin.attrib:
+                    self.job_runners.append( plugin.attrib['load'] )
         except (OSError, IOError):
             pass
 
@@ -68,6 +70,16 @@ class ConditionalDependencies( object ):
         return ( asbool( self.config["debug"] ) and
                  asbool( self.config["use_interactive"] ) )
 
+    def check_pygments( self ):
+        # pygments is a dependency of weberror and only weberror
+        return self.check_weberror()
+
+    def check_importlib( self ):
+        return version_info < (2, 7)
+
+    def check_ordereddict( self ):
+        return version_info < (2, 7)
+
 
 def optional( config_file ):
     rval = []

lib/galaxy/dependencies/conditional-requirements.txt

@@ -1,6 +1,9 @@
 # These dependencies are only required when certain config options are set
 psycopg2==2.6.1
-WebError==0.11
+WebError==0.10.3
+Pygments==2.0.2
+importlib==1.0.3
+ordereddict==1.1
 python-openid
 MySQL-python
 fluent-logger

lib/galaxy/dependencies/requirements.txt

@@ -1,5 +1,4 @@
 # packages with C extensions
-Cheetah==2.4.4
 bx-python==0.7.3
 MarkupSafe==0.23
 PyYAML==3.11
@@ -26,14 +25,15 @@ pytz==2015.4
 Babel==2.0
 Beaker==1.7.0
 
+# Cheetah and dependencies
+Cheetah==2.4.4
+Markdown==2.6.3
+
 # BioBlend and dependencies
 bioblend==0.6.1
 boto==2.38.0
 requests==2.8.1
-
-# WebError and dependences
-WebError==0.11
-Pygments==2.0.2
+requests-toolbelt==0.4.0
 
 # kombu and dependencies
 kombu==3.0.26

lib/galaxy/jobs/__init__.py

@@ -37,9 +37,6 @@ from .datasets import DatasetPath
 
 log = logging.getLogger( __name__ )
 
-DATABASE_MAX_STRING_SIZE = util.DATABASE_MAX_STRING_SIZE
-DATABASE_MAX_STRING_SIZE_PRETTY = util.DATABASE_MAX_STRING_SIZE_PRETTY
-
 # This file, if created in the job's working directory, will be used for
 # setting advanced metadata properties on the job and its associated outputs.
 # This interface is currently experimental, is only used by the upload tool,
@@ -869,7 +866,7 @@ class JobWrapper( object ):
         self.dependency_shell_commands = self.tool.build_dependency_shell_commands()
         # We need command_line persisted to the db in order for Galaxy to re-queue the job
         # if the server was stopped and restarted before the job finished
-        job.command_line = self.command_line
+        job.command_line = unicodify(self.command_line)
         self.sa_session.add( job )
         self.sa_session.flush()
         # Return list of all extra files
@@ -990,18 +987,11 @@ class JobWrapper( object ):
                 self.sa_session.add( dataset )
                 self.sa_session.flush()
             job.set_final_state( job.states.ERROR )
-            job.command_line = self.command_line
+            job.command_line = unicodify(self.command_line)
             job.info = message
             # TODO: Put setting the stdout, stderr, and exit code in one place
             # (not duplicated with the finish method).
-            if ( len( stdout ) > DATABASE_MAX_STRING_SIZE ):
-                stdout = util.shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
-                log.info( "stdout for job %d is greater than %s, only a portion will be logged to database" % ( job.id, DATABASE_MAX_STRING_SIZE_PRETTY ) )
-            job.stdout = stdout
-            if ( len( stderr ) > DATABASE_MAX_STRING_SIZE ):
-                stderr = util.shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
-                log.info( "stderr for job %d is greater than %s, only a portion will be logged to database" % ( job.id, DATABASE_MAX_STRING_SIZE_PRETTY ) )
-            job.stderr = stderr
+            job.set_streams( stdout, stderr )
             # Let the exit code be Null if one is not provided:
             if ( exit_code is not None ):
                 job.exit_code = exit_code
@@ -1093,8 +1083,6 @@ class JobWrapper( object ):
         the contents of the output files.
         """
         finish_timer = util.ExecutionTimer()
-        stdout = unicodify( stdout )
-        stderr = unicodify( stderr )
 
         # default post job setup
         self.sa_session.expunge_all()
@@ -1272,13 +1260,10 @@ class JobWrapper( object ):
         # Flush all the dataset and job changes above.  Dataset state changes
         # will now be seen by the user.
         self.sa_session.flush()
-        # Save stdout and stderr
-        if len( job.stdout ) > DATABASE_MAX_STRING_SIZE:
-            log.info( "stdout for job %d is greater than %s, only a portion will be logged to database" % ( job.id, DATABASE_MAX_STRING_SIZE_PRETTY ) )
-        job.stdout = util.shrink_string_by_size( job.stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
-        if len( job.stderr ) > DATABASE_MAX_STRING_SIZE:
-            log.info( "stderr for job %d is greater than %s, only a portion will be logged to database" % ( job.id, DATABASE_MAX_STRING_SIZE_PRETTY ) )
-        job.stderr = util.shrink_string_by_size( job.stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
+
+        # Shrink streams and ensure unicode.
+        job.set_streams( job.stdout, job.stderr )
+
         # The exit code will be null if there is no exit code to be set.
         # This is so that we don't assign an exit code, such as 0, that
         # is either incorrect or has the wrong semantics.
@@ -1324,7 +1309,7 @@ class JobWrapper( object ):
         self.tool.call_hook( 'exec_after_process', self.queue.app, inp_data=inp_data,
                              out_data=out_data, param_dict=param_dict,
                              tool=self.tool, stdout=job.stdout, stderr=job.stderr )
-        job.command_line = self.command_line
+        job.command_line = unicodify(self.command_line)
 
         collected_bytes = 0
         # Once datasets are collected, set the total dataset size (includes extra files)
@@ -1810,8 +1795,6 @@ class TaskWrapper(JobWrapper):
         the output datasets based on stderr and stdout from the command, and
         the contents of the output files.
         """
-        stdout = unicodify( stdout )
-        stderr = unicodify( stderr )
 
         # This may have ended too soon
         log.debug( 'task %s for job %d ended; exit code: %d'
@@ -1839,13 +1822,8 @@ class TaskWrapper(JobWrapper):
             task.state = task.states.ERROR
 
         # Save stdout and stderr
-        if len( stdout ) > DATABASE_MAX_STRING_SIZE:
-            log.error( "stdout for task %d is greater than %s, only a portion will be logged to database" % ( task.id, DATABASE_MAX_STRING_SIZE_PRETTY ) )
-        task.stdout = util.shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
-        if len( stderr ) > DATABASE_MAX_STRING_SIZE:
-            log.error( "stderr for task %d is greater than %s, only a portion will be logged to database" % ( task.id, DATABASE_MAX_STRING_SIZE_PRETTY ) )
+        task.set_streams( stdout, stderr )
         self._collect_metrics( task )
-        task.stderr = util.shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
         task.exit_code = tool_exit_code
         task.command_line = self.command_line
         self.sa_session.flush()

lib/galaxy/jobs/command_factory.py

@@ -3,6 +3,8 @@ from os import chmod
 from os.path import join
 from os.path import abspath
 
