[galaxy-commits] commit/galaxy-central: guerler: ToolForm: Load history summary and metadata separately, add file extension to history api, fix spinner style for select field

1 Oct 2014

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/6aad6ad39a04/
Changeset:   6aad6ad39a04
User:        guerler
Date:        2014-10-01 17:36:46+00:00
Summary:     ToolForm: Load history summary and metadata separately, add file extension to history api, fix spinner style for select field
Affected #:  17 files

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e client/galaxy/scripts/mvc/tools/tools-datasets.js

--- a/client/galaxy/scripts/mvc/tools/tools-datasets.js
+++ b/client/galaxy/scripts/mvc/tools/tools-datasets.js
@@ -1,15 +1,10 @@
-define([ 'mvc/history/history-contents', 'utils/utils' ], function( HistoryContents, Utils ){
+define(['utils/utils'], function(Utils){
     return Backbone.Model.extend({
         // initialize
         initialize: function(options) {
-            // create history contents container
-            this.currHistoryContents = new HistoryContents.HistoryContents({});
-            
-            // identify current history id
-            this.currHistoryContents.historyId = options.history_id;
-            
-            // prepare datatype structure
-            this.typedict = {};
+            // prepare datasets obects
+            this.datatypes = {};
+            this.summary = {};
             
             // link this
             var self = this;
@@ -18,70 +13,99 @@
             Utils.get({
                 url     : galaxy_config.root + 'api/datatypes/mapping',
                 cache   : true,
-                success : function(typedict) {
+                success : function(response) {
                     // backup datatype dictionary
-                    self.typedict = typedict;
+                    self.datatypes = response;
                     
-                    // make request
-                    var xhr = self.currHistoryContents.fetchAllDetails()
-                        .done( function(){
-                            // log request success
+                    // get history summary
+                    Utils.get({
+                        url     : galaxy_config.root + 'api/histories/' + options.history_id + '/contents?deleted=false',
+                        success : function(response) {
+                            // backup summary
+                            self.summary = response;
+                            
+                            // log
                             console.debug('tools-datasets::initialize() - Completed.');
                             
                             // callback
                             options.success && options.success();
-                        })
-                        .fail( function(){
+                        },
+                        error   : function(response) {
                             // log request failure
-                            console.debug('tools-datasets::initialize() - Ajax request for history datasets failed.');
-                        });
+                            console.debug('tools-datasets::initialize() - Ajax request for summary failed.');
+                            console.debug(response);
+                        }
+                    });
                 },
                 error   : function(response) {
                     // log request failure
-                    console.debug('tools-datasets::initialize() - Ajax request for datatype dictionary failed.');
+                    console.debug('tools-datasets::initialize() - Ajax request for datatypes failed.');
+                    console.debug(response);
                 }
             });
         },
         
-        /** Filters datasets by data type.
+        /**
+         * Filters datasets by data type.
         */
         filterType: function(options) {
             options = options || {};
-            var self = this;
-            return this.currHistoryContents.filter(function(content){
+            var result = [];
+            for (var i in this.summary) {
+                var dataset = this.summary[i];
+                
                 // match datatypes
                 var found = false;
                 for (var i in options.data_types) {
-                    if (self._matchType(content.get('data_type'), options.data_types[i])) {
+                    if (this._matchType(options.data_types[i], dataset.extension)) {
                         found = true;
                         break;
                     }
                 }
                 
                 // final match result
-                return  (content.get('history_content_type') === options.content_type || !options.content_type) &&
-                        (found || !options.data_types) && !content.get('deleted');
-            });
+                if ((dataset.history_content_type === options.content_type || !options.content_type) && (found || !options.data_types)) {
+                    result.push(dataset);
+                }
+            }
+            return result;
         },
         
-        /** Filter datasets by id.
+        /** Get details of a dataset by id.
+         * @param{String} Dataset id
         */
-        filter: function(filter_id) {
-            return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) );
+        getDetails: function(dataset_id, callback) {
+            Utils.get({
+                url     : galaxy_config.root + 'api/datasets/' + dataset_id,
+                success : function(response) {
+                    callback && callback(response);
+                },
+                error   : function(response) {
+                    console.debug('tools-datasets::getDetails() - Ajax request for dataset failed.');
+                    console.debug(response);
+                }
+            });
         },
         
         /** Check if datatypes match
         */
-        _matchType: function(reference, target) {
+        _matchType: function(target, reference) {
             // check if target class is available
-            var target_class = this.typedict.ext_to_class_name[target];
+            var target_class = this.datatypes.ext_to_class_name[target];
             if (!target_class) {
                 console.debug('tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.');
                 return true;
             }
             