+from galaxy import util
+
 from logging import getLogger
 log = getLogger( __name__ )
 
@@ -158,7 +160,8 @@ class CommandsBuilder(object):
     def __init__(self, initial_command):
         # Remove trailing semi-colon so we can start hacking up this command.
         # TODO: Refactor to compose a list and join with ';', would be more clean.
-        commands = initial_command.rstrip("; ")
+        initial_command = util.unicodify(initial_command)
+        commands = initial_command.rstrip(u"; ")
         self.commands = commands
 
         # Coping work dir outputs or setting metadata will mask return code of
@@ -167,17 +170,19 @@ class CommandsBuilder(object):
         self.return_code_captured = False
 
     def prepend_command(self, command):
-        self.commands = "%s; %s" % (command, self.commands)
+        self.commands = u"%s; %s" % (command,
+                                     self.commands)
         return self
 
     def prepend_commands(self, commands):
-        return self.prepend_command("; ".join(commands))
+        return self.prepend_command(u"; ".join(commands))
 
     def append_command(self, command):
-        self.commands = "%s; %s" % (self.commands, command)
+        self.commands = u"%s; %s" % (self.commands,
+                                     command)
 
     def append_commands(self, commands):
-        self.append_command("; ".join(commands))
+        self.append_command(u"; ".join(commands))
 
     def capture_return_code(self):
         if not self.return_code_captured:

lib/galaxy/jobs/output_checker.py

@@ -133,9 +133,8 @@ def check_output( tool, stdout, stderr, tool_exit_code, job ):
         success = True
 
     # Store the modified stdout and stderr in the job:
-    if None is not job:
-        job.stdout = stdout
-        job.stderr = stderr
+    if job is not None:
+        job.set_streams( stdout, stderr )
 
     return success
 

lib/galaxy/jobs/runners/__init__.py

@@ -305,6 +305,8 @@ class BaseJobRunner( object ):
 
     def write_executable_script( self, path, contents, mode=0o755 ):
         with open( path, 'w' ) as f:
+            if isinstance(contents, unicode):
+                contents = contents.encode("UTF-8")
             f.write( contents )
         os.chmod( path, mode )
         self._handle_script_integrity( path )

lib/galaxy/jobs/runners/util/job_script/__init__.py

@@ -1,5 +1,6 @@
 from string import Template
 from pkg_resources import resource_string
+from galaxy.util import unicodify
 
 DEFAULT_JOB_FILE_TEMPLATE = Template(
     resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh').decode('UTF-8')
@@ -61,6 +62,8 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
     template_params.update(**kwds)
     env_setup_commands_str = "\n".join(template_params["env_setup_commands"])
     template_params["env_setup_commands"] = env_setup_commands_str
+    for key, value in template_params.items():
+        template_params[key] = unicodify(value)
     if not isinstance(template, Template):
         template = Template(template)
     return template.safe_substitute(template_params)

lib/galaxy/managers/users.py

@@ -64,6 +64,11 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
             self.app.security_agent.user_set_default_permissions( user, default_access_private=permissions )
         return user
 
+    def delete(self, user):
+        user.deleted = True
+        self.session().add(user)
+        self.session().flush()
+
     def _error_on_duplicate_email( self, email ):
         """
         Check for a duplicate email and raise if found.
@@ -249,13 +254,12 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
         self.add_view( 'detailed', [
             # 'update_time',
             # 'create_time',
-
+            'is_admin',
             'total_disk_usage',
             'nice_total_disk_usage',
             'quota_percent',
-
-            # 'deleted',
-            # 'purged',
+            'deleted',
+            'purged',
             # 'active',
 
             # 'preferences',

lib/galaxy/model/__init__.py

@@ -99,7 +99,7 @@ class HasName:
         return name
 
 
-class HasJobMetrics:
+class JobLike:
 
     def _init_metrics( self ):
         self.text_metrics = []
@@ -130,6 +130,18 @@ class HasJobMetrics:
         # TODO: Make iterable, concatenate with chain
         return self.text_metrics + self.numeric_metrics
 
+    def set_streams( self, stdout, stderr ):
+        stdout = galaxy.util.unicodify( stdout )
+        stderr = galaxy.util.unicodify( stderr )
+        if ( len( stdout ) > galaxy.util.DATABASE_MAX_STRING_SIZE ):
+            stdout = galaxy.util.shrink_string_by_size( stdout, galaxy.util.DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
+            log.info( "stdout for %s %d is greater than %s, only a portion will be logged to database", type(self), self.id, galaxy.util.DATABASE_MAX_STRING_SIZE_PRETTY )
+        self.stdout = stdout
+        if ( len( stderr ) > galaxy.util.DATABASE_MAX_STRING_SIZE ):
+            stderr = galaxy.util.shrink_string_by_size( stderr, galaxy.util.DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
+            log.info( "stderr for %s %d is greater than %s, only a portion will be logged to database", type(self), self.id, galaxy.util.DATABASE_MAX_STRING_SIZE_PRETTY )
+        self.stderr = stderr
+
 
 class User( object, Dictifiable ):
     use_pbkdf2 = True
@@ -307,7 +319,7 @@ class TaskMetricNumeric( BaseJobMetric ):
     pass
 
 
-class Job( object, HasJobMetrics, Dictifiable ):
+class Job( object, JobLike, Dictifiable ):
     dict_collection_visible_keys = [ 'id', 'state', 'exit_code', 'update_time', 'create_time' ]
     dict_element_visible_keys = [ 'id', 'state', 'exit_code', 'update_time', 'create_time'  ]
 
@@ -356,6 +368,7 @@ class Job( object, HasJobMetrics, Dictifiable ):
         self.destination_id = None
         self.destination_params = None
         self.post_job_actions = []
+        self.state_history = []
         self.imported = False
         self.handler = None
         self.exit_code = None
@@ -657,7 +670,7 @@ class Job( object, HasJobMetrics, Dictifiable ):
             self.workflow_invocation_step.update()
 
 
-class Task( object, HasJobMetrics ):
+class Task( object, JobLike ):
     """
     A task represents a single component of a job.
     """

lib/galaxy/tools/parameters/basic.py

@@ -273,9 +273,10 @@ class TextToolParameter( ToolParameter ):
     def to_string( self, value, app ):
         """Convert a value to a string representation suitable for persisting"""
         if value is None:
-            return ''
+            rval = ''
         else:
-            return str( value )
+            rval = util.smart_str( value )
+        return rval
 
     def to_html_value( self, value, app ):
         if value is None:

lib/galaxy/web/framework/webapp.py

@@ -390,9 +390,10 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
                     # No user, associate
                     galaxy_session.user = self.get_or_create_remote_user( remote_user_email )
                     galaxy_session_requires_flush = True
-                elif ((galaxy_session.user.email != remote_user_email) and
+                elif (not remote_user_email.startswith('(null)') and  # Apache does this, see remoteuser.py
+                      (galaxy_session.user.email != remote_user_email) and
                       ((not self.app.config.allow_user_impersonation) or
-                      (remote_user_email not in self.app.config.admin_users_list))):
+                       (remote_user_email not in self.app.config.admin_users_list))):
                     # Session exists but is not associated with the correct
                     # remote user, and the currently set remote_user is not a
                     # potentially impersonating admin.