+            // check if reference class is available
+            var reference_class = this.datatypes.ext_to_class_name[reference];
+            if (!reference_class) {
+                console.debug('tools-datasets::_matchType() - Specific reference class unavailable. Accepting all formats.');
+                return true;
+            }
+            
             // check reference group
-            var reference_group = this.typedict.class_to_classes[reference];
+            var reference_group = this.datatypes.class_to_classes[reference_class];
             if (reference_group[target_class]) {
                 return true;
             }

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -414,7 +414,7 @@
                 extensions  : input_def.extensions,
                 multiple    : input_def.multiple,
                 onchange    : function(dict) {
-                    // pick the first dataset if multiple might be selected
+                    // pick the first dataset only (todo: maybe collect multiple meta information)
                     var value = dict.values[0].id;
                     
                     // get referenced columns
@@ -426,72 +426,79 @@
                         return;
                     }
                     
-                    // find selected dataset
-                    var dataset = self.app.datasets.filter(value);
-        
-                    // meta data
-                    var meta = null;
-        
-                    // check dataset
-                    if (dataset) {
-                        // log selection
-                        console.debug('tool-form::field_data() - Selected dataset ' + value + '.');
-                    
-                        // get meta data
-                        meta = dataset.get('metadata_column_types');
-                    
-                        // check meta data
-                        if (!meta) {
-                            console.debug('tool-form::field_data() - FAILED: Could not find metadata for dataset ' + value + '.');
-                        }
-                    } else {
-                        console.debug('tool-form::field_data() - FAILED: Could not find dataset ' + value + '.');
+                    // set wait mode
+                    for (var i in column_list) {
+                        var column_field = self.app.field_list[column_list[i]];
+                        column_field.wait && column_field.wait();
                     }
                     
-                    // update referenced columns
-                    for (var i in column_list) {
-                        // get column input/field
-                        var column_input = self.app.input_list[column_list[i]];
-                        var column_field = self.app.field_list[column_list[i]];
-                        if (!column_input || !column_field) {
-                            console.debug('tool-form::field_data() - FAILED: Column not found.');
+                    // find selected dataset
+                    self.app.datasets.getDetails(value,  function(dataset) {
+                        // meta data
+                        var meta = null;
+            
+                        // check dataset
+                        if (dataset) {
+                            // log selection
+                            console.debug('tool-form::field_data() - Selected dataset ' + value + '.');
+                        
+                            // get meta data
+                            meta = dataset.metadata_column_types;
+                        
+                            // check meta data
+                            if (!meta) {
+                                console.debug('tool-form::field_data() - FAILED: Could not find metadata for dataset ' + value + '.');
+                            }
+                        } else {
+                            console.debug('tool-form::field_data() - FAILED: Could not find dataset ' + value + '.');
                         }
-                    
-                        // is numerical?
-                        var numerical = column_input.numerical;
                         
-                        // identify column options
-                        var columns = [];
-                        for (var key in meta) {
-                            // get column type
-                            var column_type = meta[key];
+                        // update referenced columns
+                        for (var i in column_list) {
+                            // get column input/field
+                            var column_input = self.app.input_list[column_list[i]];
+                            var column_field = self.app.field_list[column_list[i]];
+                            if (!column_input || !column_field) {
+                                console.debug('tool-form::field_data() - FAILED: Column not found.');
+                            }
+                        
+                            // is numerical?
+                            var numerical = column_input.numerical;
                             
-                            // column index
-                            var column_index = (parseInt(key) + 1);
-                            
-                            // column type label
-                            var column_label = 'Text';
-                            if (column_type == 'int' || column_type == 'float') {
-                                column_label = 'Number';
+                            // identify column options
+                            var columns = [];
+                            for (var key in meta) {
+                                // get column type
+                                var column_type = meta[key];
+                                
+                                // column index
+                                var column_index = (parseInt(key) + 1);
+                                
+                                // column type label
+                                var column_label = 'Text';
+                                if (column_type == 'int' || column_type == 'float') {
+                                    column_label = 'Number';
+                                }
+                                
+                                // add to selection
+                                if (column_type == 'int' || column_type == 'float' || !numerical) {
+                                    columns.push({
+                                        'label' : 'Column: ' + column_index + ' [' + column_label + ']',
+                                        'value' : column_index
+                                    });
+                                }
                             }
                             