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -348,7 +348,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
         :type   history_id: str
         :param  history_id: encoded id string of the HDA's History
         :type   id:         str
-        :param  id:         the encoded id of the history to undelete
+        :param  id:         the encoded id of the history to update
         :type   payload:    dict
         :param  payload:    a dictionary containing any or all the
             fields in :func:`galaxy.model.HistoryDatasetAssociation.to_dict`

lib/galaxy/webapps/galaxy/api/users.py

@@ -6,9 +6,8 @@ import logging
 
 from sqlalchemy import false, true
 
-from galaxy import exceptions
-from galaxy import util
-from galaxy import web
+from galaxy import exceptions, util, web
+from galaxy.managers import users
 from galaxy.security.validate_user_input import validate_email
 from galaxy.security.validate_user_input import validate_password
 from galaxy.security.validate_user_input import validate_publicname
@@ -24,6 +23,11 @@ log = logging.getLogger( __name__ )
 
 class UserAPIController( BaseAPIController, UsesTagsMixin, CreatesUsersMixin, CreatesApiKeysMixin ):
 
+    def __init__(self, app):
+        super(UserAPIController, self).__init__(app)
+        self.user_manager = users.UserManager(app)
+        self.user_serializer = users.UserSerializer( app )
+
     @expose_api
     def index( self, trans, deleted='False', f_email=None, **kwd ):
         """
@@ -89,16 +93,7 @@ class UserAPIController( BaseAPIController, UsesTagsMixin, CreatesUsersMixin, Cr
                 assert not user.deleted
         except:
             raise exceptions.RequestParameterInvalidException( 'Invalid user id specified', id=id )
-
-        item = user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id,
-                                                            'total_disk_usage': float } )
-        # add a list of tags used by the user (as strings)
-        item[ 'tags_used' ] = self.get_user_tags_used( trans, user=user )
-        # TODO: move into api_values (needs trans, tho - can we do that with api_keys/@property??)
-        # TODO: works with other users (from admin)??
-        item[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans )
-        item[ 'is_admin' ] = trans.user_is_admin()
-        return item
+        return self.user_serializer.serialize_to_view(user, view='detailed')
 
     @expose_api
     def create( self, trans, payload, **kwd ):
@@ -143,10 +138,29 @@ class UserAPIController( BaseAPIController, UsesTagsMixin, CreatesUsersMixin, Cr
         raise exceptions.NotImplemented()
 
     @expose_api
-    def delete( self, trans, **kwd ):
-        raise exceptions.NotImplemented()
+    @web.require_admin
+    def delete( self, trans, id, **kwd ):
+        """
+        DELETE /api/users/{id}
+        delete the user with the given ``id``
+
+        :param id: the encoded id of the user to delete
+        :type  id: str
+
+        :param purge: (optional) if True, purge the user
+        :type  purge: bool
+        """
+        if not trans.app.config.allow_user_deletion:
+            raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow admins to delete users.' )
+        purge = util.string_as_bool(kwd.get('purge', False))
+        if purge:
+            raise exceptions.NotImplemented('Purge option has not been implemented yet')
+        user = self.get_user(trans, id)
+        self.user_manager.delete(user)
+        return self.user_serializer.serialize_to_view(user, view='detailed')
 
     @expose_api
+    @web.require_admin
     def undelete( self, trans, **kwd ):
         raise exceptions.NotImplemented()
 

lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py

@@ -998,7 +998,7 @@ class SetEnvironment( RecipeStep ):
         cmds = install_environment.environment_commands( 'set_environment' )
         env_var_dicts = action_dict.get( 'environment_variable', [] )
         root_dir_dict = dict( action='set_to',
-                              name='%s_ROOT_DIR' % tool_dependency.name.replace( '-', '_' ).upper(),
+                              name='%s_ROOT_DIR' % re.sub( r"[^A-Z0-9_]", "_", tool_dependency.name.upper() ),
                               value=install_environment.install_dir )
         env_var_dicts.append( root_dir_dict )
         for env_var_dict in env_var_dicts:

run.sh

@@ -69,6 +69,13 @@ fi
 
 python ./scripts/check_python.py || exit 1
 
+if [ ! -z "$GALAXY_RUN_WITH_TEST_TOOLS" ];
+then
+    export GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE="test/functional/tools/samples_tool_conf.xml"
+    export GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES="true"
+    export GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_TOOL_FORMATS="true"
+fi
+
 if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then
     python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"
 fi

scripts/check_eggs.py

@@ -0,0 +1 @@
+fetch_eggs.py

scripts/fetch_eggs.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+from os import pardir
+from os.path import join, abspath, dirname
+from sys import exit
+
+msg = """
+Eggs in this release of Galaxy have been replaced by Python's newer packaging
+format, wheels. Please use scripts/common_startup.sh to set up your
+environment:
+
+cd {dir} && ./scripts/common_startup.sh
+
+This will create a Python virtualenv and install Galaxy's dependencies into it.
+
+If you start Galaxy using means other than run.sh (as you probably do if you
+are seeing this message), be sure to activate the virtualenv before starting,
+using:
+
+. {venv}/bin/activate
+
+If you already run Galaxy in its own virtualenv, you can reuse your existing
+virtualenv with:
+
+cd {dir} && ./scripts/common_startup.sh --skip-venv
+"""
+
+galaxy = abspath(join(dirname(__file__), pardir))
+venv = join(galaxy, '.venv')
+print msg.format(dir=abspath(join(dirname(__file__), pardir)),
+                 venv=venv)
+exit(1)

static/maps/galaxy-app-base.js.map

@@ -1 +1 @@
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static/maps/mvc/form/form-parameters.js.map

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static/maps/mvc/form/form-select-content.js.map

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static/maps/mvc/form/form-view.js.map

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static/maps/mvc/tools/tools-jobs.js.map

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static/maps/mvc/ui/ui-select-default.js.map

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static/maps/mvc/upload/upload-button.js.map

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static/maps/utils/deferred.js.map

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static/maps/utils/uploadbox.js.map

@@ -1 +1 @@
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static/scripts/galaxy-app-base.js