-                            // add to selection
-                            if (column_type == 'int' || column_type == 'float' || !numerical) {
-                                columns.push({
-                                    'label' : 'Column: ' + column_index + ' [' + column_label + ']',
-                                    'value' : column_index
-                                });
+                            // update field
+                            if (column_field) {
+                                column_field.update(columns);
+                                if (!column_field.exists(column_field.value())) {
+                                    column_field.value(column_field.first());
+                                }
+                                column_field.show();
                             }
                         }
-                        
-                        // update field
-                        if (column_field) {
-                            column_field.update(columns);
-                            if (!column_field.exists(column_field.value())) {
-                                column_field.value(column_field.first());
-                            }
-                        }
-                    }
+                    });
                 }
             });
         },

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e client/galaxy/scripts/mvc/tools/tools-select-dataset.js
--- a/client/galaxy/scripts/mvc/tools/tools-select-dataset.js
+++ b/client/galaxy/scripts/mvc/tools/tools-select-dataset.js
@@ -40,8 +40,8 @@
         var dataset_options = [];
         for (var i in datasets) {
             dataset_options.push({
-                label: datasets[i].get('name'),
-                value: datasets[i].get('id')
+                label: datasets[i].name,
+                value: datasets[i].id
             });
         }
         
@@ -67,8 +67,8 @@
         var collection_options = [];
         for (var i in collections) {
             collection_options.push({
-                label: collections[i].get('name'),
-                value: collections[i].get('id')
+                label: collections[i].name,
+                value: collections[i].id
             });
         }
         

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e client/galaxy/scripts/mvc/ui/ui-select-default.js
--- a/client/galaxy/scripts/mvc/ui/ui-select-default.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js
@@ -124,7 +124,6 @@
     wait: function() {
         this.$icon.removeClass();
         this.$icon.addClass('fa fa-spinner fa-spin');
-        this.$select.hide();
     },
     
     /** Returns true if the field is disabled

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e client/galaxy/scripts/utils/utils.js
--- a/client/galaxy/scripts/utils/utils.js
+++ b/client/galaxy/scripts/utils/utils.js
@@ -6,12 +6,13 @@
 // dependencies
 define(["libs/underscore"], function(_) {
 
-/* request handler for GET
-    param{string}   url
-    param{function} success
-    param{function} error
-    param{boolean}  cache
-*/
+/**
+ * Request handler for GET
+ * @param{String}   url     - Url request is made to
+ * @param{Function} success - Callback on success
+ * @param{Function} error   - Callback on error
+ * @param{Boolean}  cache   - Use cached data if available
+ */
 function get (options) {
     top.__utils__get__ = top.__utils__get__ || {};
     if (options.cache && top.__utils__get__[options.url]) {
@@ -32,13 +33,14 @@
     }
 };
 
-/* request handler
-    param{string}   method
-    param{string}   url
-    param{object}   data
-    param{function} success
-    param{function} error
-*/
+/**
+ * Request handler
+ * @param{String}   method  - Request method ['GET', 'POST', 'DELETE', 'PUT']
+ * @param{String}   url     - Url request is made to
+ * @param{Object}   data    - Data send to url
+ * @param{Function} success - Callback on success
+ * @param{Function} error   - Callback on error
+ */
 function request (options) {
     // prepare ajax
     var ajaxConfig = {
@@ -79,7 +81,11 @@
     });
 };
 
-// get css value
+/** 
+ * Read a property value from CSS
+ * @param{String}   classname   - CSS class
+ * @param{String}   name        - CSS property
+ */
 function cssGetAttribute (classname, name) {
     // place dummy element
     var el = $('<div class="' + classname + '"></div>');
@@ -97,14 +103,21 @@
     return value;
 };
     
-// load css
+/**
+ * Load a CSS file
+ * @param{String}   url - Url of CSS file
+ */
 function cssLoadFile (url) {
     // check if css is already available
     if (!$('link[href^="' + url + '"]').length)
         $('<link href="' + galaxy_config.root + url + '" rel="stylesheet">').appendTo('head');
 };
 
-// merge
+/**
+ * Safely merge to dictionaries
+ * @param{Object}   options         - Target dictionary
+ * @param{Object}   optionsDefault  - Source dictionary
+ */
 function merge (options, optionsDefault) {
     if (options)
         return _.defaults(options, optionsDefault);
@@ -112,7 +125,11 @@
         return optionsDefault;
 };
 
-// to string
+/**
+ * Format byte size to string with units
+ * @param{Integer}   size           - Size in bytes
+ * @param{Boolean}   normal_font    - Switches font between normal and bold
+ */
 function bytesToString (size, normal_font) {
     // identify unit
     var unit = "";
@@ -132,19 +149,26 @@
     }
 };
 
-// unique ide
+/**
+ * Create a unique id
+ */
 function uuid(){
     return 'x' + Math.random().toString(36).substring(2, 9);
 };
 
-// wrap
+/**
+ * Wrap an dom element into a paragraph
+ * @param{Element}  $el - DOM element to be wrapped
+ */
 function wrap($el) {
     var wrapper = $('<p></p>');
     wrapper.append($el);
     return wrapper;
 };
 
-// time
+/**
+ * Create a time stamp
+ */
 function time() {
     // get date object
     var d = new Date();
@@ -162,7 +186,6 @@
     return datetime;
 };
 
-// return
 return {
     cssLoadFile   : cssLoadFile,
     cssGetAttribute : cssGetAttribute,

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e lib/galaxy/webapps/galaxy/api/history_contents.py
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -139,6 +139,7 @@
             'type'  : api_type,
             'state'  : hda.dataset.state,
             'deleted': hda.deleted,
+            'extension': hda.extension,
             'visible': hda.visible,
             'purged': hda.purged,
             'resubmitted': hda._state == trans.app.model.Dataset.states.RESUBMITTED,

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/scripts/mvc/tools/tools-datasets.js
--- a/static/scripts/mvc/tools/tools-datasets.js
+++ b/static/scripts/mvc/tools/tools-datasets.js
@@ -1,15 +1,10 @@
-define([ 'mvc/history/history-contents', 'utils/utils' ], function( HistoryContents, Utils ){
+define(['utils/utils'], function(Utils){
     return Backbone.Model.extend({
         // initialize
         initialize: function(options) {
-            // create history contents container
-            this.currHistoryContents = new HistoryContents.HistoryContents({});
-            
-            // identify current history id
-            this.currHistoryContents.historyId = options.history_id;
-            
-            // prepare datatype structure
-            this.typedict = {};
+            // prepare datasets obects
+            this.datatypes = {};
+            this.summary = {};
             
             // link this
             var self = this;
@@ -18,70 +13,99 @@
             Utils.get({
                 url     : galaxy_config.root + 'api/datatypes/mapping',
                 cache   : true,
-                success : function(typedict) {
+                success : function(response) {
                     // backup datatype dictionary
-                    self.typedict = typedict;
+                    self.datatypes = response;
                     
-                    // make request
-                    var xhr = self.currHistoryContents.fetchAllDetails()
-                        .done( function(){
-                            // log request success
+                    // get history summary
+                    Utils.get({
+                        url     : galaxy_config.root + 'api/histories/' + options.history_id + '/contents?deleted=false',
+                        success : function(response) {
+                            // backup summary
+                            self.summary = response;
+                            
+                            // log
                             console.debug('tools-datasets::initialize() - Completed.');
                             
                             // callback
                             options.success && options.success();
-                        })
-                        .fail( function(){
+                        },
+                        error   : function(response) {
                             // log request failure
-                            console.debug('tools-datasets::initialize() - Ajax request for history datasets failed.');
-                        });
+                            console.debug('tools-datasets::initialize() - Ajax request for summary failed.');
+                            console.debug(response);
+                        }
+                    });
                 },
                 error   : function(response) {
                     // log request failure
-                    console.debug('tools-datasets::initialize() - Ajax request for datatype dictionary failed.');
+                    console.debug('tools-datasets::initialize() - Ajax request for datatypes failed.');
+                    console.debug(response);
                 }
             });
         },
         
-        /** Filters datasets by data type.
+        /**
+         * Filters datasets by data type.
         */
         filterType: function(options) {
             options = options || {};
-            var self = this;
-            return this.currHistoryContents.filter(function(content){
+            var result = [];
+            for (var i in this.summary) {
+                var dataset = this.summary[i];
+                
                 // match datatypes
                 var found = false;
                 for (var i in options.data_types) {
-                    if (self._matchType(content.get('data_type'), options.data_types[i])) {
+                    if (this._matchType(options.data_types[i], dataset.extension)) {
                         found = true;
                         break;
                     }
                 }
                 
                 // final match result
-                return  (content.get('history_content_type') === options.content_type || !options.content_type) &&
-                        (found || !options.data_types) && !content.get('deleted');
-            });
+                if ((dataset.history_content_type === options.content_type || !options.content_type) && (found || !options.data_types)) {
+                    result.push(dataset);
+                }
+            }
+            return result;
         },
         