@@ -1,2 +1,2 @@
-define(["libs/underscore","libs/backbone","mvc/base-mvc","mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(a,b,c,d,e,f,g){function h(a,b){var c=this;return c._init(a||{},b||{})}f(h,"GalaxyApp");var i="galaxy:debug",j=i+":namespaces",k=!1;try{k="true"==localStorage.getItem(i)}catch(l){console.log(g("localStorage not available for debug flag retrieval"))}return h.prototype._init=function(c,d){var e=this;return a.extend(e,b.Events),k&&(e.logger=console,console.debug("debugging galaxy:","options:",c,"bootstrapped:",d)),e._processOptions(c),e.root=c.root||"/",e._initConfig(c.config||d.config||{}),e._patchGalaxy(window.Galaxy),e._initLogger(e.options.loggerOptions||{}),e.debug("GalaxyApp.options: ",e.options),e.debug("GalaxyApp.config: ",e.config),e.debug("GalaxyApp.logger: ",e.logger),e._initLocale(),e.debug("GalaxyApp.localize: ",e.localize),e.config=c.config||{},e.debug("GalaxyApp.config: ",e.config),e._initUser(c.user||{}),e.debug("GalaxyApp.user: ",e.user),e._setUpListeners(),e.trigger("ready",e),e},h.prototype.defaultOptions={patchExisting:!0,root:"/"},h.prototype._processOptions=function(a){var b=this,c=b.defaultOptions;b.options={};for(var d in c)c.hasOwnProperty(d)&&(b.options[d]=a.hasOwnProperty(d)?a[d]:c[d]);return b},h.prototype._initConfig=function(a){var b=this;return b.config=a,b.config.debug=k||b.config.debug,b},h.prototype._patchGalaxy=function(a){var b=this;if(b.options.patchExisting&&a)for(var c in a)a.hasOwnProperty(c)&&(b[c]=a[c])},h.prototype._initLogger=function(a){var b=this;if(b.config.debug){a.consoleLogger=a.consoleLogger||console,a.consoleLevel=a.consoleLevel||e.MetricsLogger.ALL;try{a.consoleNamespaceWhitelist=localStorage.getItem(j).split(",")}catch(d){}}return b.logger=new e.MetricsLogger(a),b.config.debug&&(c.LoggableMixin.logger=b.logger),b},h.prototype._initLocale=function(a){var b=this;return b.debug("_initLocale:",a),b.localize=g,window._l=b.localize,b},h.prototype._initUser=function(a){var b=this;return b.debug("_initUser:",a),b.user=new d.User(a),b.user.logger=b.logger,b.currUser=b.user,b},h.prototype._setUpListeners=function(){var a=this;return a.lastAjax={},$(document).bind("ajaxSend",function(b,c,d){var e=d.data;try{e=JSON.parse(e)}catch(f){}a.lastAjax={url:location.href.slice(0,-1)+d.url,data:e}}),a},h.prototype.debugging=function(a){var b=this;try{if(void 0===a)return"true"===localStorage.getItem(i);if(a)return localStorage.setItem(i,!0),!0;localStorage.removeItem(i),b.debuggingNamespaces(null)}catch(c){console.log(g("localStorage not available for debug flag retrieval"))}return!1},h.prototype.debuggingNamespaces=function(a){var b=this;try{if(void 0===a){var c=localStorage.getItem(j);return"string"==typeof c?c.split(","):[]}null===a?localStorage.removeItem(j):localStorage.setItem(j,a);var d=b.debuggingNamespaces();return b.logger&&(b.logger.options.consoleNamespaceWhitelist=d),d}catch(e){console.log(g("localStorage not available for debug namespace retrieval"))}},h.prototype.toString=function(){var a=this.user?this.user.get("email")||"(anonymous)":"uninitialized";return"GalaxyApp("+a+")"},{GalaxyApp:h}});
+define(["libs/underscore","libs/backbone","mvc/base-mvc","mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(a,b,c,d,e,f,g){function h(a,b){var c=this;return c._init(a||{},b||{})}f(h,"GalaxyApp");var i="galaxy:debug",j=i+":namespaces",k=!1;try{k="true"==localStorage.getItem(i)}catch(l){console.log(g("localStorage not available for debug flag retrieval"))}return h.prototype._init=function(c,d){var e=this;return a.extend(e,b.Events),k&&(e.logger=console,console.debug("debugging galaxy:","options:",c,"bootstrapped:",d)),e._processOptions(c),e.root=c.root||"/",e._initConfig(c.config||d.config||{}),e._patchGalaxy(window.Galaxy),e._initLogger(e.options.loggerOptions||{}),e.debug("GalaxyApp.options: ",e.options),e.debug("GalaxyApp.config: ",e.config),e.debug("GalaxyApp.logger: ",e.logger),e._initLocale(),e.debug("GalaxyApp.localize: ",e.localize),e.config=c.config||{},e.debug("GalaxyApp.config: ",e.config),e._initUser(c.user||{}),e.debug("GalaxyApp.user: ",e.user),e._setUpListeners(),e.trigger("ready",e),e},h.prototype.defaultOptions={patchExisting:!0,root:"/"},h.prototype._processOptions=function(a){var b=this,c=b.defaultOptions;b.options={};for(var d in c)c.hasOwnProperty(d)&&(b.options[d]=a.hasOwnProperty(d)?a[d]:c[d]);return b},h.prototype._initConfig=function(a){var b=this;return b.config=a,b.config.debug=k||b.config.debug,b},h.prototype._patchGalaxy=function(a){var b=this;if(b.options.patchExisting&&a)for(var c in a)a.hasOwnProperty(c)&&(b[c]=a[c])},h.prototype._initLogger=function(a){var b=this;if(b.config.debug){a.consoleLogger=a.consoleLogger||console,a.consoleLevel=a.consoleLevel||e.MetricsLogger.ALL;try{a.consoleNamespaceWhitelist=localStorage.getItem(j).split(",")}catch(d){}}return b.logger=new e.MetricsLogger(a),b.emit={},["log","debug","info","warn","error","metric"].map(function(a){b.emit[a]=function(){b.logger.emit(a,arguments[0],Array.prototype.slice.call(arguments,1))}}),b.config.debug&&(c.LoggableMixin.logger=b.logger),b},h.prototype._initLocale=function(a){var b=this;return b.debug("_initLocale:",a),b.localize=g,window._l=b.localize,b},h.prototype._initUser=function(a){var b=this;return b.debug("_initUser:",a),b.user=new d.User(a),b.user.logger=b.logger,b.currUser=b.user,b},h.prototype._setUpListeners=function(){var a=this;return a.lastAjax={},$(document).bind("ajaxSend",function(b,c,d){var e=d.data;try{e=JSON.parse(e)}catch(f){}a.lastAjax={url:location.href.slice(0,-1)+d.url,data:e}}),a},h.prototype.debugging=function(a){var b=this;try{if(void 0===a)return"true"===localStorage.getItem(i);if(a)return localStorage.setItem(i,!0),!0;localStorage.removeItem(i),b.debuggingNamespaces(null)}catch(c){console.log(g("localStorage not available for debug flag retrieval"))}return!1},h.prototype.debuggingNamespaces=function(a){var b=this;try{if(void 0===a){var c=localStorage.getItem(j);return"string"==typeof c?c.split(","):[]}null===a?localStorage.removeItem(j):localStorage.setItem(j,a);var d=b.debuggingNamespaces();return b.logger&&(b.logger.options.consoleNamespaceWhitelist=d),d}catch(e){console.log(g("localStorage not available for debug namespace retrieval"))}},h.prototype.toString=function(){var a=this.user?this.user.get("email")||"(anonymous)":"uninitialized";return"GalaxyApp("+a+")"},{GalaxyApp:h}});
 //# sourceMappingURL=../maps/galaxy-app-base.js.map

static/scripts/mvc/form/form-parameters.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-select-ftp","mvc/ui/ui-color-picker"],function(a,b,c,d,e,f){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a),console.debug("tools-form::_addRow() : Auto matched field type ("+a.type+").")),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(this.app.options.is_workflow)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value="";var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new f({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})},_fieldFtp:function(a){var b=this;return new e.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
+define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-select-ftp","mvc/ui/ui-color-picker"],function(a,b,c,d,e,f){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+a.type+").")),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(this.app.options.is_workflow)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value="";var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new f({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})},_fieldFtp:function(a){var b=this;return new e.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-parameters.js.map