-        /** Filter datasets by id.
+        /** Get details of a dataset by id.
+         * @param{String} Dataset id
         */
-        filter: function(filter_id) {
-            return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) );
+        getDetails: function(dataset_id, callback) {
+            Utils.get({
+                url     : galaxy_config.root + 'api/datasets/' + dataset_id,
+                success : function(response) {
+                    callback && callback(response);
+                },
+                error   : function(response) {
+                    console.debug('tools-datasets::getDetails() - Ajax request for dataset failed.');
+                    console.debug(response);
+                }
+            });
         },
         
         /** Check if datatypes match
         */
-        _matchType: function(reference, target) {
+        _matchType: function(target, reference) {
             // check if target class is available
-            var target_class = this.typedict.ext_to_class_name[target];
+            var target_class = this.datatypes.ext_to_class_name[target];
             if (!target_class) {
                 console.debug('tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.');
                 return true;
             }
             
+            // check if reference class is available
+            var reference_class = this.datatypes.ext_to_class_name[reference];
+            if (!reference_class) {
+                console.debug('tools-datasets::_matchType() - Specific reference class unavailable. Accepting all formats.');
+                return true;
+            }
+            
             // check reference group
-            var reference_group = this.typedict.class_to_classes[reference];
+            var reference_group = this.datatypes.class_to_classes[reference_class];
             if (reference_group[target_class]) {
                 return true;
             }

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -414,7 +414,7 @@
                 extensions  : input_def.extensions,
                 multiple    : input_def.multiple,
                 onchange    : function(dict) {
-                    // pick the first dataset if multiple might be selected
+                    // pick the first dataset only (todo: maybe collect multiple meta information)
                     var value = dict.values[0].id;
                     
                     // get referenced columns
@@ -426,72 +426,79 @@
                         return;
                     }
                     
-                    // find selected dataset
-                    var dataset = self.app.datasets.filter(value);
-        
-                    // meta data
-                    var meta = null;
-        
-                    // check dataset
-                    if (dataset) {
-                        // log selection
-                        console.debug('tool-form::field_data() - Selected dataset ' + value + '.');
-                    
-                        // get meta data
-                        meta = dataset.get('metadata_column_types');
-                    
-                        // check meta data
-                        if (!meta) {
-                            console.debug('tool-form::field_data() - FAILED: Could not find metadata for dataset ' + value + '.');
-                        }
-                    } else {
-                        console.debug('tool-form::field_data() - FAILED: Could not find dataset ' + value + '.');
+                    // set wait mode
+                    for (var i in column_list) {
+                        var column_field = self.app.field_list[column_list[i]];
+                        column_field.wait && column_field.wait();
                     }
                     
-                    // update referenced columns
-                    for (var i in column_list) {
-                        // get column input/field
-                        var column_input = self.app.input_list[column_list[i]];
-                        var column_field = self.app.field_list[column_list[i]];
-                        if (!column_input || !column_field) {
-                            console.debug('tool-form::field_data() - FAILED: Column not found.');
+                    // find selected dataset
+                    self.app.datasets.getDetails(value,  function(dataset) {
+                        // meta data
+                        var meta = null;
+            
+                        // check dataset
+                        if (dataset) {
+                            // log selection
+                            console.debug('tool-form::field_data() - Selected dataset ' + value + '.');
+                        
+                            // get meta data
+                            meta = dataset.metadata_column_types;
+                        
+                            // check meta data
+                            if (!meta) {
+                                console.debug('tool-form::field_data() - FAILED: Could not find metadata for dataset ' + value + '.');
+                            }
+                        } else {
+                            console.debug('tool-form::field_data() - FAILED: Could not find dataset ' + value + '.');
                         }
-                    
-                        // is numerical?
-                        var numerical = column_input.numerical;
                         
-                        // identify column options
-                        var columns = [];
-                        for (var key in meta) {
-                            // get column type
-                            var column_type = meta[key];
+                        // update referenced columns
+                        for (var i in column_list) {
+                            // get column input/field
+                            var column_input = self.app.input_list[column_list[i]];
+                            var column_field = self.app.field_list[column_list[i]];
+                            if (!column_input || !column_field) {
+                                console.debug('tool-form::field_data() - FAILED: Column not found.');
+                            }
+                        
+                            // is numerical?
+                            var numerical = column_input.numerical;
                             