static/scripts/mvc/form/form-repeat.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(a,b,c,d){var e=Backbone.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(c){this.options=a.merge(c,this.optionsDefault),this.setElement("<div/>");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("<div/>").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(!a.id||this.list[a.id])return void console.debug("form-repeat::add - Duplicate repeat block id.");this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(a){if(!this.list[a])return void console.debug("form-repeat::del - Invalid repeat block id.");this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}});
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(a,b,c,d){var e=Backbone.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(c){this.options=a.merge(c,this.optionsDefault),this.setElement("<div/>");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("<div/>").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(!a.id||this.list[a.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate repeat block id.");this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(a){if(!this.list[a])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}});
 //# sourceMappingURL=../../../maps/mvc/form/form-repeat.js.map

static/scripts/mvc/form/form-select-content.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d,this.history={};var e=this;this.setElement('<div class="ui-select-content"/>'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var d=[];for(var e in b){var f=b[e];d.push({label:f.hid+": "+f.name,value:f.id}),c.history[f.id+"_"+f.src]=f}a.update(d)}}var c=this;b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){console.debug("tools-select-content::value() - Skipped.")}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=this.history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=this.history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}});return{View:c}});
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d,this.history={};var e=this;this.setElement('<div class="ui-select-content"/>'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var d=[];for(var e in b){var f=b[e];d.push({label:f.hid+": "+f.name,value:f.id}),c.history[f.id+"_"+f.src]=f}a.update(d)}}var c=this;b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){Galaxy.emit.debug("tools-select-content::value()","Skipped.")}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=this.history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=this.history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/form/form-select-content.js.map

static/scripts/mvc/form/form-view.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),!c))if(self==top){var e=this.$el.parents().filter(function(){return"auto"==$(this).css("overflow")}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-50},500)}else $("html, body").animate({scrollTop:d.$el.offset().top-20},500)},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),$(".tooltip").remove(),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),console.debug("tools-form-base::initialize() - Completed.")}})});
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),Galaxy.emit.debug("form-view::initialize()","Ready to build form.",this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),!c))if(self==top){var e=this.$el.parents().filter(function(){return"auto"==$(this).css("overflow")}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-50},500)}else $("html, body").animate({scrollTop:d.$el.offset().top-20},500)},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),$(".tooltip").remove(),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map

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

@@ -1,2 +1,2 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){if(this.options=a.merge(c,{}),this.setElement("<div/>"),this.deferred=new b,c.inputs)this._buildForm(c);else{var d=this;this.deferred.execute(function(a){d._buildModel(a,c,!0)})}},remove:function(){var a=this;this.$el.hide(),this.deferred.execute(function(){Backbone.View.prototype.remove.call(a),console.debug("tools-form-base::remove() - Destroy view.")})},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(a){c._updateModel(a)})}},this.options),this.options.customize&&this.options.customize(this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,d,e){var f=this;this.options.id=d.id,this.options.version=d.version;var g="",h={};d.job_id?g=Galaxy.root+"api/jobs/"+d.job_id+"/build_for_rerun":(g=Galaxy.root+"api/tools/"+d.id+"/build",Galaxy.params&&Galaxy.params.tool_id==d.id&&(h=$.extend({},Galaxy.params),d.version&&(h.tool_version=d.version))),a.request({type:"GET",url:g,data:h,success:function(a){f._buildForm(a.tool_model||a),!e&&f.form.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:!1}),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a),b.resolve()},error:function(a){var d=a&&a.err_msg||"Uncaught error.";f.$el.is(":empty")?f.$el.prepend(new c.Message({message:d,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:d,buttons:{Close:function(){Galaxy.modal.hide()}}}),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a),b.reject()}})},_updateModel:function(b){var c=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",d=this,e=this.form,f={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},d.form.data.create())};e.wait(!0),console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(f),a.request({type:"POST",url:c,data:f,success:function(a){d.form.update(a.tool_model||a),d.options.update&&d.options.update(a),e.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),b.resolve()},error:function(a){console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a),b.reject()}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(b){a._buildModel(b,{id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
+define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){if(this.options=a.merge(c,{}),this.setElement("<div/>"),this.deferred=new b,c.inputs)this._buildForm(c);else{var d=this;this.deferred.execute(function(a){d._buildModel(a,c,!0)})}},remove:function(){var a=this;this.$el.hide(),this.deferred.execute(function(){Backbone.View.prototype.remove.call(a),Galaxy.emit.debug("tools-form-base::remove()","Destroy view.")})},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(a){c._updateModel(a)})}},this.options),this.options.customize&&this.options.customize(this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,d,e){var f=this;this.options.id=d.id,this.options.version=d.version;var g="",h={};d.job_id?g=Galaxy.root+"api/jobs/"+d.job_id+"/build_for_rerun":(g=Galaxy.root+"api/tools/"+d.id+"/build",Galaxy.params&&Galaxy.params.tool_id==d.id&&(h=$.extend({},Galaxy.params),d.version&&(h.tool_version=d.version))),a.request({type:"GET",url:g,data:h,success:function(a){f._buildForm(a.tool_model||a),!e&&f.form.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:!1}),Galaxy.emit.debug("tools-form-base::initialize()","Initial tool model ready.",a),b.resolve()},error:function(a){var d=a&&a.err_msg||"Uncaught error.";f.$el.is(":empty")?f.$el.prepend(new c.Message({message:d,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:d,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tools-form::initialize()","Initial tool model request failed.",a),b.reject()}})},_updateModel:function(b){var c=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",d=this,e=this.form,f={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},d.form.data.create())};e.wait(!0),Galaxy.emit.debug("tools-form-base::_updateModel()","Sending current state.",f),a.request({type:"POST",url:c,data:f,success:function(a){d.form.update(a.tool_model||a),d.options.update&&d.options.update(a),e.wait(!1),Galaxy.emit.debug("tools-form-base::_updateModel()","Received new model.",a),b.resolve()},error:function(a){Galaxy.emit.debug("tools-form-base::_updateModel()","Refresh request failed.",a),b.reject()}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(b){a._buildModel(b,{id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map