-                            // column index
-                            var column_index = (parseInt(key) + 1);
-                            
-                            // column type label
-                            var column_label = 'Text';
-                            if (column_type == 'int' || column_type == 'float') {
-                                column_label = 'Number';
+                            // identify column options
+                            var columns = [];
+                            for (var key in meta) {
+                                // get column type
+                                var column_type = meta[key];
+                                
+                                // column index
+                                var column_index = (parseInt(key) + 1);
+                                
+                                // column type label
+                                var column_label = 'Text';
+                                if (column_type == 'int' || column_type == 'float') {
+                                    column_label = 'Number';
+                                }
+                                
+                                // add to selection
+                                if (column_type == 'int' || column_type == 'float' || !numerical) {
+                                    columns.push({
+                                        'label' : 'Column: ' + column_index + ' [' + column_label + ']',
+                                        'value' : column_index
+                                    });
+                                }
                             }
                             
-                            // add to selection
-                            if (column_type == 'int' || column_type == 'float' || !numerical) {
-                                columns.push({
-                                    'label' : 'Column: ' + column_index + ' [' + column_label + ']',
-                                    'value' : column_index
-                                });
+                            // update field
+                            if (column_field) {
+                                column_field.update(columns);
+                                if (!column_field.exists(column_field.value())) {
+                                    column_field.value(column_field.first());
+                                }
+                                column_field.show();
                             }
                         }
-                        
-                        // update field
-                        if (column_field) {
-                            column_field.update(columns);
-                            if (!column_field.exists(column_field.value())) {
-                                column_field.value(column_field.first());
-                            }
-                        }
-                    }
+                    });
                 }
             });
         },

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/scripts/mvc/tools/tools-select-dataset.js
--- a/static/scripts/mvc/tools/tools-select-dataset.js
+++ b/static/scripts/mvc/tools/tools-select-dataset.js
@@ -40,8 +40,8 @@
         var dataset_options = [];
         for (var i in datasets) {
             dataset_options.push({
-                label: datasets[i].get('name'),
-                value: datasets[i].get('id')
+                label: datasets[i].name,
+                value: datasets[i].id
             });
         }
         
@@ -67,8 +67,8 @@
         var collection_options = [];
         for (var i in collections) {
             collection_options.push({
-                label: collections[i].get('name'),
-                value: collections[i].get('id')
+                label: collections[i].name,
+                value: collections[i].id
             });
         }
         

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/scripts/mvc/ui/ui-select-default.js
--- a/static/scripts/mvc/ui/ui-select-default.js
+++ b/static/scripts/mvc/ui/ui-select-default.js
@@ -124,7 +124,6 @@
     wait: function() {
         this.$icon.removeClass();
         this.$icon.addClass('fa fa-spinner fa-spin');
-        this.$select.hide();
     },
     
     /** Returns true if the field is disabled

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/scripts/packed/mvc/tools/tools-datasets.js
--- a/static/scripts/packed/mvc/tools/tools-datasets.js
+++ b/static/scripts/packed/mvc/tools/tools-datasets.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-contents","utils/utils"],function(b,a){return Backbone.Model.extend({initialize:function(d){this.currHistoryContents=new b.HistoryContents({});this.currHistoryContents.historyId=d.history_id;this.typedict={};var c=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(e){c.typedict=e;var f=c.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");d.success&&d.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request for history datasets failed.")})},error:function(e){console.debug("tools-datasets::initialize() - Ajax request for datatype dictionary failed.")}})},filterType:function(d){d=d||{};var c=this;return this.currHistoryContents.filter(function(f){var g=false;for(var e in d.data_types){if(c._matchType(f.get("data_type"),d.data_types[e])){g=true;break}}return(f.get("history_content_type")===d.content_type||!d.content_type)&&(g||!d.data_types)&&!f.get("deleted")})},filter:function(c){return _.first(this.currHistoryContents.filter(function(d){return d.get("id")===c}))},_matchType:function(c,f){var d=this.typedict.ext_to_class_name[f];if(!d){console.debug("tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var e=this.typedict.class_to_classes[c];if(e[d]){return true}return false}})});
\ No newline at end of file
+define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:galaxy_config.root+"api/histories/"+c.history_id+"/contents?deleted=false",success:function(e){b.summary=e;console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-datasets::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-datasets::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];for(var d in this.summary){var f=this.summary[d];var e=false;for(var d in c.data_types){if(this._matchType(c.data_types[d],f.extension)){e=true;break}}if((f.history_content_type===c.content_type||!c.content_type)&&(e||!c.data_types)){b.push(f)}}return b},getDetails:function(b,c){a.get({url:galaxy_config.root+"api/datasets/"+b,success:function(d){c&&c(d)},error:function(d){console.debug("tools-datasets::getDetails() - Ajax request for dataset failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-datasets::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})});
\ No newline at end of file

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-dataset"],function(d,a,g,c,b){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new a.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_field_conditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(h){var i=this;var j=h.id;return new b.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(l){var v=l.values[0].id;var t=i.app.tree.references(j,"data_column");if(t.length<=0){console.debug("tool-form::field_data() -  Data column parameters unavailable.");return}var o=i.app.datasets.filter(v);var x=null;if(o){console.debug("tool-form::field_data() - Selected dataset "+v+".");x=o.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+v+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+v+".")}for(var p in t){var r=i.app.input_list[t[p]];var s=i.app.field_list[t[p]];if(!r||!s){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=r.numerical;var m=[];for(var w in x){var u=x[w];var k=(parseInt(w)+1);var q="Text";if(u=="int"||u=="float"){q="Number"}if(u=="int"||u=="float"||!n){m.push({label:"Column: "+k+" ["+q+"]",value:k})}}if(s){s.update(m);if(!s.exists(s.value())){s.value(s.first())}}}}})},_field_select:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_field_hidden:function(h){return new g.Hidden({id:"field-"+h.id})},_field_boolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-dataset"],function(d,a,g,c,b){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new a.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_field_conditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(h){var i=this;var j=h.id;return new b.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(o){var n=o.values[0].id;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() -  Data column parameters unavailable.");return}for(var m in l){var k=i.app.field_list[l[m]];k.wait&&k.wait()}i.app.datasets.getDetails(n,function(r){var z=null;if(r){console.debug("tool-form::field_data() - Selected dataset "+n+".");z=r.metadata_column_types;if(!z){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+n+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+n+".")}for(var t in l){var v=i.app.input_list[l[t]];var w=i.app.field_list[l[t]];if(!v||!w){console.debug("tool-form::field_data() - FAILED: Column not found.")}var s=v.numerical;var q=[];for(var y in z){var x=z[y];var p=(parseInt(y)+1);var u="Text";if(x=="int"||x=="float"){u="Number"}if(x=="int"||x=="float"||!s){q.push({label:"Column: "+p+" ["+u+"]",value:p})}}if(w){w.update(q);if(!w.exists(w.value())){w.value(w.first())}w.show()}}})}})},_field_select:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_field_hidden:function(h){return new g.Hidden({id:"field-"+h.id})},_field_boolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/scripts/packed/mvc/tools/tools-select-dataset.js
--- a/static/scripts/packed/mvc/tools/tools-select-dataset.js
+++ b/static/scripts/packed/mvc/tools/tools-select-dataset.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.datasets.filterType({content_type:"dataset",data_types:h.extensions});var k=[];for(var j in l){k.push({label:l[j].get("name"),value:l[j].get("id")})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.datasets.filterType({content_type:"collection",data_types:h.extensions});var f=[];for(var j in m){f.push({label:m[j].get("name"),value:m[j].get("id")})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(){var g=null;switch(this.current){case"hda":g=this.select_datasets;break;case"hdca":g=this.select_collection;break}var j=g.value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.current})}return f},validate:function(){switch(this.current){case"hda":return this.select_datasets.validate();case"hdca":return this.select_collection.validate()}},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}}});return{View:d}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.datasets.filterType({content_type:"dataset",data_types:h.extensions});var k=[];for(var j in l){k.push({label:l[j].name,value:l[j].id})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.datasets.filterType({content_type:"collection",data_types:h.extensions});var f=[];for(var j in m){f.push({label:m[j].name,value:m[j].id})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(){var g=null;switch(this.current){case"hda":g=this.select_datasets;break;case"hdca":g=this.select_collection;break}var j=g.value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.current})}return f},validate:function(){switch(this.current){case"hda":return this.select_datasets.validate();case"hdca":return this.select_collection.validate()}},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}}});return{View:d}});
\ No newline at end of file

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/scripts/packed/mvc/ui/ui-select-default.js
--- a/static/scripts/packed/mvc/ui/ui-select-default.js
+++ b/static/scripts/packed/mvc/ui/ui-select-default.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if(d[c]==="null"){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if(d[c]==="null"){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}});
\ No newline at end of file