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

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;return this.node=c.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!1)}),this._makeSections(c),void b.prototype.initialize.call(this,c)):void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.")},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var f=b.inputs[e];if(f.action){if(f.name="pja__"+a+"__"+f.action,f.pja_arg&&(f.name+="__"+f.pja_arg),f.payload)for(var h in f.payload){var i=f.payload[h];f.payload[f.name+"__"+h]=i,delete i}var j=g.post_job_actions[f.action+a];if(j){for(var k in d)d[k].expanded=!0;f.value=f.pja_arg?j.action_arguments&&j.action_arguments[f.pja_arg]||f.value:"true"}}f.inputs&&c(f,d.slice(0))}}var d=[],e=[];for(key in b)d.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)e.push(this.node.input_terminals[key].name);d.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),d.unshift({0:"Sequences",1:"Sequences"}),d.unshift({0:"Roadmaps",1:"Roadmaps"}),d.unshift({0:"Leave unchanged",1:"__empty__"});var f={title:"Add Actions: '"+a+"'",type:"section",flat:!0,inputs:[{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>'+e.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},g=this;return c(f),f}});return{View:c}});
+define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;return this.node=c.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!1)}),this._makeSections(c),void b.prototype.initialize.call(this,c)):void Galaxy.emit.debug("tools-form-workflow::initialize()","Node not found in workflow.")},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var f=b.inputs[e];if(f.action){if(f.name="pja__"+a+"__"+f.action,f.pja_arg&&(f.name+="__"+f.pja_arg),f.payload)for(var h in f.payload){var i=f.payload[h];f.payload[f.name+"__"+h]=i,delete i}var j=g.post_job_actions[f.action+a];if(j){for(var k in d)d[k].expanded=!0;f.value=f.pja_arg?j.action_arguments&&j.action_arguments[f.pja_arg]||f.value:"true"}}f.inputs&&c(f,d.slice(0))}}var d=[],e=[];for(key in b)d.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)e.push(this.node.input_terminals[key].name);d.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),d.unshift({0:"Sequences",1:"Sequences"}),d.unshift({0:"Roadmaps",1:"Roadmaps"}),d.unshift({0:"Leave unchanged",1:"__empty__"});var f={title:"Add Actions: '"+a+"'",type:"section",flat:!0,inputs:[{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>'+e.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},g=this;return c(f),f}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map

static/scripts/mvc/tools/tools-jobs.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(console.debug(g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.$el.replaceWith(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),console.debug(a),a&&a.err_data){var d=c.data.matchResponse(a.err_data);for(var f in d){c.highlight(f,d[f]);break}}else c.modal.show({title:"Job submission failed",body:a&&a.err_msg||b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(console.debug("tools-jobs::submit - Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+k+"</b> selection(s) while a previous field contains <b>"+d+"</b>."),!1}}else console.debug("tools-jobs::_validation - Retrieving input objects failed.")}return!0},_refreshHdas:function(a,b){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(a,b)}}});
+define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(Galaxy.emit.debug("tools-jobs::submit()","Validation complete.",g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.$el.replaceWith(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),Galaxy.emit.debug("tools-jobs::submit","Submission failed.",a),a&&a.err_data){var d=c.data.matchResponse(a.err_data);for(var f in d){c.highlight(f,d[f]);break}}else c.modal.show({title:"Job submission failed",body:a&&a.err_msg||b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(Galaxy.emit.debug("tools-jobs::submit()","Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+k+"</b> selection(s) while a previous field contains <b>"+d+"</b>."),!1}}else Galaxy.emit.debug("tools-jobs::_validation()","Retrieving input objects failed.")}return!0},_refreshHdas:function(a,b){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(a,b)}}});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-jobs.js.map

static/scripts/mvc/ui/ui-select-default.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-buttons"],function(a,b){var c=Backbone.View.extend({optionsDefault:{id:a.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(c){var d=this;this.options=a.merge(c,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.options.searchable&&(this.all_button=new b.ButtonCheck({onclick:function(){var a=[];0!==d.all_button.value()&&(a=d._availableOptions()),d.value(a),d.trigger("change")}}),this.$el.prepend(this.all_button.$el)),this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){d.trigger("change")}),this.on("change",function(){d.options.onchange&&d.options.onchange(this.value())})},value:function(a){void 0!==a&&(null===a&&(a="__null__"),(this.exists(a)||this.options.multiple)&&(this.$select.val(a),this.$select.select2&&this.$select.select2("val",a)));var b=this._getValue();return this.all_button&&this.all_button.value($.isArray(b)&&b.length||0,this._size()),b},first:function(){var a=this.$select.find("option").first();return a.length>0?a.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},update:function(a){var b=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var c in a)this.$select.append(this._templateOption(a[c]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2(),this.$(".select2-container .select2-search input").off("blur")),this.value(b),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(a){this.options.onchange=a},exists:function(a){return this.$select.find('option[value="'+a+'"]').length>0},_getValue:function(){var b=this.$select.val();return a.validate(b)?b:null},_availableOptions:function(){var a=[];return this.$select.find("option").each(function(b,c){a.push($(c).attr("value"))}),a},_size:function(){return this.$select.find("option").length},_templateOption:function(a){return'<option value="'+a.value+'">'+a.label+"</option>"},_template:function(a){return'<div id="'+a.id+'" class="'+a.cls+'"><select id="'+a.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:c}});
+define(["utils/utils","mvc/ui/ui-buttons"],function(a,b){var c=Backbone.View.extend({optionsDefault:{id:a.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(c){var d=this;this.options=a.merge(c,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon_dropdown=this.$el.find(".icon-dropdown");var e=null;this.$(".icon-resize").on("mousedown",function(a){var b=a.pageY,c=d.$select.height();e=e||c,$("#dd-helper").show().on("mousemove",function(a){d.$select.height(Math.max(c+(a.pageY-b),e))}).on("mouseup mouseleave",function(){$("#dd-helper").hide().off()})}),this.options.multiple&&(this.options.searchable?(this.all_button=new b.ButtonCheck({onclick:function(){var a=[];0!==d.all_button.value()&&(a=d._availableOptions()),d.value(a),d.trigger("change")}}),this.$el.prepend(this.all_button.$el)):this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$icon_dropdown.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){d.trigger("change")}),this.on("change",function(){d.options.onchange&&d.options.onchange(this.value())})},value:function(a){void 0!==a&&(null===a&&(a="__null__"),(this.exists(a)||this.options.multiple)&&(this.$select.val(a),this.$select.select2&&this.$select.select2("val",a)));var b=this._getValue();return this.all_button&&this.all_button.value($.isArray(b)&&b.length||0,this._size()),b},first:function(){var a=this.$select.find("option").first();return a.length>0?a.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-spinner fa-spin")},unwait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},update:function(a){var b=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var c in a)this.$select.append(this._templateOption(a[c]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2({closeOnSelect:!this.options.multiple}),this.$(".select2-container .select2-search input").off("blur")),this.value(b),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(a){this.options.onchange=a},exists:function(a){return this.$select.find('option[value="'+a+'"]').length>0},_getValue:function(){var b=this.$select.val();return a.validate(b)?b:null},_availableOptions:function(){var a=[];return this.$select.find("option").each(function(b,c){a.push($(c).attr("value"))}),a},_size:function(){return this.$select.find("option").length},_templateOption:function(a){return'<option value="'+a.value+'">'+a.label+"</option>"},_template:function(a){return'<div id="'+a.id+'" class="'+a.cls+'"><select id="'+a.id+'_select" class="select"/><div class="icon-dropdown"/><div class="icon-resize"><i class="fa fa-angle-double-right fa-rotate-45"/></div></div>'}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/ui/ui-select-default.js.map

static/scripts/mvc/upload/upload-button.js

@@ -1,2 +1,2 @@
-define([],function(){var a=Backbone.Model.extend({defaults:{icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",percentage:0,status:""}}),b=Backbone.View.extend({model:null,initialize:function(a){var b=this,c=a.model;this.setElement(this._template()),this.$el.on("click",function(b){a.onclick(b)}),this.$el.tooltip({title:c.get("tooltip"),placement:"bottom"}),c.on("change:percentage",function(){b._percentage(c.get("percentage"))}),c.on("change:status",function(){b._status(c.get("status"))});var b=this;$(window).on("beforeunload",function(){var b="";return a.onunload&&(b=a.onunload()),""!=b?b:void 0})},_status:function(a){var b=this.$el.find(".progress-bar");b.removeClass(),b.addClass("progress-bar"),b.addClass("progress-bar-notransition"),""!=a&&b.addClass("progress-bar-"+a)},_percentage:function(a){var b=this.$el.find(".progress-bar");b.css({width:a+"%"})},_template:function(){return'<div class="upload-button"><div class="progress"><div class="progress-bar"></div></div><div id="label" class="label"><a class="panel-header-button" href="javascript:void(0)"><span class="fa fa-upload"></span></a></div></div>'}});return{Model:a,View:b}});
+define([],function(){var a=Backbone.Model.extend({defaults:{icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",percentage:0,status:""}}),b=Backbone.View.extend({model:null,initialize:function(a){var b=this,c=a.model;this.setElement(this._template()),this.$el.on("click",function(b){a.onclick(b)}),this.$el.tooltip({title:c.get("tooltip"),placement:"bottom"}),c.on("change:percentage",function(){b._percentage(c.get("percentage"))}),c.on("change:status",function(){b._status(c.get("status"))});var b=this;$(window).on("beforeunload",function(){var b="";return a.onunload&&(b=a.onunload()),""!=b?b:void 0})},_status:function(a){var b=this.$el.find(".progress-bar");b.removeClass(),b.addClass("progress-bar"),b.addClass("progress-bar-notransition"),""!=a&&b.addClass("progress-bar-"+a)},_percentage:function(a){var b=this.$el.find(".progress-bar");b.css({width:a+"%"})},_template:function(){return'<div class="upload-button"><div class="progress"><div class="progress-bar"/><a class="panel-header-button" href="javascript:void(0)"><span class="fa fa-upload"/></a></div></div>'}});return{Model:a,View:b}});
 //# sourceMappingURL=../../../maps/mvc/upload/upload-button.js.map

static/scripts/utils/deferred.js

@@ -1,2 +1,2 @@
-define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(){this.active={},this.last=null},execute:function(b){var c=this,d=a.uid(),e=b.length>0;this.active[d]=!0;var f=$.Deferred();f.promise().always(function(){delete c.active[d],e&&console.debug("Deferred::execute() - "+this.state()+" "+d)}),$.when(this.last).always(function(){c.active[d]?(e&&console.debug("Deferred::execute() - running "+d),b(f),!e&&f.resolve()):f.reject()}),this.last=f.promise()},reset:function(){console.debug("Deferred::execute() - reset");for(var a in this.active)this.active[a]=!1},ready:function(){return $.isEmptyObject(this.active)}})});
+define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(){this.active={},this.last=null},execute:function(b){var c=this,d=a.uid(),e=b.length>0;this.active[d]=!0;var f=$.Deferred();f.promise().always(function(){delete c.active[d],e&&Galaxy.emit.debug("deferred::execute()",this.state().charAt(0).toUpperCase()+this.state().slice(1)+" "+d)}),$.when(this.last).always(function(){c.active[d]?(e&&Galaxy.emit.debug("deferred::execute()","Running "+d),b(f),!e&&f.resolve()):f.reject()}),this.last=f.promise()},reset:function(){Galaxy.emit.debug("deferred::execute()","Reset");for(var a in this.active)this.active[a]=!1},ready:function(){return $.isEmptyObject(this.active)}})});
 //# sourceMappingURL=../../maps/utils/deferred.js.map

static/scripts/utils/uploadbox.js

@@ -1,2 +1,2 @@
-!function(a){jQuery.event.props.push("dataTransfer"),a.uploadpost=function(b){var c=a.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},b),d=c.data;if(d.error_message)return void c.error(d.error_message);var e=new FormData;for(var f in d.payload)e.append(f,d.payload[f]);var g=0;for(var f in d.files){var h=d.files[f];e.append(h.name,h.file,h.file.name),g+=h.file.size}return g>1048576*c.maxfilesize?void c.error(c.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",c.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var a=null;if(xhr.responseText)try{a=jQuery.parseJSON(xhr.responseText)}catch(b){a=xhr.responseText}if(xhr.status<200||xhr.status>299){var d=xhr.statusText;403==xhr.status?d=c.error_login:0==xhr.status?d=c.error_server:d||(d=c.error_default),c.error(d+" ("+xhr.status+")")}else c.success(a)}},xhr.upload.addEventListener("progress",function(a){a.lengthComputable&&c.progress(Math.round(100*a.loaded/a.total))},!1),console.debug("uploadbox::uploadpost() - Posting following data:"),console.debug(c),void xhr.send(e))},a.fn.uploadinput=function(b){var c=this,d=a.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},b),e=a('<input type="file" style="display: none" '+(d.multiple&&"multiple"||"")+"/>");return c.append(e).change(function(b){d.onchange(b.target.files),a(this).val("")}),c.on("drop",function(a){d.ondragleave(a),a.dataTransfer&&(d.onchange(a.dataTransfer.files),a.preventDefault())}),c.on("dragover",function(a){a.preventDefault(),d.ondragover(a)}),c.on("dragleave",function(a){a.stopPropagation(),d.ondragleave(a)}),{dialog:function(){e.trigger("click")}}},a.fn.uploadbox=function(b){function c(a){if(a&&a.length&&!p){for(var b=n,c=0;c<a.length;c++){var d=String(n++);m[d]=a[c],l.announce(d,m[d]),o++}return b}}function d(a){m[a]&&(delete m[a],o--)}function e(){if(0==o||q)return q=!1,p=!1,void l.complete();p=!0;var b=-1;for(var c in m){b=c;break}m[b];d(b),a.uploadpost({url:l.url,data:l.initialize(b),success:function(a){l.success(b,a),e()},error:function(a){l.error(b,a),e()},progress:function(a){l.progress(b,a)}})}function f(){r.dialog()}function g(a){for(a in m)d(a)}function h(){p||(p=!0,e())}function i(){q=!0}function j(b){return l=a.extend({},l,b)}function k(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var l=a.extend({},{dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(a,b){alert(b)},complete:function(){}},b),m={},n=0,o=0,p=!1,q=!1,r=a(this).uploadinput({multiple:!0,onchange:function(a){c(a)},ondragover:b.ondragover,ondragleave:b.ondragleave});return{select:f,add:c,remove:d,start:h,stop:i,reset:g,configure:j,compatible:k}}}(jQuery);
+!function(a){jQuery.event.props.push("dataTransfer"),a.uploadpost=function(b){var c=a.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},b),d=c.data;if(d.error_message)return void c.error(d.error_message);var e=new FormData;for(var f in d.payload)e.append(f,d.payload[f]);var g=0;for(var f in d.files){var h=d.files[f];e.append(h.name,h.file,h.file.name),g+=h.file.size}return g>1048576*c.maxfilesize?void c.error(c.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",c.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var a=null;if(xhr.responseText)try{a=jQuery.parseJSON(xhr.responseText)}catch(b){a=xhr.responseText}if(xhr.status<200||xhr.status>299){var d=xhr.statusText;403==xhr.status?d=c.error_login:0==xhr.status?d=c.error_server:d||(d=c.error_default),c.error(d+" ("+xhr.status+")")}else c.success(a)}},xhr.upload.addEventListener("progress",function(a){a.lengthComputable&&c.progress(Math.round(100*a.loaded/a.total))},!1),Galaxy.emit.debug("uploadbox::uploadpost()","Posting following data.",c),void xhr.send(e))},a.fn.uploadinput=function(b){var c=this,d=a.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},b),e=a('<input type="file" style="display: none" '+(d.multiple&&"multiple"||"")+"/>");return c.append(e).change(function(b){d.onchange(b.target.files),a(this).val("")}),c.on("drop",function(a){d.ondragleave(a),a.dataTransfer&&(d.onchange(a.dataTransfer.files),a.preventDefault())}),c.on("dragover",function(a){a.preventDefault(),d.ondragover(a)}),c.on("dragleave",function(a){a.stopPropagation(),d.ondragleave(a)}),{dialog:function(){e.trigger("click")}}},a.fn.uploadbox=function(b){function c(a){if(a&&a.length&&!p){for(var b=n,c=0;c<a.length;c++){var d=String(n++);m[d]=a[c],l.announce(d,m[d]),o++}return b}}function d(a){m[a]&&(delete m[a],o--)}function e(){if(0==o||q)return q=!1,p=!1,void l.complete();p=!0;var b=-1;for(var c in m){b=c;break}m[b];d(b),a.uploadpost({url:l.url,data:l.initialize(b),success:function(a){l.success(b,a),e()},error:function(a){l.error(b,a),e()},progress:function(a){l.progress(b,a)}})}function f(){r.dialog()}function g(a){for(a in m)d(a)}function h(){p||(p=!0,e())}function i(){q=!0}function j(b){return l=a.extend({},l,b)}function k(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var l=a.extend({},{dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(a,b){alert(b)},complete:function(){}},b),m={},n=0,o=0,p=!1,q=!1,r=a(this).uploadinput({multiple:!0,onchange:function(a){c(a)},ondragover:b.ondragover,ondragleave:b.ondragleave});return{select:f,add:c,remove:d,start:h,stop:i,reset:g,configure:j,compatible:k}}}(jQuery);
 //# sourceMappingURL=../../maps/utils/uploadbox.js.map