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/scripts/utils/utils.js
--- a/static/scripts/utils/utils.js
+++ b/static/scripts/utils/utils.js
@@ -6,12 +6,13 @@
 // dependencies
 define(["libs/underscore"], function(_) {
 
-/* request handler for GET
-    param{string}   url
-    param{function} success
-    param{function} error
-    param{boolean}  cache
-*/
+/**
+ * Request handler for GET
+ * @param{String}   url     - Url request is made to
+ * @param{Function} success - Callback on success
+ * @param{Function} error   - Callback on error
+ * @param{Boolean}  cache   - Use cached data if available
+ */
 function get (options) {
     top.__utils__get__ = top.__utils__get__ || {};
     if (options.cache && top.__utils__get__[options.url]) {
@@ -32,13 +33,14 @@
     }
 };
 
-/* request handler
-    param{string}   method
-    param{string}   url
-    param{object}   data
-    param{function} success
-    param{function} error
-*/
+/**
+ * Request handler
+ * @param{String}   method  - Request method ['GET', 'POST', 'DELETE', 'PUT']
+ * @param{String}   url     - Url request is made to
+ * @param{Object}   data    - Data send to url
+ * @param{Function} success - Callback on success
+ * @param{Function} error   - Callback on error
+ */
 function request (options) {
     // prepare ajax
     var ajaxConfig = {
@@ -79,7 +81,11 @@
     });
 };
 
-// get css value
+/** 
+ * Read a property value from CSS
+ * @param{String}   classname   - CSS class
+ * @param{String}   name        - CSS property
+ */
 function cssGetAttribute (classname, name) {
     // place dummy element
     var el = $('<div class="' + classname + '"></div>');
@@ -97,14 +103,21 @@
     return value;
 };
     
-// load css
+/**
+ * Load a CSS file
+ * @param{String}   url - Url of CSS file
+ */
 function cssLoadFile (url) {
     // check if css is already available
     if (!$('link[href^="' + url + '"]').length)
         $('<link href="' + galaxy_config.root + url + '" rel="stylesheet">').appendTo('head');
 };
 
-// merge
+/**
+ * Safely merge to dictionaries
+ * @param{Object}   options         - Target dictionary
+ * @param{Object}   optionsDefault  - Source dictionary
+ */
 function merge (options, optionsDefault) {
     if (options)
         return _.defaults(options, optionsDefault);
@@ -112,7 +125,11 @@
         return optionsDefault;
 };
 
-// to string
+/**
+ * Format byte size to string with units
+ * @param{Integer}   size           - Size in bytes
+ * @param{Boolean}   normal_font    - Switches font between normal and bold
+ */
 function bytesToString (size, normal_font) {
     // identify unit
     var unit = "";
@@ -132,19 +149,26 @@
     }
 };
 
-// unique ide
+/**
+ * Create a unique id
+ */
 function uuid(){
     return 'x' + Math.random().toString(36).substring(2, 9);
 };
 
-// wrap
+/**
+ * Wrap an dom element into a paragraph
+ * @param{Element}  $el - DOM element to be wrapped
+ */
 function wrap($el) {
     var wrapper = $('<p></p>');
     wrapper.append($el);
     return wrapper;
 };
 
-// time
+/**
+ * Create a time stamp
+ */
 function time() {
     // get date object
     var d = new Date();
@@ -162,7 +186,6 @@
     return datetime;
 };
 
-// return
 return {
     cssLoadFile   : cssLoadFile,
     cssGetAttribute : cssGetAttribute,

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1313,7 +1313,7 @@
 .ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px}
 .ui-radiobutton{width:100%}.ui-radiobutton label{height:23px;line-height:1em}
 .ui-radiobutton i{padding-right:5px}
-.ui-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2}
+.ui-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;background:#f2f2f2;text-align:center;line-height:25px}
 .ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none}
 .ui-select-multiple{height:100% !important;width:100% !important}
 .libraryRow{background-color:#ebd9b2}

diff -r 264079ecc6f0c3fe23b854791e22a181cd8ce11e -r 6aad6ad39a04c8897198f64af0797397a03d112e static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -280,9 +280,9 @@
         height: 100%;
         float: right;
         border-left: 1px solid @border-default-color;
-        padding-left: 9px;
-        padding-top: 4px;
         background: @btn-default-bg;
+        text-align: center;
+        line-height: 25px;
     }
 
     select {

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: guerler: ToolForm: Load history summary and metadata separately, add file extension to history api, fix spinner style for select field

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