test/api/helpers.py

@@ -83,7 +83,10 @@ class BaseDatasetPopulator( object ):
             raise
 
     def wait_for_job( self, job_id, assert_ok=False, timeout=DEFAULT_TIMEOUT ):
-        return wait_on_state( lambda: self._get( "jobs/%s" % job_id ), assert_ok=assert_ok, timeout=timeout )
+        return wait_on_state( lambda: self.get_job_details( job_id ), assert_ok=assert_ok, timeout=timeout )
+
+    def get_job_details( self, job_id, full=False ):
+        return self._get( "jobs/%s?full=%s" % (job_id, full) )
 
     def _summarize_history_errors( self, history_id ):
         pass

test/functional/tools/samples_tool_conf.xml

@@ -18,6 +18,7 @@
   <tool file="dbkey_filter_input.xml" />
   <tool file="dbkey_filter_multi_input.xml" />
   <tool file="composite_output.xml" />
+  <tool file="unicode_stream.xml" />
   <tool file="metadata.xml" />
   <tool file="metadata_bam.xml" />
   <tool file="metadata_bcf.xml" />

test/functional/tools/unicode_stream.xml

@@ -0,0 +1,41 @@
+<tool id="unicode_stream" name="unicode_stream" version="0.1.0">
+    <description>
+    </description>
+    <configfiles>
+        <configfile name="cf">ვეპხის ტყაოსანი შოთა რუსთაველი
+</configfile>
+    </configfiles>
+    <command detect_errors="exit_code">
+        echo '$input1' > $out_file1;
+        cat $cf;
+        >&amp;2 cat $cf;
+        sh -c "exit $exit"
+    </command>
+    <inputs>
+        <param name="input1" type="text" label="Input">
+            <sanitizer sanitize="False">
+            </sanitizer>
+        </param>
+        <param name="exit" type="integer" value="0" label="Exit Code" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test expect_exit_code="0" expect_failure="false">
+            <param name="input1" value="This is a line of text."/>
+            <param name="exit" value="0" />
+            <output name="out_file1" file="simple_line.txt" />
+        </test>
+        <test expect_exit_code="1" expect_failure="true">
+            <param name="input1" value="This is a line of text."/>
+            <param name="exit" value="1" />
+        </test>
+        <test expect_exit_code="0" expect_failure="false">
+            <param name="input1" value="ვვვვვ"/>
+            <param name="exit" value="0" />
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>

test/unit/jobs/test_job_output_checker.py

@@ -3,6 +3,7 @@ from galaxy.util.bunch import Bunch
 from galaxy.jobs.output_checker import check_output
 from galaxy.jobs.error_level import StdioErrorLevel
 from galaxy.tools.parser.interface import ToolStdioRegex
+from galaxy.model import Job
 
 
 class OutputCheckerTestCase( TestCase ):
@@ -12,11 +13,8 @@ class OutputCheckerTestCase( TestCase ):
             stdio_regexes=[],
             stdio_exit_codes=[],
         )
-        self.job = Bunch(
-            stdout=None,
-            stderr=None,
-            get_id_tag=lambda: "test_id",
-        )
+        self.job = Job()
+        self.job.id = "test_id"
         self.stdout = ''
         self.stderr = ''
         self.tool_exit_code = None

tools/filters/wig_to_bigwig.xml

@@ -1,15 +1,25 @@
 <tool id="wig_to_bigWig" name="Wig/BedGraph-to-bigWig" version="1.1.0">
   <description>converter</description>
-  <command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 
+  <requirements>
+    <requirement type="package">ucsc_tools</requirement>
+  </requirements>
+  <stdio>
+      <!-- Anything other than zero is an error -->
+      <regex match="needLargeMem: trying to allocate 0 bytes"
+          description="Your input file might be empty or wrongly formatted"/>
+      <regex match="^Error"/>
+  </stdio>
+  <command>
+      <![CDATA[
+      grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1
     #if $settings.settingsType == "full":
       -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.clip} ${settings.unc}
     #else:
       -clip
     #end if
-    2&gt;&amp;1 || echo "Error running wigToBigWig." >&amp;2</command>
-  <requirements>
-    <requirement type="package">ucsc_tools</requirement>
-  </requirements>
+    2>&1 || echo "Error running wigToBigWig." >&2
+    ]]>
+  </command>
   <inputs>
     <param format="wig,bedgraph" name="input1" type="data" label="Convert">
       <validator type="unspecified_build" />

tools/stats/gsummary.py

@@ -107,7 +107,12 @@ def main():
             stop_err( "Computation resulted in the following error: %s" % str( s ) )
         summary = summary.as_py( BASIC_CONVERSION )
         outfile.write( "#%s\n" % headings_str )
-        outfile.write( "%s\n" % "\t".join( [ "%g" % k for k in summary ] ) )
+        if type(summary) is dict:
+            # using rpy
+            outfile.write( "%s\n" % "\t".join( [ "%g" % summary[k] for k in headings ] ) )
+        else:
+            # using rpy2
+            outfile.write( "%s\n" % "\t".join( [ "%g" % k for k in summary ] ) )
         outfile.close()
 
         if skipped_lines: