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commit/galaxy-central: guerler: ToolForm/Ui: Improve and extend option fields, add dataset/collection selector
by commits-noreply＠bitbucket.org 19 Sep '14
by commits-noreply＠bitbucket.org 19 Sep '14
19 Sep '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/afdd7586c0e6/
Changeset: afdd7586c0e6
User: guerler
Date: 2014-09-19 16:47:17+00:00
Summary: ToolForm/Ui: Improve and extend option fields, add dataset/collection selector
Affected #: 23 files
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 client/galaxy/scripts/mvc/tools/tools-repeat.js
--- a/client/galaxy/scripts/mvc/tools/tools-repeat.js
+++ b/client/galaxy/scripts/mvc/tools/tools-repeat.js
@@ -93,7 +93,7 @@
// append to dom
this.table.add(portlet.$el);
- this.table.prepend('row_' + options.id);
+ this.table.prepend('row_' + options.id, true);
// validate maximum
if (this.options.max > 0 && this.size() >= this.options.max) {
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 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
@@ -411,67 +411,70 @@
// find selected dataset
var dataset = self.app.datasets.filter(value);
+ // meta data
+ var meta = null;
+
// check dataset
if (dataset && column_list.length > 0) {
// log selection
console.debug('tool-form::field_data() - Selected dataset ' + value + '.');
// get meta data
- var meta = dataset.get('metadata_column_types');
+ 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 + '.');
}
-
- // 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;
-
- // 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
- });
- }
- }
-
- // update field
- if (column_field) {
- column_field.update(columns);
- if (!column_field.exists(column_field.value())) {
- column_field.value(column_field.first());
- }
- }
- }
} else {
// log failure
console.debug('tool-form::field_data() - FAILED: Could not find dataset ' + value + '.');
}
+
+ // 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;
+
+ // 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
+ });
+ }
+ }
+
+ // update field
+ if (column_field) {
+ column_field.update(columns);
+ if (!column_field.exists(column_field.value())) {
+ column_field.value(column_field.first());
+ }
+ }
+ }
}
});
},
@@ -495,7 +498,7 @@
SelectClass = Ui.Checkbox;
break;
case 'radio':
- SelectClass = Ui.RadioButton;
+ SelectClass = Ui.Radio;
break;
}
@@ -506,14 +509,6 @@
multiple: input_def.multiple
});
},
-
- // column field
- _field_data_colum : function (input_def) {
- return new Ui.Select.View({
- id : 'field-' + input_def.id,
- multiple: input_def.multiple
- });
- },
// text input field
_field_text : function(input_def) {
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 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
@@ -7,9 +7,20 @@
// link this
var self = this;
- // tabs
- this.tabs = new Tabs.View({
- onchange: function() {
+ // add element
+ this.setElement('<div/>');
+
+ // current selection
+ this.current = 'dataset';
+
+ // create button
+ this.button_new = new Ui.RadioButton.View({
+ value : this.current,
+ data : [ { icon: 'fa-file-o', label : 'Select datasets', value : 'dataset' },
+ { icon: 'fa-files-o', label : 'Select a collection', value : 'collection' }],
+ onchange: function(value) {
+ self.current = value;
+ self.refresh();
self.trigger('change');
}
});
@@ -41,13 +52,6 @@
}
});
- // add tab
- this.tabs.add({
- id : 'datasets',
- title : 'Select datasets',
- $el : this.select_datasets.$el
- });
-
//
// collections
//
@@ -74,15 +78,13 @@
}
});
- // add tab
- this.tabs.add({
- id : 'collection',
- title : 'Select a dataset collection',
- $el : this.select_collection.$el
- });
+ // add elements to dom
+ this.$el.append(Utils.wrap(this.button_new.$el));
+ this.$el.append(this.select_datasets.$el);
+ this.$el.append(this.select_collection.$el);
- // add element
- this.setElement(this.tabs.$el);
+ // refresh view
+ this.refresh();
// add change event. fires on trigger
this.on('change', function() {
@@ -93,10 +95,9 @@
},
// value
- value : function (new_value) {
- var current_tab = this.tabs.current();
- switch(current_tab) {
- case 'datasets':
+ value : function () {
+ switch(this.current) {
+ case 'dataset':
return this.select_datasets.value();
case 'collection':
return this.select_collection.value();
@@ -106,6 +107,20 @@
// render
update: function(options) {
this.select.update(options);
+ },
+
+ // refresh
+ refresh: function() {
+ switch (this.current) {
+ case 'dataset':
+ this.select_datasets.$el.fadeIn();
+ this.select_collection.$el.hide();
+ break;
+ case 'collection':
+ this.select_datasets.$el.hide();
+ this.select_collection.$el.fadeIn();
+ break;
+ }
}
});
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 client/galaxy/scripts/mvc/ui/ui-misc.js
--- a/client/galaxy/scripts/mvc/ui/ui-misc.js
+++ b/client/galaxy/scripts/mvc/ui/ui-misc.js
@@ -437,6 +437,7 @@
Modal : Modal,
RadioButton : Options.RadioButton,
Checkbox : Options.Checkbox,
+ Radio : Options.Radio,
Searchbox : Searchbox,
Select : Select,
Hidden : Hidden,
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 client/galaxy/scripts/mvc/ui/ui-options.js
--- a/client/galaxy/scripts/mvc/ui/ui-options.js
+++ b/client/galaxy/scripts/mvc/ui/ui-options.js
@@ -18,7 +18,15 @@
this.options = Utils.merge(options, this.optionsDefault);
// create new element
- this.setElement(this._template(this.options));
+ this.setElement('<div/>');
+
+ // create elements
+ this.$error = $(this._templateError(options));
+ this.$options = $(this._template(options));
+
+ // append
+ this.$el.append(this.$error);
+ this.$el.append(this.$options);
// hide input field
if (!this.options.visible) {
@@ -50,7 +58,12 @@
// add new options
for (var key in options) {
- this.$el.append(this._templateOption(options[key]));
+ // load option template
+ var $option = $(this._templateOption(options[key]));
+ $option.addClass('ui-option');
+
+ // append to dom
+ this.$options.append($option);
}
// add change events
@@ -99,13 +112,14 @@
// refresh
_refresh: function() {
- // remove placeholder
- this.$el.find('.ui-error').remove();
-
// count remaining options
- var remaining = this.$el.find('input').length;
+ var remaining = this.$el.find('.ui-option').length;
if (remaining == 0) {
- this.$el.append(this._templateEmpty());
+ this.$error.show();
+ this.$options.hide();
+ } else {
+ this.$error.hide();
+ this.$options.css('display', 'inline-block');
}
},
@@ -129,18 +143,16 @@
}
},
- // template for options
- _templateEmpty: function() {
- return '<div class="ui-error">' + this.options.empty + '</div>';
+ _templateError: function(options) {
+ return '<div class="ui-error" style="display: none;">' + options.empty + '</div>';
}
});
-/** checkbox options field **/
-var Checkbox = {};
-Checkbox.View = OptionsBase.extend({
+/** radio button field **/
+var Radio = {};
+Radio.View = OptionsBase.extend({
// initialize
initialize: function(options) {
- options.multiple = true;
OptionsBase.prototype.initialize.call(this, options);
},
@@ -168,18 +180,35 @@
// template for options
_templateOption: function(pair) {
- return '<div class="ui-option">' +
- '<input type="checkbox" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
+ return '<div>' +
+ '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
'</div>';
},
// template
_template: function() {
- return '<div class="ui-checkbox"/>';
+ return '<div class="ui-options"/>';
}
});
-/** radio button options field **/
+/** checkbox options field **/
+var Checkbox = {};
+Checkbox.View = Radio.View.extend({
+ // initialize
+ initialize: function(options) {
+ options.multiple = true;
+ Radio.View.prototype.initialize.call(this, options);
+ },
+
+ // template for options
+ _templateOption: function(pair) {
+ return '<div>' +
+ '<input type="checkbox" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
+ '</div>';
+ }
+});
+
+/** radio button options field styled as classic buttons **/
var RadioButton = {};
RadioButton.View = OptionsBase.extend({
// initialize
@@ -202,9 +231,13 @@
// template for options
_templateOption: function(pair) {
- return '<label class="ui-option btn btn-default">' +
- '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '">' + pair.label +
- '</label>';
+ var tmpl = '<label class="btn btn-default">';
+ if (pair.icon) {
+ tmpl += '<i class="fa ' + pair.icon + '"/>';
+ }
+ tmpl += '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '">' + pair.label +
+ '</label>';
+ return tmpl;
},
// template
@@ -214,8 +247,9 @@
});
return {
- Checkbox : Checkbox,
- RadioButton : RadioButton
+ Radio : Radio,
+ RadioButton : RadioButton,
+ Checkbox : Checkbox
};
});
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 client/galaxy/scripts/mvc/ui/ui-table.js
--- a/client/galaxy/scripts/mvc/ui/ui-table.js
+++ b/client/galaxy/scripts/mvc/ui/ui-table.js
@@ -77,13 +77,13 @@
},
// append
- append: function(id) {
- this._commit(id);
+ append: function(id, fade) {
+ this._commit(id, fade, false);
},
// prepend
- prepend: function(id) {
- this._commit(id, true);
+ prepend: function(id, fade) {
+ this._commit(id, fade, true);
},
// get element
@@ -142,13 +142,13 @@
},
// commit
- _commit: function(id, prepend) {
+ _commit: function(id, fade, prepend) {
// remove previous item with same id
this.del(id);
// add
this.row.attr('id', id);
-
+
// add row
if (prepend) {
this.$tbody.prepend(this.row);
@@ -156,6 +156,12 @@
this.$tbody.append(this.row);
}
+ // fade mode
+ if (fade) {
+ this.row.hide();
+ this.row.fadeIn();
+ }
+
// row
this.row = this._row();
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 config/plugins/visualizations/charts/static/app.css
--- a/config/plugins/visualizations/charts/static/app.css
+++ b/config/plugins/visualizations/charts/static/app.css
@@ -48,6 +48,7 @@
.charts-grid .header {
font-size: 0.9em;
font-weight: bold;
+ padding-bottom: 10px;
}
.charts-viewport {
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$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",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("mvc/ui/ui-checkbox",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="ui-checkbox">';for(key in e.data){var n=e.data[key];t+='<input type="checkbox" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"<br>"}return t+="</div>",t}});return{View:t}}),define("mvc/ui/ui-radiobutton",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{View:t}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r,Checkbox:n,Searchbox:p,Select:t,Textarea:v}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="'+e.cls+'">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3 class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-title-text" class="portlet-title-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1,multiple:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.options.multiple?(this.$select.prop("multiple",!0),this.$select.addClass("ui-select-multiple"),this.$icon.remove()):this.$el.addClass("ui-select"),this.update(this.options.data),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&this.$select.val(e),this.$select.val()},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},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.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:1,max:100,step:1},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$slider=this.$el.find("#slider"),this.$text=this.$el.find("#text"),this.$slider.slider(this.options),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==13||t==8||t==37||t==39||t==189||t>=48&&t<=57||n.options.step!=1&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()}),this.$slider.on("slide",function(e,t){n.value(t.value)})},value:function(e){return e!==undefined&&(e=Math.max(Math.min(e,this.options.max),this.options.min),this.options.onchange&&this.options.onchange(e),this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),empty:"No data available"},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$error=$(this._templateError(t)),this.$options=$(this._template(t)),this.$el.append(this.$error),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){var e=this.$el.find(".ui-option").length;e==0?(this.$error.show(),this.$options.hide()):(this.$error.hide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return null;if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_templateError:function(e){return'<div class="ui-error" style="display: none;">'+e.empty+"</div>"}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",query_limit:1e3,library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/library/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})});
\ No newline at end of file
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 config/plugins/visualizations/charts/static/views/types.js
--- a/config/plugins/visualizations/charts/static/views/types.js
+++ b/config/plugins/visualizations/charts/static/views/types.js
@@ -133,10 +133,10 @@
var $el = $('<div style="clear: both;"/>')
// add header label
- $el.append(Utils.wrap(this._template_header({
+ $el.append(this._template_header({
id : 'types-header-' + this.categories_index[category],
title : category
- })));
+ }));
// add chart types
for (var id in this.categories[category]) {
@@ -150,15 +150,15 @@
}
// append type to screen
- $el.append(Utils.wrap(this._template_item({
+ $el.append(this._template_item({
id : id,
title : title,
url : config.app_root + 'charts/' + this.app.chartPath(id) + '/logo.png'
- })));
+ }));
}
// add to view
- this.$el.append(Utils.wrap($el));
+ this.$el.append($el);
}
},
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/mvc/tools/tools-repeat.js
--- a/static/scripts/mvc/tools/tools-repeat.js
+++ b/static/scripts/mvc/tools/tools-repeat.js
@@ -93,7 +93,7 @@
// append to dom
this.table.add(portlet.$el);
- this.table.prepend('row_' + options.id);
+ this.table.prepend('row_' + options.id, true);
// validate maximum
if (this.options.max > 0 && this.size() >= this.options.max) {
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -411,67 +411,70 @@
// find selected dataset
var dataset = self.app.datasets.filter(value);
+ // meta data
+ var meta = null;
+
// check dataset
if (dataset && column_list.length > 0) {
// log selection
console.debug('tool-form::field_data() - Selected dataset ' + value + '.');
// get meta data
- var meta = dataset.get('metadata_column_types');
+ 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 + '.');
}
-
- // 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;
-
- // 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
- });
- }
- }
-
- // update field
- if (column_field) {
- column_field.update(columns);
- if (!column_field.exists(column_field.value())) {
- column_field.value(column_field.first());
- }
- }
- }
} else {
// log failure
console.debug('tool-form::field_data() - FAILED: Could not find dataset ' + value + '.');
}
+
+ // 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;
+
+ // 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
+ });
+ }
+ }
+
+ // update field
+ if (column_field) {
+ column_field.update(columns);
+ if (!column_field.exists(column_field.value())) {
+ column_field.value(column_field.first());
+ }
+ }
+ }
}
});
},
@@ -495,7 +498,7 @@
SelectClass = Ui.Checkbox;
break;
case 'radio':
- SelectClass = Ui.RadioButton;
+ SelectClass = Ui.Radio;
break;
}
@@ -506,14 +509,6 @@
multiple: input_def.multiple
});
},
-
- // column field
- _field_data_colum : function (input_def) {
- return new Ui.Select.View({
- id : 'field-' + input_def.id,
- multiple: input_def.multiple
- });
- },
// text input field
_field_text : function(input_def) {
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 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
@@ -7,9 +7,20 @@
// link this
var self = this;
- // tabs
- this.tabs = new Tabs.View({
- onchange: function() {
+ // add element
+ this.setElement('<div/>');
+
+ // current selection
+ this.current = 'dataset';
+
+ // create button
+ this.button_new = new Ui.RadioButton.View({
+ value : this.current,
+ data : [ { icon: 'fa-file-o', label : 'Select datasets', value : 'dataset' },
+ { icon: 'fa-files-o', label : 'Select a collection', value : 'collection' }],
+ onchange: function(value) {
+ self.current = value;
+ self.refresh();
self.trigger('change');
}
});
@@ -41,13 +52,6 @@
}
});
- // add tab
- this.tabs.add({
- id : 'datasets',
- title : 'Select datasets',
- $el : this.select_datasets.$el
- });
-
//
// collections
//
@@ -74,15 +78,13 @@
}
});
- // add tab
- this.tabs.add({
- id : 'collection',
- title : 'Select a dataset collection',
- $el : this.select_collection.$el
- });
+ // add elements to dom
+ this.$el.append(Utils.wrap(this.button_new.$el));
+ this.$el.append(this.select_datasets.$el);
+ this.$el.append(this.select_collection.$el);
- // add element
- this.setElement(this.tabs.$el);
+ // refresh view
+ this.refresh();
// add change event. fires on trigger
this.on('change', function() {
@@ -93,10 +95,9 @@
},
// value
- value : function (new_value) {
- var current_tab = this.tabs.current();
- switch(current_tab) {
- case 'datasets':
+ value : function () {
+ switch(this.current) {
+ case 'dataset':
return this.select_datasets.value();
case 'collection':
return this.select_collection.value();
@@ -106,6 +107,20 @@
// render
update: function(options) {
this.select.update(options);
+ },
+
+ // refresh
+ refresh: function() {
+ switch (this.current) {
+ case 'dataset':
+ this.select_datasets.$el.fadeIn();
+ this.select_collection.$el.hide();
+ break;
+ case 'collection':
+ this.select_datasets.$el.hide();
+ this.select_collection.$el.fadeIn();
+ break;
+ }
}
});
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/mvc/ui/ui-misc.js
--- a/static/scripts/mvc/ui/ui-misc.js
+++ b/static/scripts/mvc/ui/ui-misc.js
@@ -437,6 +437,7 @@
Modal : Modal,
RadioButton : Options.RadioButton,
Checkbox : Options.Checkbox,
+ Radio : Options.Radio,
Searchbox : Searchbox,
Select : Select,
Hidden : Hidden,
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/mvc/ui/ui-options.js
--- a/static/scripts/mvc/ui/ui-options.js
+++ b/static/scripts/mvc/ui/ui-options.js
@@ -18,7 +18,15 @@
this.options = Utils.merge(options, this.optionsDefault);
// create new element
- this.setElement(this._template(this.options));
+ this.setElement('<div/>');
+
+ // create elements
+ this.$error = $(this._templateError(options));
+ this.$options = $(this._template(options));
+
+ // append
+ this.$el.append(this.$error);
+ this.$el.append(this.$options);
// hide input field
if (!this.options.visible) {
@@ -50,7 +58,12 @@
// add new options
for (var key in options) {
- this.$el.append(this._templateOption(options[key]));
+ // load option template
+ var $option = $(this._templateOption(options[key]));
+ $option.addClass('ui-option');
+
+ // append to dom
+ this.$options.append($option);
}
// add change events
@@ -99,13 +112,14 @@
// refresh
_refresh: function() {
- // remove placeholder
- this.$el.find('.ui-error').remove();
-
// count remaining options
- var remaining = this.$el.find('input').length;
+ var remaining = this.$el.find('.ui-option').length;
if (remaining == 0) {
- this.$el.append(this._templateEmpty());
+ this.$error.show();
+ this.$options.hide();
+ } else {
+ this.$error.hide();
+ this.$options.css('display', 'inline-block');
}
},
@@ -129,18 +143,16 @@
}
},
- // template for options
- _templateEmpty: function() {
- return '<div class="ui-error">' + this.options.empty + '</div>';
+ _templateError: function(options) {
+ return '<div class="ui-error" style="display: none;">' + options.empty + '</div>';
}
});
-/** checkbox options field **/
-var Checkbox = {};
-Checkbox.View = OptionsBase.extend({
+/** radio button field **/
+var Radio = {};
+Radio.View = OptionsBase.extend({
// initialize
initialize: function(options) {
- options.multiple = true;
OptionsBase.prototype.initialize.call(this, options);
},
@@ -168,18 +180,35 @@
// template for options
_templateOption: function(pair) {
- return '<div class="ui-option">' +
- '<input type="checkbox" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
+ return '<div>' +
+ '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
'</div>';
},
// template
_template: function() {
- return '<div class="ui-checkbox"/>';
+ return '<div class="ui-options"/>';
}
});
-/** radio button options field **/
+/** checkbox options field **/
+var Checkbox = {};
+Checkbox.View = Radio.View.extend({
+ // initialize
+ initialize: function(options) {
+ options.multiple = true;
+ Radio.View.prototype.initialize.call(this, options);
+ },
+
+ // template for options
+ _templateOption: function(pair) {
+ return '<div>' +
+ '<input type="checkbox" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
+ '</div>';
+ }
+});
+
+/** radio button options field styled as classic buttons **/
var RadioButton = {};
RadioButton.View = OptionsBase.extend({
// initialize
@@ -202,9 +231,13 @@
// template for options
_templateOption: function(pair) {
- return '<label class="ui-option btn btn-default">' +
- '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '">' + pair.label +
- '</label>';
+ var tmpl = '<label class="btn btn-default">';
+ if (pair.icon) {
+ tmpl += '<i class="fa ' + pair.icon + '"/>';
+ }
+ tmpl += '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '">' + pair.label +
+ '</label>';
+ return tmpl;
},
// template
@@ -214,8 +247,9 @@
});
return {
- Checkbox : Checkbox,
- RadioButton : RadioButton
+ Radio : Radio,
+ RadioButton : RadioButton,
+ Checkbox : Checkbox
};
});
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/mvc/ui/ui-table.js
--- a/static/scripts/mvc/ui/ui-table.js
+++ b/static/scripts/mvc/ui/ui-table.js
@@ -77,13 +77,13 @@
},
// append
- append: function(id) {
- this._commit(id);
+ append: function(id, fade) {
+ this._commit(id, fade, false);
},
// prepend
- prepend: function(id) {
- this._commit(id, true);
+ prepend: function(id, fade) {
+ this._commit(id, fade, true);
},
// get element
@@ -142,13 +142,13 @@
},
// commit
- _commit: function(id, prepend) {
+ _commit: function(id, fade, prepend) {
// remove previous item with same id
this.del(id);
// add
this.row.attr('id', id);
-
+
// add row
if (prepend) {
this.$tbody.prepend(this.row);
@@ -156,6 +156,12 @@
this.$tbody.append(this.row);
}
+ // fade mode
+ if (fade) {
+ this.row.hide();
+ this.row.fadeIn();
+ }
+
// row
this.row = this._row();
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/packed/mvc/tools/tools-repeat.js
--- a/static/scripts/packed/mvc/tools/tools-repeat.js
+++ b/static/scripts/packed/mvc/tools/tools-repeat.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(c,a,b,e){var d=Backbone.View.extend({optionsDefault:{max:null},initialize:function(g){this.options=c.merge(g,this.optionsDefault);this.setElement("<div/>");var f=this;this.button_new=new e.ButtonIcon({icon:"fa-plus",title:"Insert "+g.title_new,tooltip:"Add new "+g.title_new+" block",floating:"clear",onclick:function(){if(g.onnew){g.onnew()}}});this.table=new a.View({cls:"ui-table-plain",content:""});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.table.$el);this.list={}},size:function(){return _.size(this.list)},add:function(g){var f=new e.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){if(g.ondel){g.ondel()}}});var h=new b.View({id:g.id,title:"<b>"+g.title+"</b>",cls:"ui-portlet-repeat",operations:{button_delete:f}});if(!g.ondel){f.remove()}h.append(g.$el);h.$el.addClass("section-row");this.list[g.id]=h;this.table.add(h.$el);this.table.prepend("row_"+g.id);if(this.options.max>0&&this.size()>=this.options.max){this.button_new.disable()}},del:function(g){if(this.list[g]){var f=this.table.get("row_"+g);f.remove();delete this.list[g];this.button_new.enable()}},retitle:function(g){var f=0;for(var h in this.list){this.list[h].title(++f+": "+g)}}});return{View:d}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(c,a,b,e){var d=Backbone.View.extend({optionsDefault:{max:null},initialize:function(g){this.options=c.merge(g,this.optionsDefault);this.setElement("<div/>");var f=this;this.button_new=new e.ButtonIcon({icon:"fa-plus",title:"Insert "+g.title_new,tooltip:"Add new "+g.title_new+" block",floating:"clear",onclick:function(){if(g.onnew){g.onnew()}}});this.table=new a.View({cls:"ui-table-plain",content:""});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.table.$el);this.list={}},size:function(){return _.size(this.list)},add:function(g){var f=new e.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){if(g.ondel){g.ondel()}}});var h=new b.View({id:g.id,title:"<b>"+g.title+"</b>",cls:"ui-portlet-repeat",operations:{button_delete:f}});if(!g.ondel){f.remove()}h.append(g.$el);h.$el.addClass("section-row");this.list[g.id]=h;this.table.add(h.$el);this.table.prepend("row_"+g.id,true);if(this.options.max>0&&this.size()>=this.options.max){this.button_new.disable()}},del:function(g){if(this.list[g]){var f=this.table.get("row_"+g);f.remove();delete this.list[g];this.button_new.enable()}},retitle:function(g){var f=0;for(var h in this.list){this.list[h].title(++f+": "+g)}}});return{View:d}});
\ No newline at end of file
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-dataset"],function(d,a,g,c,b){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn()},reset:function(){this.$el.find(".ui-table-form-error").hide()},_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.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$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(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_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.RadioButton;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_data_colum:function(h){return new g.Select.View({id:"field-"+h.id,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){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||0,max:h.max||1000,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()},reset:function(){this.$el.find(".ui-table-form-error").hide()},_template:function(h){var i=$('<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 m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$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-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el});n.$el.addClass("ui-table-form-section");this.table.add(n.$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(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);var w=null;if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.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){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||0,max:h.max||1000,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 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 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"],function(b,d,a){var c=Backbone.View.extend({initialize:function(m,g){var f=this;this.tabs=new a.View({onchange:function(){f.trigger("change")}});var k=m.datasets.filterType({content_type:"dataset",data_types:g.extensions});var j=[];for(var h in k){j.push({label:k[h].get("name"),value:k[h].get("id")})}this.select_datasets=new d.Select.View({multiple:true,data:j,value:j[0]&&j[0].value,onchange:function(){f.trigger("change")}});this.tabs.add({id:"datasets",title:"Select datasets",$el:this.select_datasets.$el});var l=m.datasets.filterType({content_type:"collection",data_types:g.extensions});var e=[];for(var h in l){e.push({label:l[h].get("name"),value:l[h].get("id")})}this.select_collection=new d.Select.View({data:e,value:e[0]&&e[0].value,onchange:function(){f.trigger("change")}});this.tabs.add({id:"collection",title:"Select a dataset collection",$el:this.select_collection.$el});this.setElement(this.tabs.$el);this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},value:function(e){var f=this.tabs.current();switch(f){case"datasets":return this.select_datasets.value();case"collection":return this.select_collection.value()}},update:function(e){this.select.update(e)}});return{View:c}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(b,d,a){var c=Backbone.View.extend({initialize:function(m,g){var f=this;this.setElement("<div/>");this.current="dataset";this.button_new=new d.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"dataset"},{icon:"fa-files-o",label:"Select a collection",value:"collection"}],onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});var k=m.datasets.filterType({content_type:"dataset",data_types:g.extensions});var j=[];for(var h in k){j.push({label:k[h].get("name"),value:k[h].get("id")})}this.select_datasets=new d.Select.View({multiple:true,data:j,value:j[0]&&j[0].value,onchange:function(){f.trigger("change")}});var l=m.datasets.filterType({content_type:"collection",data_types:g.extensions});var e=[];for(var h in l){e.push({label:l[h].get("name"),value:l[h].get("id")})}this.select_collection=new d.Select.View({data:e,value:e[0]&&e[0].value,onchange:function(){f.trigger("change")}});this.$el.append(b.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},value:function(){switch(this.current){case"dataset":return this.select_datasets.value();case"collection":return this.select_collection.value()}},update:function(e){this.select.update(e)},refresh:function(){switch(this.current){case"dataset":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"collection":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}}});return{View:c}});
\ No newline at end of file
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/packed/mvc/ui/ui-misc.js
--- a/static/scripts/packed/mvc/ui/ui-misc.js
+++ b/static/scripts/packed/mvc/ui/ui-misc.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,n,p,l){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'<label class="ui-label '+q.cls+'">'+q.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/> '+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(q.onclick){q.onclick()}});$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='<button id="'+q.id+'" type="submit" style="float: '+q.floating+';" type="button" class="ui-button '+q.cls+'">';if(q.icon){r+='<i class="icon fa '+q.icon+'"></i> '}r+=q.title+"</button>";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var q=this;$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick&&!q.disabled){r.onclick()}});$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="'+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/> <span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'<div><a href="javascript:void(0)" class="ui-anchor '+q.cls+'">'+q.title+"</a></div>"}});var m=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=k.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){if(q.area){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'"></textarea>'}else{return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}}});var o=Backbone.View.extend({optionsDefault:{value:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<hidden id="'+q.id+'" value="'+q.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:i,Label:j,Message:m,Modal:l,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Searchbox:a,Select:b,Hidden:o,Slider:e}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,n,p,l){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'<label class="ui-label '+q.cls+'">'+q.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/> '+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(q.onclick){q.onclick()}});$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='<button id="'+q.id+'" type="submit" style="float: '+q.floating+';" type="button" class="ui-button '+q.cls+'">';if(q.icon){r+='<i class="icon fa '+q.icon+'"></i> '}r+=q.title+"</button>";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var q=this;$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick&&!q.disabled){r.onclick()}});$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="'+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/> <span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'<div><a href="javascript:void(0)" class="ui-anchor '+q.cls+'">'+q.title+"</a></div>"}});var m=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=k.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){if(q.area){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'"></textarea>'}else{return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}}});var o=Backbone.View.extend({optionsDefault:{value:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<hidden id="'+q.id+'" value="'+q.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:i,Label:j,Message:m,Modal:l,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Searchbox:a,Select:b,Hidden:o,Slider:e}});
\ No newline at end of file
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/packed/mvc/ui/ui-options.js
--- a/static/scripts/packed/mvc/ui/ui-options.js
+++ b/static/scripts/packed/mvc/ui/ui-options.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(f){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(f,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var e=this;this.on("change",function(){e._change()})},update:function(f){var h=this._getValue();this.$el.find(".ui-option").remove();for(var g in f){this.$el.append(this._templateOption(f[g]))}var e=this;this.$el.find("input").on("change",function(){e.value(e._getValue());e._change()});this._refresh();this.value(h)},exists:function(f){if(typeof f==="string"){f=[f]}for(var e in f){if(this.$el.find('input[value="'+f[e]+'"]').length>0){return true}}return false},first:function(){var e=this.$el.find("input");if(e.length>0){return e.val()}else{return undefined}},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){this.$el.find(".ui-error").remove();var e=this.$el.find("input").length;if(e==0){this.$el.append(this._templateEmpty())}},_getValue:function(){var f=this.$el.find(":checked");if(f.length==0){return null}if(this.options.multiple){var e=[];f.each(function(){e.push($(this).val())});return e}else{return f.val()}},_templateEmpty:function(){return'<div class="ui-error">'+this.options.empty+"</div>"}});var c={};c.View=a.extend({initialize:function(e){e.multiple=true;a.prototype.initialize.call(this,e)},value:function(e){if(typeof e==="string"){e=[e]}if(e!==undefined){this.$el.find("input").prop("checked",false);for(var f in e){this.$el.find("input[value="+e[f]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(e){return'<div class="ui-option"><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br></div>"},_template:function(){return'<div class="ui-checkbox"/>'}});var d={};d.View=a.extend({initialize:function(e){a.prototype.initialize.call(this,e)},value:function(e){if(e!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+e+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(e){return'<label class="ui-option btn btn-default"><input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>"},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Checkbox:c,RadioButton:d}});
\ No newline at end of file
+define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$error=$(this._templateError(g));this.$options=$(this._template(g));this.$el.append(this.$error);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){var f=this.$el.find(".ui-option").length;if(f==0){this.$error.show();this.$options.hide()}else{this.$error.hide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return null}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_templateError:function(f){return'<div class="ui-error" style="display: none;">'+f.empty+"</div>"}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}});
\ No newline at end of file
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/scripts/packed/mvc/ui/ui-table.js
--- a/static/scripts/packed/mvc/ui/ui-table.js
+++ b/static/scripts/packed/mvc/ui/ui-table.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(c){this.options=a.merge(c,this.optionsDefault);var d=$(this._template(this.options));this.$thead=d.find("thead");this.$tbody=d.find("tbody");this.$tmessage=d.find("tmessage");this.setElement(d);this.row=this._row()},addHeader:function(c){var d=$("<th></th>");d.append(c);this.row.append(d)},appendHeader:function(){this.$thead.append(this.row);this.row=$("<tr></tr>")},add:function(c,d,f){var e=$("<td></td>");if(d){e.css("width",d)}if(f){e.css("text-align",f)}e.append(c);this.row.append(e)},append:function(c){this._commit(c)},prepend:function(c){this._commit(c,true)},get:function(c){return this.$el.find("#"+c)},del:function(d){var c=this.$tbody.find("#"+d);if(c.length>0){c.remove();this.row_count--;this._refresh()}},delAll:function(){this.$tbody.empty();this.row_count=0;this._refresh()},value:function(c){this.before=this.$tbody.find(".current").attr("id");if(c!==undefined){this.$tbody.find("tr").removeClass("current");if(c){this.$tbody.find("#"+c).addClass("current")}}var d=this.$tbody.find(".current").attr("id");if(d===undefined){return null}else{if(d!=this.before&&this.options.onchange){this.options.onchange(c)}return d}},size:function(){return this.$tbody.find("tr").length},_commit:function(d,c){this.del(d);this.row.attr("id",d);if(c){this.$tbody.prepend(this.row)}else{this.$tbody.append(this.row)}this.row=this._row();this.row_count++;this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(f){var c=this.value();var d=$(f.target).closest("tr").attr("id");if(d!=""){if(d&&c!=d){if(this.options.onconfirm){this.options.onconfirm(d)}else{this.value(d)}}}},_ondblclick:function(d){var c=this.value();if(c&&this.options.ondblclick){this.options.ondblclick(c)}},_refresh:function(){if(this.row_count==0){this.$tmessage.show()}else{this.$tmessage.hide()}},_template:function(c){return'<div><table class="'+c.cls+'"><thead></thead><tbody></tbody></table><tmessage>'+c.content+"</tmessage><div>"}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(c){this.options=a.merge(c,this.optionsDefault);var d=$(this._template(this.options));this.$thead=d.find("thead");this.$tbody=d.find("tbody");this.$tmessage=d.find("tmessage");this.setElement(d);this.row=this._row()},addHeader:function(c){var d=$("<th></th>");d.append(c);this.row.append(d)},appendHeader:function(){this.$thead.append(this.row);this.row=$("<tr></tr>")},add:function(c,d,f){var e=$("<td></td>");if(d){e.css("width",d)}if(f){e.css("text-align",f)}e.append(c);this.row.append(e)},append:function(d,c){this._commit(d,c,false)},prepend:function(d,c){this._commit(d,c,true)},get:function(c){return this.$el.find("#"+c)},del:function(d){var c=this.$tbody.find("#"+d);if(c.length>0){c.remove();this.row_count--;this._refresh()}},delAll:function(){this.$tbody.empty();this.row_count=0;this._refresh()},value:function(c){this.before=this.$tbody.find(".current").attr("id");if(c!==undefined){this.$tbody.find("tr").removeClass("current");if(c){this.$tbody.find("#"+c).addClass("current")}}var d=this.$tbody.find(".current").attr("id");if(d===undefined){return null}else{if(d!=this.before&&this.options.onchange){this.options.onchange(c)}return d}},size:function(){return this.$tbody.find("tr").length},_commit:function(e,d,c){this.del(e);this.row.attr("id",e);if(c){this.$tbody.prepend(this.row)}else{this.$tbody.append(this.row)}if(d){this.row.hide();this.row.fadeIn()}this.row=this._row();this.row_count++;this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(f){var c=this.value();var d=$(f.target).closest("tr").attr("id");if(d!=""){if(d&&c!=d){if(this.options.onconfirm){this.options.onconfirm(d)}else{this.value(d)}}}},_ondblclick:function(d){var c=this.value();if(c&&this.options.ondblclick){this.options.ondblclick(c)}},_refresh:function(){if(this.row_count==0){this.$tmessage.show()}else{this.$tmessage.hide()}},_template:function(c){return'<div><table class="'+c.cls+'"><thead></thead><tbody></tbody></table><tmessage>'+c.content+"</tmessage><div>"}});return{View:b}});
\ No newline at end of file
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -148,7 +148,7 @@
.form-control::-moz-placeholder{color:#999}
.form-control:-ms-input-placeholder{color:#999}
.form-control::-webkit-input-placeholder{color:#999}
-.form-control,.ui-checkbox,.ui-form-slider .ui-form-slider-text,.ui-input,.ui-textarea{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)}
+.form-control,.ui-options,.ui-form-slider .ui-form-slider-text,.ui-input,.ui-textarea{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)}
.form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee}
textarea.form-control{height:auto}
.form-group{margin-bottom:15px}
@@ -1279,11 +1279,12 @@
.upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop}
.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-repeat{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;}
.ui-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px}
-.ui-checkbox{height:100% !important}
+.ui-options{height:100% !important}
.ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px}
.ui-form-slider .ui-form-slider-text{width:100px;float:left}
.ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px}
-.ui-radiobutton label{height:23px;line-height:1em}
+.ui-radiobutton{width:100%}.ui-radiobutton label{height:23px;line-height:1em}
+.ui-radiobutton i{padding-right:5px}
.ui-table tbody{cursor:pointer}
.ui-table-plain tbody td{padding:5px 0px 5px 0px !important;border:none !important}
.ui-table-plain tbody{cursor:auto !important}
diff -r 4a3b213b261c391119c46bbfd0123fdde494a28e -r afdd7586c0e66d84c2da3401b1b1c1fc79a48cc7 static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -12,7 +12,7 @@
padding: 5px;
}
-.ui-checkbox {
+.ui-options {
&:extend(.form-control);
height: 100% !important;
}
@@ -40,10 +40,15 @@
}
.ui-radiobutton {
+ width: 100%;
label {
height: 23px;
line-height: 1em;
}
+
+ i {
+ padding-right: 5px;
+ }
}
.ui-table {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: davebgx: Fix page title on tool shed categories page, as pointed out by Greg.
by commits-noreply＠bitbucket.org 19 Sep '14
by commits-noreply＠bitbucket.org 19 Sep '14
19 Sep '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4a3b213b261c/
Changeset: 4a3b213b261c
User: davebgx
Date: 2014-09-19 14:11:21+00:00
Summary: Fix page title on tool shed categories page, as pointed out by Greg.
Affected #: 1 file
diff -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa -r 4a3b213b261c391119c46bbfd0123fdde494a28e lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -123,7 +123,7 @@
**kwd ) )
title = trans.app.repository_grid_filter_manager.get_grid_title( trans,
trailing_string='by Category',
- default='Categories' )
+ default='Repositories' )
self.category_grid.title = title
return self.category_grid( trans, **kwd )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/cda6be2edfe6/
Changeset: cda6be2edfe6
User: guerler
Date: 2014-09-18 18:57:46+00:00
Summary: Ui: Fix option fields
Affected #: 10 files
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d 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
@@ -25,12 +25,8 @@
// template
_template: function(options) {
- var $input;
- if (options.highlight) {
- $input = $('<div class="ui-table-element ui-table-form-section"/>');
- } else {
- $input = $('<div class="ui-table-element"/>');
- }
+ // create table element
+ var $input = $('<div class="ui-table-element"/>');
// add error
$input.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');
@@ -226,10 +222,12 @@
var input_element = new InputElement({
label : input_def.title,
help : input_def.help,
- $el : repeat.$el,
- highlight : true
+ $el : repeat.$el
});
+ // displays as grouped subsection
+ input_element.$el.addClass('ui-table-form-section');
+
// create table row
this.table.add(input_element.$el);
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d client/galaxy/scripts/mvc/ui/ui-checkbox.js
--- a/client/galaxy/scripts/mvc/ui/ui-checkbox.js
+++ /dev/null
@@ -1,91 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// plugin
-var View = Backbone.View.extend({
- // options
- optionsDefault: {
- value : '',
- visible : true,
- cls : '',
- data : [],
- id : Utils.uuid()
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // hide input field
- if (!this.options.visible) {
- this.$el.hide();
- }
-
- // set initial value
- if (this.options.value) {
- this.value(this.options.value);
- }
-
- // current value
- this.current = this.options.value;
-
- // onchange event handler. fires on user activity.
- var self = this;
- this.$el.find('input').on('change', function() {
- self.value(self._getValue());
- });
- },
-
- // value
- value : function (new_val) {
- // get current value
- var before = this.current;
-
- // set new value
- if (new_val !== undefined) {
- this.$el.find('label').removeClass('active');
- this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
- this.current = new_val;
- }
-
- // check value
- var after = this.current;
- if (after != before && this.options.onchange) {
- this.options.onchange(this.current);
- }
-
- // get and return value
- return this.current;
- },
-
- // get value
- _getValue: function() {
- var selected = this.$el.find(':checked');
- var value = null;
- if (selected.length > 0) {
- value = selected.val();
- }
- return value;
- },
-
- // element
- _template: function(options) {
- var tmpl = '<div class="ui-checkbox">';
- for (key in options.data) {
- var pair = options.data[key];
- tmpl += '<input type="checkbox" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + '<br>';
- }
- tmpl += '</div>';
- return tmpl;
- }
-});
-
-return {
- View : View
-};
-
-});
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d client/galaxy/scripts/mvc/ui/ui-options.js
--- /dev/null
+++ b/client/galaxy/scripts/mvc/ui/ui-options.js
@@ -0,0 +1,221 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+/** base class for options based ui elements **/
+var OptionsBase = Backbone.View.extend({
+ // initialize
+ initialize: function(options) {
+ // options
+ this.optionsDefault = {
+ value : [],
+ visible : true,
+ data : [],
+ id : Utils.uuid(),
+ empty : 'No data available'
+ };
+
+ // configure options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // create new element
+ this.setElement(this._template(this.options));
+
+ // hide input field
+ if (!this.options.visible) {
+ this.$el.hide();
+ }
+
+ // initialize data
+ this.update(this.options.data);
+
+ // set initial value
+ if (this.options.value) {
+ this.value(this.options.value);
+ }
+
+ // add change event. fires on trigger
+ var self = this;
+ this.on('change', function() {
+ self._change();
+ });
+ },
+
+ // update options
+ update: function(options) {
+ // backup current value
+ var current = this._getValue();
+
+ // remove all options
+ this.$el.find('.ui-option').remove();
+
+ // add new options
+ for (var key in options) {
+ this.$el.append(this._templateOption(options[key]));
+ }
+
+ // add change events
+ var self = this;
+ this.$el.find('input').on('change', function() {
+ self.value(self._getValue());
+ self._change();
+ });
+
+ // refresh
+ this._refresh();
+
+ // set previous value
+ this.value(current);
+ },
+
+ // check if selected value exists (or any if multiple)
+ exists: function(value) {
+ if (typeof value === 'string') {
+ value = [value];
+ }
+ for (var i in value) {
+ if (this.$el.find('input[value="' + value[i] + '"]').length > 0) {
+ return true;
+ }
+ }
+ return false;
+ },
+
+ // first
+ first: function() {
+ var options = this.$el.find('input');
+ if (options.length > 0) {
+ return options.val();
+ } else {
+ return undefined;
+ }
+ },
+
+ // change
+ _change: function() {
+ if (this.options.onchange) {
+ this.options.onchange(this._getValue());
+ }
+ },
+
+ // refresh
+ _refresh: function() {
+ // remove placeholder
+ this.$el.find('.ui-error').remove();
+
+ // count remaining options
+ var remaining = this.$el.find('input').length;
+ if (remaining == 0) {
+ this.$el.append(this._templateEmpty());
+ }
+ },
+
+ // get value
+ _getValue: function() {
+ // get selected values
+ var selected = this.$el.find(':checked');
+ if (selected.length == 0) {
+ return null;
+ }
+
+ // return multiple or single value
+ if (this.options.multiple) {
+ var values = [];
+ selected.each(function() {
+ values.push($(this).val());
+ });
+ return values;
+ } else {
+ return selected.val();
+ }
+ },
+
+ // template for options
+ _templateEmpty: function() {
+ return '<div class="ui-error">' + this.options.empty + '</div>';
+ }
+});
+
+/** checkbox options field **/
+var Checkbox = {};
+Checkbox.View = OptionsBase.extend({
+ // initialize
+ initialize: function(options) {
+ options.multiple = true;
+ OptionsBase.prototype.initialize.call(this, options);
+ },
+
+ // value
+ value: function (new_val) {
+ // check if its an array
+ if (typeof new_val === 'string') {
+ new_val = [new_val];
+ }
+
+ // set new value
+ if (new_val !== undefined) {
+ // reset selection
+ this.$el.find('input').prop('checked', false);
+
+ // update to new selection
+ for (var i in new_val) {
+ this.$el.find('input[value=' + new_val[i] + ']').prop('checked', true);
+ };
+ }
+
+ // get and return value
+ return this._getValue();
+ },
+
+ // template for options
+ _templateOption: function(pair) {
+ return '<div class="ui-option">' +
+ '<input type="checkbox" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
+ '</div>';
+ },
+
+ // template
+ _template: function() {
+ return '<div class="ui-checkbox"/>';
+ }
+});
+
+/** radio button options field **/
+var RadioButton = {};
+RadioButton.View = OptionsBase.extend({
+ // initialize
+ initialize: function(options) {
+ OptionsBase.prototype.initialize.call(this, options);
+ },
+
+ // value
+ value: function (new_val) {
+ // set new value
+ if (new_val !== undefined) {
+ this.$el.find('input').prop('checked', false);
+ this.$el.find('label').removeClass('active');
+ this.$el.find('[value="' + new_val + '"]').prop('checked', true).closest('label').addClass('active');
+ }
+
+ // get and return value
+ return this._getValue();
+ },
+
+ // template for options
+ _templateOption: function(pair) {
+ return '<label class="ui-option btn btn-default">' +
+ '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '">' + pair.label +
+ '</label>';
+ },
+
+ // template
+ _template: function() {
+ return '<div class="btn-group ui-radiobutton" data-toggle="buttons"/>';
+ }
+});
+
+return {
+ Checkbox : Checkbox,
+ RadioButton : RadioButton
+};
+
+});
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d client/galaxy/scripts/mvc/ui/ui-radiobutton.js
--- a/client/galaxy/scripts/mvc/ui/ui-radiobutton.js
+++ /dev/null
@@ -1,93 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// plugin
-var View = Backbone.View.extend({
- // options
- optionsDefault: {
- value : '',
- visible : true,
- cls : '',
- data : [],
- id : Utils.uuid()
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // hide input field
- if (!this.options.visible) {
- this.$el.hide();
- }
-
- // set initial value
- if (this.options.value) {
- this.value(this.options.value);
- }
-
- // current value
- this.current = this.options.value;
-
- // onchange event handler. fires on user activity.
- var self = this;
- this.$el.find('input').on('change', function() {
- self.value(self._getValue());
- });
- },
-
- // value
- value : function (new_val) {
- // get current value
- var before = this.current;
-
- // set new value
- if (new_val !== undefined) {
- this.$el.find('label').removeClass('active');
- this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
- this.current = new_val;
- }
-
- // check value
- var after = this.current;
- if (after != before && this.options.onchange) {
- this.options.onchange(this.current);
- }
-
- // get and return value
- return this.current;
- },
-
- // get value
- _getValue: function() {
- var selected = this.$el.find(':checked');
- var value = null;
- if (selected.length > 0) {
- value = selected.val();
- }
- return value;
- },
-
- // element
- _template: function(options) {
- var tmpl = '<div class="btn-group ui-radiobutton" data-toggle="buttons">';
- for (key in options.data) {
- var pair = options.data[key];
- tmpl += '<label class="btn btn-default">' +
- '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label +
- '</label>';
- }
- tmpl += '</div>';
- return tmpl;
- }
-});
-
-return {
- View : View
-};
-
-});
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -25,12 +25,8 @@
// template
_template: function(options) {
- var $input;
- if (options.highlight) {
- $input = $('<div class="ui-table-element ui-table-form-section"/>');
- } else {
- $input = $('<div class="ui-table-element"/>');
- }
+ // create table element
+ var $input = $('<div class="ui-table-element"/>');
// add error
$input.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');
@@ -226,10 +222,12 @@
var input_element = new InputElement({
label : input_def.title,
help : input_def.help,
- $el : repeat.$el,
- highlight : true
+ $el : repeat.$el
});
+ // displays as grouped subsection
+ input_element.$el.addClass('ui-table-form-section');
+
// create table row
this.table.add(input_element.$el);
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d static/scripts/mvc/ui/ui-checkbox.js
--- a/static/scripts/mvc/ui/ui-checkbox.js
+++ /dev/null
@@ -1,91 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// plugin
-var View = Backbone.View.extend({
- // options
- optionsDefault: {
- value : '',
- visible : true,
- cls : '',
- data : [],
- id : Utils.uuid()
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // hide input field
- if (!this.options.visible) {
- this.$el.hide();
- }
-
- // set initial value
- if (this.options.value) {
- this.value(this.options.value);
- }
-
- // current value
- this.current = this.options.value;
-
- // onchange event handler. fires on user activity.
- var self = this;
- this.$el.find('input').on('change', function() {
- self.value(self._getValue());
- });
- },
-
- // value
- value : function (new_val) {
- // get current value
- var before = this.current;
-
- // set new value
- if (new_val !== undefined) {
- this.$el.find('label').removeClass('active');
- this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
- this.current = new_val;
- }
-
- // check value
- var after = this.current;
- if (after != before && this.options.onchange) {
- this.options.onchange(this.current);
- }
-
- // get and return value
- return this.current;
- },
-
- // get value
- _getValue: function() {
- var selected = this.$el.find(':checked');
- var value = null;
- if (selected.length > 0) {
- value = selected.val();
- }
- return value;
- },
-
- // element
- _template: function(options) {
- var tmpl = '<div class="ui-checkbox">';
- for (key in options.data) {
- var pair = options.data[key];
- tmpl += '<input type="checkbox" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + '<br>';
- }
- tmpl += '</div>';
- return tmpl;
- }
-});
-
-return {
- View : View
-};
-
-});
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d static/scripts/mvc/ui/ui-radiobutton.js
--- a/static/scripts/mvc/ui/ui-radiobutton.js
+++ /dev/null
@@ -1,93 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// plugin
-var View = Backbone.View.extend({
- // options
- optionsDefault: {
- value : '',
- visible : true,
- cls : '',
- data : [],
- id : Utils.uuid()
- },
-
- // initialize
- initialize : function(options) {
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- // create new element
- this.setElement(this._template(this.options));
-
- // hide input field
- if (!this.options.visible) {
- this.$el.hide();
- }
-
- // set initial value
- if (this.options.value) {
- this.value(this.options.value);
- }
-
- // current value
- this.current = this.options.value;
-
- // onchange event handler. fires on user activity.
- var self = this;
- this.$el.find('input').on('change', function() {
- self.value(self._getValue());
- });
- },
-
- // value
- value : function (new_val) {
- // get current value
- var before = this.current;
-
- // set new value
- if (new_val !== undefined) {
- this.$el.find('label').removeClass('active');
- this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
- this.current = new_val;
- }
-
- // check value
- var after = this.current;
- if (after != before && this.options.onchange) {
- this.options.onchange(this.current);
- }
-
- // get and return value
- return this.current;
- },
-
- // get value
- _getValue: function() {
- var selected = this.$el.find(':checked');
- var value = null;
- if (selected.length > 0) {
- value = selected.val();
- }
- return value;
- },
-
- // element
- _template: function(options) {
- var tmpl = '<div class="btn-group ui-radiobutton" data-toggle="buttons">';
- for (key in options.data) {
- var pair = options.data[key];
- tmpl += '<label class="btn btn-default">' +
- '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label +
- '</label>';
- }
- tmpl += '</div>';
- return tmpl;
- }
-});
-
-return {
- View : View
-};
-
-});
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d 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()},reset:function(){this.$el.find(".ui-table-form-error").hide()},_template:function(h){var i;if(h.highlight){i=$('<div class="ui-table-element ui-table-form-section"/>')}else{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.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el,highlight:true});this.table.add(n.$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(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_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.RadioButton;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_data_colum:function(h){return new g.Select.View({id:"field-"+h.id,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){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||0,max:h.max||1000,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.$el.find(".ui-table-form-error").fadeIn()},reset:function(){this.$el.find(".ui-table-form-error").hide()},_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.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$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(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_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.RadioButton;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_data_colum:function(h){return new g.Select.View({id:"field-"+h.id,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){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||0,max:h.max||1000,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 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d static/scripts/packed/mvc/ui/ui-checkbox.js
--- a/static/scripts/packed/mvc/ui/ui-checkbox.js
+++ /dev/null
@@ -1,1 +0,0 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="ui-checkbox">';for(key in d.data){var e=d.data[key];c+='<input type="checkbox" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"<br>"}c+="</div>";return c}});return{View:b}});
\ No newline at end of file
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d static/scripts/packed/mvc/ui/ui-radiobutton.js
--- a/static/scripts/packed/mvc/ui/ui-radiobutton.js
+++ /dev/null
@@ -1,1 +0,0 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in d.data){var e=d.data[key];c+='<label class="btn btn-default"><input type="radio" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"</label>"}c+="</div>";return c}});return{View:b}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/37e5c86d9fc0/
Changeset: 37e5c86d9fc0
User: guerler
Date: 2014-09-18 18:58:12+00:00
Summary: Merge
Affected #: 16 files
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa client/galaxy/scripts/galaxy.base.js
--- a/client/galaxy/scripts/galaxy.base.js
+++ b/client/galaxy/scripts/galaxy.base.js
@@ -237,7 +237,8 @@
$.fn.refresh_select2 = function() {
var select_elt = $(this);
var options = { width: "resolve",
- closeOnSelect: !select_elt.is("[MULTIPLE]")
+ closeOnSelect: !select_elt.is("[MULTIPLE]"),
+ dropdownAutoWidth : true
};
return select_elt.select2( options );
}
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa client/galaxy/scripts/mvc/library/library-folderlist-view.js
--- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
@@ -1,4 +1,3 @@
-// dependencies
define([
"galaxy.masthead",
"utils/utils",
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -2,11 +2,15 @@
"galaxy.masthead",
"utils/utils",
"libs/toastr",
- "mvc/library/library-model"],
+ "mvc/library/library-model",
+ "mvc/ui/ui-select"
+ ],
function( mod_masthead,
- mod_utils,
- mod_toastr,
- mod_library_model ) {
+ mod_utils,
+ mod_toastr,
+ mod_library_model,
+ mod_select
+ ){
var FolderToolbarView = Backbone.View.extend({
el: '#center',
@@ -37,8 +41,28 @@
// user's histories
histories : null,
+ // genome select
+ select_genome : null,
+
+ // extension select
+ select_extension : null,
+
+ // extension types
+ list_extensions :[],
+
+ // datatype placeholder for extension auto-detection
+ auto: {
+ id : 'auto',
+ text : 'Auto-detect',
+ description : 'This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.'
+ },
+
+ // genomes
+ list_genomes : [],
+
initialize: function(options){
this.options = _.defaults( options || {}, this.defaults );
+ this.fetchExtAndGenomes();
this.render();
},
@@ -321,7 +345,7 @@
var template_modal = this.templateImportPathModal();
this.modal.show({
closing_events : true,
- title : 'Enter paths relative to Galaxy root',
+ title : 'Please enter paths to import',
body : template_modal({}),
buttons : {
'Import' : function() {that.importFromPathsClicked(that);},
@@ -332,9 +356,65 @@
Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
}
});
+ this.renderSelectBoxes();
},
/**
+ * Request all extensions and genomes from Galaxy
+ * and save them sorted in arrays.
+ */
+ fetchExtAndGenomes: function(){
+ var that = this;
+ mod_utils.get(galaxy_config.root + "api/datatypes?extension_only=False",
+ function(datatypes) {
+ for (key in datatypes) {
+ that.list_extensions.push({
+ id : datatypes[key].extension,
+ text : datatypes[key].extension,
+ description : datatypes[key].description,
+ description_url : datatypes[key].description_url
+ });
+ }
+ that.list_extensions.sort(function(a, b) {
+ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
+ });
+ that.list_extensions.unshift(that.auto);
+
+ });
+ mod_utils.get(galaxy_config.root + "api/genomes",
+ function(genomes) {
+ for (key in genomes) {
+ that.list_genomes.push({
+ id : genomes[key][1],
+ text : genomes[key][0]
+ });
+ }
+ that.list_genomes.sort(function(a, b) {
+ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
+ });
+ });
+ },
+
+ renderSelectBoxes: function(){
+ // This won't work properly unlesss we already have the data fetched.
+ // See this.fetchExtAndGenomes()
+ // TODO switch to common resources:
+ // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy…
+ var that = this;
+ this.select_genome = new mod_select.View( {
+ css: 'genome',
+ data: that.list_genomes,
+ container: Galaxy.modal.$el.find( '#genome' ),
+ value: '?'
+ } );
+ this.select_extension = new mod_select.View({
+ css: 'extension',
+ data: that.list_extensions,
+ container: Galaxy.modal.$el.find('#extension'),
+ value: 'auto'
+ });
+ },
+ /**
* Create modal for importing form user's directory
* on Galaxy. Bind jQuery events.
*/
@@ -343,18 +423,20 @@
this.modal = Galaxy.modal;
var template_modal = this.templateBrowserModal();
this.modal.show({
- closing_events : true,
- title : 'Select folders or files to import',
- body : template_modal({}),
- buttons : {
- 'Import' : function() {that.importFromUserdirClicked(that);},
- 'Close' : function() {Galaxy.modal.hide();}
- },
- closing_callback: function(){
- // TODO: should not trigger routes outside of the router
- Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
- }
- });
+ closing_events : true,
+ title : 'Please select folders or files',
+ body : template_modal({}),
+ buttons : {
+ 'Import' : function() {that.importFromUserdirClicked(that);},
+ 'Close' : function() {Galaxy.modal.hide();}
+ },
+ closing_callback: function(){
+ // TODO: should not trigger routes outside of the router
+ Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
+ }
+ });
+
+ this.renderSelectBoxes();
this.renderJstree({disabled_jstree_element: 'folders'});
$('input[type=radio]').change(function(event){
@@ -431,6 +513,8 @@
importFromPathsClicked: function(){
var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
+ var file_type = this.select_extension.value();
+ var dbkey = this.select_genome.value();
var paths = $('textarea#import_paths').val();
var valid_paths = [];
if (!paths){
@@ -445,7 +529,12 @@
}
};
this.initChainCallControl( { length: valid_paths.length, action: 'adding_datasets' } );
- this.chainCallImportingFolders(valid_paths, preserve_dirs, link_data, 'admin_path');
+ this.chainCallImportingFolders( { paths: valid_paths,
+ preserve_dirs: preserve_dirs,
+ link_data: link_data,
+ source: 'admin_path',
+ file_type: file_type,
+ dbkey: dbkey } );
}
},
@@ -494,6 +583,8 @@
var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' );
var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' );
+ var file_type = this.select_extension.value();
+ var dbkey = this.select_genome.value();
var selection_type = selected_nodes[0].type;
var paths = [];
if ( selected_nodes.length < 1 ){
@@ -507,9 +598,17 @@
}
this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } );
if ( selection_type === 'folder' ){
- this.chainCallImportingFolders( paths, preserve_dirs, link_data, 'userdir_folder' );
+
+ this.chainCallImportingFolders( { paths: paths,
+ preserve_dirs: preserve_dirs,
+ link_data: link_data,
+ source: 'userdir_folder',
+ file_type: file_type,
+ dbkey: dbkey } );
} else if ( selection_type === 'file' ){
- this.chainCallImportingUserdirFiles( paths );
+ this.chainCallImportingUserdirFiles( { paths : paths,
+ file_type: file_type,
+ dbkey: dbkey } );
}
}
},
@@ -600,9 +699,10 @@
* calling them in chain. Update the progress bar in between each.
* @param {array} paths paths relative to user folder on Galaxy
*/
- chainCallImportingUserdirFiles: function( paths ){
+ chainCallImportingUserdirFiles: function( options ){
+
var that = this;
- var popped_item = paths.pop();
+ var popped_item = options.paths.pop();
if ( typeof popped_item === "undefined" ) {
if ( this.options.chain_call_control.failed_number === 0 ){
mod_toastr.success( 'Selected files imported into the current folder' );
@@ -614,15 +714,17 @@
}
var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
'&source=userdir_file' +
- '&path=' + popped_item ) )
+ '&path=' + popped_item +
+ '&file_type=' + options.file_type +
+ '&dbkey=' + options.dbkey ) )
promise.done( function( response ){
that.updateProgress();
- that.chainCallImportingUserdirFiles( paths );
+ that.chainCallImportingUserdirFiles( options );
} )
.fail( function(){
that.options.chain_call_control.failed_number += 1;
that.updateProgress();
- that.chainCallImportingUserdirFiles( paths );
+ that.chainCallImportingUserdirFiles( options );
} );
},
@@ -635,10 +737,10 @@
* @param {str} source string representing what type of folder
* is the source of import
*/
- chainCallImportingFolders: function(paths, preserve_dirs, link_data, source){
- // need to check which paths to call
+ chainCallImportingFolders: function( options ){
+ // TODO need to check which paths to call
var that = this;
- var popped_item = paths.pop();
+ var popped_item = options.paths.pop();
if (typeof popped_item == "undefined") {
if (this.options.chain_call_control.failed_number === 0){
mod_toastr.success('Selected folders and their contents imported into the current folder.');
@@ -649,19 +751,31 @@
}
return true;
}
- var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id +
- '&source=' + source +
- '&path=' + popped_item +
- '&preserve_dirs=' + preserve_dirs +
- '&link_data=' + link_data))
+ var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
+ '&source=' + options.source +
+ '&path=' + popped_item +
+ '&preserve_dirs=' + options.preserve_dirs +
+ '&link_data=' + options.link_data +
+ '&file_type=' + options.file_type +
+ '&dbkey=' + options.dbkey ) )
promise.done(function(response){
that.updateProgress();
- that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+ that.chainCallImportingFolders( { paths: options.paths,
+ preserve_dirs: options.preserve_dirs,
+ link_data: options.link_data,
+ source: options.source,
+ file_type: options.file_type,
+ dbkey: options.dbkey } );
})
.fail(function(){
that.options.chain_call_control.failed_number += 1;
that.updateProgress();
- that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+ that.chainCallImportingFolders( { paths: options.paths,
+ preserve_dirs: options.preserve_dirs,
+ link_data: options.link_data,
+ source: options.source,
+ file_type: options.file_type,
+ dbkey: options.dbkey } );
});
},
@@ -1012,7 +1126,10 @@
var tmpl_array = [];
tmpl_array.push('<div id="file_browser_modal">');
+ tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
+ tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
+
tmpl_array.push('<div style="margin-bottom:1em;">');
tmpl_array.push('<label class="radio-inline">');
tmpl_array.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');
@@ -1020,22 +1137,25 @@
tmpl_array.push('<label class="radio-inline">');
tmpl_array.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');
tmpl_array.push('</label>');
-
+ tmpl_array.push('</div>');
+ tmpl_array.push('<div style="margin-bottom:1em;">');
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
tmpl_array.push('Preserve directory structure');
tmpl_array.push(' </label>');
-
tmpl_array.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
tmpl_array.push('Link files instead of copying');
tmpl_array.push(' </label>');
tmpl_array.push('</div>');
+ tmpl_array.push('<div id="jstree_browser">');
+ tmpl_array.push('</div>');
- tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
- tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
-
- tmpl_array.push('<div id="jstree_browser">');
+ tmpl_array.push('<hr />');
+ tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
+ tmpl_array.push('<div>');
+ tmpl_array.push('Type: <span id="extension" class="extension" />');
+ tmpl_array.push(' Genome: <span id="genome" class="genome" />');
tmpl_array.push('</div>');
tmpl_array.push('</div>');
@@ -1046,21 +1166,28 @@
var tmpl_array = [];
tmpl_array.push('<div id="file_browser_modal">');
+ tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
+ tmpl_array.push('<div style="margin-bottom: 0.5em;">');
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure">');
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
tmpl_array.push('Preserve directory structure');
tmpl_array.push(' </label>');
-
tmpl_array.push('<label class="checkbox-inline jstree-link-files">');
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
tmpl_array.push('Link files instead of copying');
tmpl_array.push(' </label>');
tmpl_array.push('</div>');
- tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
+ tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');
- tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');
+ tmpl_array.push('<hr />');
+ tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
+ tmpl_array.push('<div>');
+ tmpl_array.push('Type: <span id="extension" class="extension" />');
+ tmpl_array.push(' Genome: <span id="genome" class="genome" />');
+ tmpl_array.push('</div>');
+
tmpl_array.push('</div>');
return _.template(tmpl_array.join(''));
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa client/galaxy/scripts/mvc/ui/ui-select.js
--- a/client/galaxy/scripts/mvc/ui/ui-select.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select.js
@@ -155,6 +155,8 @@
data : this.select_data,
containerCssClass : this.options.css,
placeholder : this.options.placeholder,
+ width : 'resolve',
+ dropdownAutoWidth : true
};
this.$el.select2(select_opt);
// select previous value (if exists)
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa lib/galaxy/visualization/registry.py
--- a/lib/galaxy/visualization/registry.py
+++ b/lib/galaxy/visualization/registry.py
@@ -159,7 +159,7 @@
# config file is required, otherwise skip this visualization
plugin[ 'config_file' ] = os.path.join( plugin_path, 'config', ( plugin.name + '.xml' ) )
config = self.config_parser.parse_file( plugin.config_file )
-
+
if not config:
return None
plugin[ 'config' ] = config
@@ -390,14 +390,9 @@
Parse the given XML file for visualizations data.
:returns: visualization config dictionary
"""
- try:
- xml_tree = galaxy.util.parse_xml( xml_filepath )
- visualization = self.parse_visualization( xml_tree.getroot() )
- return visualization
- # skip vis' with parsing errors - don't shutdown the startup
- except ParsingException, parse_exc:
- log.exception( 'Skipped visualization config "%s" due to parsing errors', xml_filepath )
- return None
+ xml_tree = galaxy.util.parse_xml( xml_filepath )
+ visualization = self.parse_visualization( xml_tree.getroot() )
+ return visualization
def parse_visualization( self, xml_tree ):
"""
@@ -406,16 +401,16 @@
"""
returned = {}
- # allow manually turning off a vis by checking for a disabled property
- if 'disabled' in xml_tree.attrib:
-#TODO: differentiate between disabled and failed to parse, log.warn only on failure, log.info otherwise
- return None
-
# a text display name for end user links
returned[ 'name' ] = xml_tree.attrib.get( 'name', None )
if not returned[ 'name' ]:
raise ParsingException( 'visualization needs a name attribute' )
+ # allow manually turning off a vis by checking for a disabled property
+ if 'disabled' in xml_tree.attrib:
+ log.info( '%s, plugin disabled: %s. Skipping...', self, returned[ 'name' ] )
+ return None
+
# record the embeddable flag - defaults to false
# this is a design by contract promise that the visualization can be rendered inside another page
# often by rendering only a DOM fragment. Since this is an advanced feature that requires a bit more
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa lib/galaxy/web/base/pluginframework.py
--- a/lib/galaxy/web/base/pluginframework.py
+++ b/lib/galaxy/web/base/pluginframework.py
@@ -118,15 +118,14 @@
for plugin_path in self.find_plugins():
try:
plugin = self.load_plugin( plugin_path )
- if not plugin:
- log.warn( '%s, plugin load failed or disabled: %s. Skipping...', self, plugin_path )
+
+ if plugin and plugin.name not in self.plugins:
+ self.plugins[ plugin.name ] = plugin
+ log.info( '%s, loaded plugin: %s', self, plugin.name )
#NOTE: prevent silent, implicit overwrite here (two plugins in two diff directories)
#TODO: overwriting may be desired
- elif plugin.name in self.plugins:
+ elif plugin and plugin.name in self.plugins:
log.warn( '%s, plugin with name already exists: %s. Skipping...', self, plugin.name )
- else:
- self.plugins[ plugin.name ] = plugin
- log.info( '%s, loaded plugin: %s', self, plugin.name )
except Exception, exc:
if not self.skip_bad_plugins:
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa lib/galaxy/webapps/galaxy/api/lda_datasets.py
--- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
@@ -414,9 +414,9 @@
kwd[ 'space_to_tab' ] = 'False'
kwd[ 'to_posix_lines' ] = 'True'
- kwd[ 'dbkey' ] = '?'
- kwd[ 'file_type' ] = 'auto'
-
+
+ kwd[ 'dbkey' ] = kwd.get( 'dbkey', '?' )
+ kwd[ 'file_type' ] = kwd.get( 'file_type', 'auto' )
kwd[' link_data_only' ] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files'
encoded_folder_id = kwd.get( 'encoded_folder_id', None )
if encoded_folder_id is not None:
@@ -473,9 +473,6 @@
trans, 'api', params, os.path.basename( file ), file, 'server_dir', library_bunch ) )
# user wants to import whole folder
if source == "userdir_folder":
- # import_folder_root = [next(part for part in path.split(os.path.sep) if part) for path in [os.path.splitdrive(path_to_root_import_folder)[1]]]
- # new_folder = self.folder_manager.create( trans, folder_id, import_folder_root[0] )
-
uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets(
trans, 'api', params, library_bunch, 200, '' )
uploaded_datasets = uploaded_datasets_bunch[0]
@@ -495,7 +492,6 @@
for ud in uploaded_datasets:
ud.path = os.path.abspath( ud.path )
abspath_datasets.append( ud )
-
json_file_path = upload_common.create_paramfile( trans, abspath_datasets )
data_list = [ ud.data for ud in abspath_datasets ]
job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=folder )
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa static/scripts/galaxy.base.js
--- a/static/scripts/galaxy.base.js
+++ b/static/scripts/galaxy.base.js
@@ -237,7 +237,8 @@
$.fn.refresh_select2 = function() {
var select_elt = $(this);
var options = { width: "resolve",
- closeOnSelect: !select_elt.is("[MULTIPLE]")
+ closeOnSelect: !select_elt.is("[MULTIPLE]"),
+ dropdownAutoWidth : true
};
return select_elt.select2( options );
}
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa static/scripts/mvc/library/library-folderlist-view.js
--- a/static/scripts/mvc/library/library-folderlist-view.js
+++ b/static/scripts/mvc/library/library-folderlist-view.js
@@ -1,4 +1,3 @@
-// dependencies
define([
"galaxy.masthead",
"utils/utils",
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa static/scripts/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/mvc/library/library-foldertoolbar-view.js
@@ -2,11 +2,15 @@
"galaxy.masthead",
"utils/utils",
"libs/toastr",
- "mvc/library/library-model"],
+ "mvc/library/library-model",
+ "mvc/ui/ui-select"
+ ],
function( mod_masthead,
- mod_utils,
- mod_toastr,
- mod_library_model ) {
+ mod_utils,
+ mod_toastr,
+ mod_library_model,
+ mod_select
+ ){
var FolderToolbarView = Backbone.View.extend({
el: '#center',
@@ -37,8 +41,28 @@
// user's histories
histories : null,
+ // genome select
+ select_genome : null,
+
+ // extension select
+ select_extension : null,
+
+ // extension types
+ list_extensions :[],
+
+ // datatype placeholder for extension auto-detection
+ auto: {
+ id : 'auto',
+ text : 'Auto-detect',
+ description : 'This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.'
+ },
+
+ // genomes
+ list_genomes : [],
+
initialize: function(options){
this.options = _.defaults( options || {}, this.defaults );
+ this.fetchExtAndGenomes();
this.render();
},
@@ -321,7 +345,7 @@
var template_modal = this.templateImportPathModal();
this.modal.show({
closing_events : true,
- title : 'Enter paths relative to Galaxy root',
+ title : 'Please enter paths to import',
body : template_modal({}),
buttons : {
'Import' : function() {that.importFromPathsClicked(that);},
@@ -332,9 +356,65 @@
Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
}
});
+ this.renderSelectBoxes();
},
/**
+ * Request all extensions and genomes from Galaxy
+ * and save them sorted in arrays.
+ */
+ fetchExtAndGenomes: function(){
+ var that = this;
+ mod_utils.get(galaxy_config.root + "api/datatypes?extension_only=False",
+ function(datatypes) {
+ for (key in datatypes) {
+ that.list_extensions.push({
+ id : datatypes[key].extension,
+ text : datatypes[key].extension,
+ description : datatypes[key].description,
+ description_url : datatypes[key].description_url
+ });
+ }
+ that.list_extensions.sort(function(a, b) {
+ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
+ });
+ that.list_extensions.unshift(that.auto);
+
+ });
+ mod_utils.get(galaxy_config.root + "api/genomes",
+ function(genomes) {
+ for (key in genomes) {
+ that.list_genomes.push({
+ id : genomes[key][1],
+ text : genomes[key][0]
+ });
+ }
+ that.list_genomes.sort(function(a, b) {
+ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
+ });
+ });
+ },
+
+ renderSelectBoxes: function(){
+ // This won't work properly unlesss we already have the data fetched.
+ // See this.fetchExtAndGenomes()
+ // TODO switch to common resources:
+ // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy…
+ var that = this;
+ this.select_genome = new mod_select.View( {
+ css: 'genome',
+ data: that.list_genomes,
+ container: Galaxy.modal.$el.find( '#genome' ),
+ value: '?'
+ } );
+ this.select_extension = new mod_select.View({
+ css: 'extension',
+ data: that.list_extensions,
+ container: Galaxy.modal.$el.find('#extension'),
+ value: 'auto'
+ });
+ },
+ /**
* Create modal for importing form user's directory
* on Galaxy. Bind jQuery events.
*/
@@ -343,18 +423,20 @@
this.modal = Galaxy.modal;
var template_modal = this.templateBrowserModal();
this.modal.show({
- closing_events : true,
- title : 'Select folders or files to import',
- body : template_modal({}),
- buttons : {
- 'Import' : function() {that.importFromUserdirClicked(that);},
- 'Close' : function() {Galaxy.modal.hide();}
- },
- closing_callback: function(){
- // TODO: should not trigger routes outside of the router
- Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
- }
- });
+ closing_events : true,
+ title : 'Please select folders or files',
+ body : template_modal({}),
+ buttons : {
+ 'Import' : function() {that.importFromUserdirClicked(that);},
+ 'Close' : function() {Galaxy.modal.hide();}
+ },
+ closing_callback: function(){
+ // TODO: should not trigger routes outside of the router
+ Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
+ }
+ });
+
+ this.renderSelectBoxes();
this.renderJstree({disabled_jstree_element: 'folders'});
$('input[type=radio]').change(function(event){
@@ -431,6 +513,8 @@
importFromPathsClicked: function(){
var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
+ var file_type = this.select_extension.value();
+ var dbkey = this.select_genome.value();
var paths = $('textarea#import_paths').val();
var valid_paths = [];
if (!paths){
@@ -445,7 +529,12 @@
}
};
this.initChainCallControl( { length: valid_paths.length, action: 'adding_datasets' } );
- this.chainCallImportingFolders(valid_paths, preserve_dirs, link_data, 'admin_path');
+ this.chainCallImportingFolders( { paths: valid_paths,
+ preserve_dirs: preserve_dirs,
+ link_data: link_data,
+ source: 'admin_path',
+ file_type: file_type,
+ dbkey: dbkey } );
}
},
@@ -494,6 +583,8 @@
var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' );
var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' );
+ var file_type = this.select_extension.value();
+ var dbkey = this.select_genome.value();
var selection_type = selected_nodes[0].type;
var paths = [];
if ( selected_nodes.length < 1 ){
@@ -507,9 +598,17 @@
}
this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } );
if ( selection_type === 'folder' ){
- this.chainCallImportingFolders( paths, preserve_dirs, link_data, 'userdir_folder' );
+
+ this.chainCallImportingFolders( { paths: paths,
+ preserve_dirs: preserve_dirs,
+ link_data: link_data,
+ source: 'userdir_folder',
+ file_type: file_type,
+ dbkey: dbkey } );
} else if ( selection_type === 'file' ){
- this.chainCallImportingUserdirFiles( paths );
+ this.chainCallImportingUserdirFiles( { paths : paths,
+ file_type: file_type,
+ dbkey: dbkey } );
}
}
},
@@ -600,9 +699,10 @@
* calling them in chain. Update the progress bar in between each.
* @param {array} paths paths relative to user folder on Galaxy
*/
- chainCallImportingUserdirFiles: function( paths ){
+ chainCallImportingUserdirFiles: function( options ){
+
var that = this;
- var popped_item = paths.pop();
+ var popped_item = options.paths.pop();
if ( typeof popped_item === "undefined" ) {
if ( this.options.chain_call_control.failed_number === 0 ){
mod_toastr.success( 'Selected files imported into the current folder' );
@@ -614,15 +714,17 @@
}
var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
'&source=userdir_file' +
- '&path=' + popped_item ) )
+ '&path=' + popped_item +
+ '&file_type=' + options.file_type +
+ '&dbkey=' + options.dbkey ) )
promise.done( function( response ){
that.updateProgress();
- that.chainCallImportingUserdirFiles( paths );
+ that.chainCallImportingUserdirFiles( options );
} )
.fail( function(){
that.options.chain_call_control.failed_number += 1;
that.updateProgress();
- that.chainCallImportingUserdirFiles( paths );
+ that.chainCallImportingUserdirFiles( options );
} );
},
@@ -635,10 +737,10 @@
* @param {str} source string representing what type of folder
* is the source of import
*/
- chainCallImportingFolders: function(paths, preserve_dirs, link_data, source){
- // need to check which paths to call
+ chainCallImportingFolders: function( options ){
+ // TODO need to check which paths to call
var that = this;
- var popped_item = paths.pop();
+ var popped_item = options.paths.pop();
if (typeof popped_item == "undefined") {
if (this.options.chain_call_control.failed_number === 0){
mod_toastr.success('Selected folders and their contents imported into the current folder.');
@@ -649,19 +751,31 @@
}
return true;
}
- var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id +
- '&source=' + source +
- '&path=' + popped_item +
- '&preserve_dirs=' + preserve_dirs +
- '&link_data=' + link_data))
+ var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
+ '&source=' + options.source +
+ '&path=' + popped_item +
+ '&preserve_dirs=' + options.preserve_dirs +
+ '&link_data=' + options.link_data +
+ '&file_type=' + options.file_type +
+ '&dbkey=' + options.dbkey ) )
promise.done(function(response){
that.updateProgress();
- that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+ that.chainCallImportingFolders( { paths: options.paths,
+ preserve_dirs: options.preserve_dirs,
+ link_data: options.link_data,
+ source: options.source,
+ file_type: options.file_type,
+ dbkey: options.dbkey } );
})
.fail(function(){
that.options.chain_call_control.failed_number += 1;
that.updateProgress();
- that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+ that.chainCallImportingFolders( { paths: options.paths,
+ preserve_dirs: options.preserve_dirs,
+ link_data: options.link_data,
+ source: options.source,
+ file_type: options.file_type,
+ dbkey: options.dbkey } );
});
},
@@ -1012,7 +1126,10 @@
var tmpl_array = [];
tmpl_array.push('<div id="file_browser_modal">');
+ tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
+ tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
+
tmpl_array.push('<div style="margin-bottom:1em;">');
tmpl_array.push('<label class="radio-inline">');
tmpl_array.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');
@@ -1020,22 +1137,25 @@
tmpl_array.push('<label class="radio-inline">');
tmpl_array.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');
tmpl_array.push('</label>');
-
+ tmpl_array.push('</div>');
+ tmpl_array.push('<div style="margin-bottom:1em;">');
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
tmpl_array.push('Preserve directory structure');
tmpl_array.push(' </label>');
-
tmpl_array.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
tmpl_array.push('Link files instead of copying');
tmpl_array.push(' </label>');
tmpl_array.push('</div>');
+ tmpl_array.push('<div id="jstree_browser">');
+ tmpl_array.push('</div>');
- tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
- tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
-
- tmpl_array.push('<div id="jstree_browser">');
+ tmpl_array.push('<hr />');
+ tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
+ tmpl_array.push('<div>');
+ tmpl_array.push('Type: <span id="extension" class="extension" />');
+ tmpl_array.push(' Genome: <span id="genome" class="genome" />');
tmpl_array.push('</div>');
tmpl_array.push('</div>');
@@ -1046,21 +1166,28 @@
var tmpl_array = [];
tmpl_array.push('<div id="file_browser_modal">');
+ tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
+ tmpl_array.push('<div style="margin-bottom: 0.5em;">');
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure">');
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
tmpl_array.push('Preserve directory structure');
tmpl_array.push(' </label>');
-
tmpl_array.push('<label class="checkbox-inline jstree-link-files">');
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
tmpl_array.push('Link files instead of copying');
tmpl_array.push(' </label>');
tmpl_array.push('</div>');
- tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
+ tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');
- tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');
+ tmpl_array.push('<hr />');
+ tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
+ tmpl_array.push('<div>');
+ tmpl_array.push('Type: <span id="extension" class="extension" />');
+ tmpl_array.push(' Genome: <span id="genome" class="genome" />');
+ tmpl_array.push('</div>');
+
tmpl_array.push('</div>');
return _.template(tmpl_array.join(''));
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa static/scripts/mvc/ui/ui-select.js
--- a/static/scripts/mvc/ui/ui-select.js
+++ b/static/scripts/mvc/ui/ui-select.js
@@ -155,6 +155,8 @@
data : this.select_data,
containerCssClass : this.options.css,
placeholder : this.options.placeholder,
+ width : 'resolve',
+ dropdownAutoWidth : true
};
this.$el.select2(select_opt);
// select previous value (if exists)
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa static/scripts/packed/galaxy.base.js
--- a/static/scripts/packed/galaxy.base.js
+++ b/static/scripts/packed/galaxy.base.js
@@ -1,1 +1,1 @@
-(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){var l=i.action||i;g.append($("<li></li>").append($("<a>").attr("href",i.url).html(j).click(l)))}else{g.append($("<li></li>").addClass("head").append($("<a href='#'></a>").html(j)))}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>").append(g).appendTo("body");var e=d.pageX-h.width()/2;e=Math.min(e,$(document).scrollLeft()+$(window).width()-$(h).width()-5);e=Math.max(e,$(document).scrollLeft()+5);h.css({top:d.pageY,left:e})},10);setTimeout(function(){var f=function(h){$(h).bind("click.close_popup",function(){$(".popmenu-wrapper").remove();h.unbind("click.close_popup")})};f($(window.document));f($(window.top.document));for(var e=window.top.frames.length;e--;){var g=$(window.top.frames[e].document);f(g)}},50);return false})}function make_popup_menus(a){a=a||document;$(a).find("div[popupmenu]").each(function(){var b={};var d=$(this);d.find("a").each(function(){var g=$(this),i=g.get(0),e=i.getAttribute("confirm"),f=i.getAttribute("href"),h=i.getAttribute("target");if(!f){b[g.text()]=null}else{b[g.text()]={url:f,action:function(){if(!e||confirm(e)){if(h){window.open(f,h);return false}else{g.click()}}}}}});var c=$(a).find("#"+d.attr("popupmenu"));c.find("a").bind("click",function(f){f.stopPropagation();return 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d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=("cur_text" in g?g.cur_text:a.text()),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input 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\ No newline at end of file
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GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}jQuery.fn.preventDoubleSubmission=function(){$(this).on("submit",function(b){var a=$(this);if(a.data("submitted")===true){b.preventDefault()}else{a.data("submitted",true)}});return this};$(document).ready(function(){init_refresh_on_change();if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip()}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})});
\ No newline at end of file
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa static/scripts/packed/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){g.is_admin=Galaxy.currUser.isAdmin();g.is_anonym=Galaxy.currUser.isAnonymous();if(g.user_library_import_dir!==null||g.allow_library_path_paste!==false||g.library_import_dir!==null){g.mutiple_add_dataset_options=true}}this.$el.html(h(g))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(h){h.preventDefault();h.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created.");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})}else{e.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(h){var g=h.templateBulkImportInModal();h.modal=Galaxy.modal;h.modal.show({closing_events:true,title:"Import into History",body:g({histories:h.histories.models}),buttons:{Import:function(){h.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var j=$("select[name=dataset_import_bulk] option:selected").val();var m=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=j;var g=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});var l=[];for(var h=g.length-1;h>=0;h--){var f=g[h];var k=new c.HistoryItem();k.url=k.urlRoot+j+"/contents";k.content=f;k.source="library";l.push(k)}this.initChainCallControl({length:l.length,action:"to_history",history_name:m});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+j);this.chainCallImportingIntoHistory(l,m)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon.")}else{e.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesFromHistory();var h=f.options.full_path[f.options.full_path.length-1][1];f.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+h,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(i){f.fetchAndDisplayHistoryContents(i.target.value)})}else{e.error("An error ocurred.")}})},importFilesFromPathModal:function(){var g=this;this.modal=Galaxy.modal;var f=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Enter paths relative to Galaxy root",body:f({}),buttons:{Import:function(){g.importFromPathsClicked(g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+g.id,{trigger:true})}})},importFilesFromUserdirModal:function(){var g=this;this.modal=Galaxy.modal;var f=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Select folders or files to import",body:f({}),buttons:{Import:function(){g.importFromUserdirClicked(g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+g.id,{trigger:true})}});this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(h){if(h.target.value==="jstree-disable-folders"){g.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(h.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(f){var h=this;this.options=_.extend(this.options,f);var g=this.options.disabled_jstree_element;this.jstree=new c.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+g;this.jstree.fetch({success:function(j,i){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(k){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:j},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},importFromPathsClicked:function(){var f=this.modal.$el.find(".preserve-checkbox").is(":checked");var k=this.modal.$el.find(".link-checkbox").is(":checked");var j=$("textarea#import_paths").val();var h=[];if(!j){e.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");j=j.split("\n");for(var g=j.length-1;g>=0;g--){trimmed=j[g].trim();if(trimmed.length!==0){h.push(trimmed)}}this.initChainCallControl({length:h.length,action:"adding_datasets"});this.chainCallImportingFolders(h,f,k,"admin_path")}},initChainCallControl:function(f){var g;switch(f.action){case"adding_datasets":g=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(g({folder_name:this.options.folder_name}));break;case"deleting_datasets":g=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(g());break;case"to_history":g=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(g({history_name:f.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/f.length;this.options.chain_call_control.total_number=f.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(k){var g=$("#jstree_browser").jstree().get_selected(true);var f=this.modal.$el.find(".preserve-checkbox").is(":checked");var m=this.modal.$el.find(".link-checkbox").is(":checked");var j=g[0].type;var l=[];if(g.length<1){e.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var h=g.length-1;h>=0;h--){if(g[h].li_attr.full_path!==undefined){l.push(g[h].li_attr.full_path)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders(l,f,m,"userdir_folder")}else{if(j==="file"){this.chainCallImportingUserdirFiles(l)}}}},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var k=this.modal.$el.find("#selected_history_content").find(":checked");var f=[];var j=[];if(k.length<1){e.info("You must select some datasets first.")}else{this.modal.disableButton("Add");k.each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.initChainCallControl({length:j.length,action:"adding_datasets"});this.chainCallAddingHdas(j)}},chainCallImportingIntoHistory:function(g,j){var f=this;var h=g.pop();if(typeof h=="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCallImportingIntoHistory(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallImportingIntoHistory(g,j)})},chainCallImportingUserdirFiles:function(i){var f=this;var g=i.pop();if(typeof g==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{e.error("An error occured.")}return true}var h=$.when($.post("/api/libraries/datasets?encoded_folder_id="+f.id+"&source=userdir_file&path="+g));h.done(function(j){f.updateProgress();f.chainCallImportingUserdirFiles(i)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallImportingUserdirFiles(i)})},chainCallImportingFolders:function(k,f,l,i){var g=this;var h=k.pop();if(typeof h=="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{e.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+g.id+"&source="+i+"&path="+h+"&preserve_dirs="+f+"&link_data="+l));j.done(function(m){g.updateProgress();g.chainCallImportingFolders(k,f,l,i)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingFolders(k,f,l,i)})},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h=="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You must select at least one dataset for deletion.")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},showLibInfo:function(){var g=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var f=null;var h=this;if(Galaxy.libraries.libraryListView!==null){f=Galaxy.libraries.libraryListView.collection.get(g);this.showLibInfoModal(f)}else{f=new c.Library({id:g});f.fetch({success:function(){h.showLibInfoModal(f)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})}},showLibInfoModal:function(f){var g=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:g({library:f}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(f){switch(f.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();e.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateBrowserModal:function(){var f=[];f.push('<div id="file_browser_modal">');f.push('<div style="margin-bottom:1em;">');f.push('<label class="radio-inline">');f.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');f.push("</label>");f.push('<label class="radio-inline">');f.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');f.push("</label>");f.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');f.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');f.push("Preserve directory structure");f.push(" </label>");f.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');f.push(' <input class="link-checkbox" type="checkbox" value="link_files">');f.push("Link files instead of copying");f.push(" </label>");f.push("</div>");f.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');f.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');f.push('<div id="jstree_browser">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateImportPathModal:function(){var f=[];f.push('<div id="file_browser_modal">');f.push('<label class="checkbox-inline jstree-preserve-structure">');f.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');f.push("Preserve directory structure");f.push(" </label>");f.push('<label class="checkbox-inline jstree-link-files">');f.push(' <input class="link-checkbox" type="checkbox" value="link_files">');f.push("Link files instead of copying");f.push(" </label>");f.push("</div>");f.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');f.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');f.push("</div>");return _.template(f.join(""))},templateAddFilesFromHistory:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push("<br/>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("<strong>Choose the datasets to import:</strong>");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}});
\ No newline at end of file
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa static/scripts/packed/mvc/ui/ui-select.js
--- a/static/scripts/packed/mvc/ui/ui-select.js
+++ b/static/scripts/packed/mvc/ui/ui-select.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:false,minimumInputLength:0,initialData:""},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(!this.options.multiple){if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){if(!this.options.multiple){var d=this._getValue();var c={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,};this.$el.select2(c);this._setValue(d)}else{var c={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(c)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:false,minimumInputLength:0,initialData:""},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(!this.options.multiple){if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){if(!this.options.multiple){var d=this._getValue();var c={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,width:"resolve",dropdownAutoWidth:true};this.$el.select2(c);this._setValue(d)}else{var c={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(c)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}});
\ No newline at end of file
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1232,8 +1232,7 @@
.select2-offscreen,.select2-offscreen:focus{clip:rect(0 0 0 0) !important;width:1px !important;height:1px !important;border:0 !important;margin:0 !important;padding:0 !important;overflow:hidden !important;position:absolute !important;outline:0 !important;left:0px !important;top:0px !important}
.select2-display-none{display:none}
.select2-measure-scrollbar{position:absolute;top:-10000px;left:-10000px;width:100px;height:100px;overflow:scroll}
-@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.select2-container{min-width:256px}
-.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px}
+@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px}
.galaxy-frame .toggle{color:gold}
.galaxy-frame .frame-background{z-index:1000;position:absolute;display:none;top:0px;left:0px;height:100%;width:100%;opacity:0.6;background:#000;overflow:auto}
.galaxy-frame .frame-shadow{z-index:1001;position:absolute;display:none;top:0px;left:0px;opacity:0.5;background:#2c3143;border:1px solid #888}
diff -r cda6be2edfe6dbc07d97d18a0d0f1160376a6b9d -r 37e5c86d9fc0d5c1c9defd3cc8a4c37c24ed13fa static/style/src/less/base.less
--- a/static/style/src/less/base.less
+++ b/static/style/src/less/base.less
@@ -15,10 +15,6 @@
}
@import "select2.less";
-/* fix for zero width select2 - remove when fixed there */
-.select2-container {
- min-width: 256px;
-}
// galaxy sub-components
@import "frame.less";
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/366f58570550/
Changeset: 366f58570550
User: martenson
Date: 2014-09-18 16:45:04+00:00
Summary: removed the fix setting min-width to all select2 containers, I believe it is unnecessary with width: 'resolve' and dropdownAutoWidth: true settings
Affected #: 8 files
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 366f5857055021b69fe623acd4101707c9fe569a client/galaxy/scripts/galaxy.base.js
--- a/client/galaxy/scripts/galaxy.base.js
+++ b/client/galaxy/scripts/galaxy.base.js
@@ -237,7 +237,8 @@
$.fn.refresh_select2 = function() {
var select_elt = $(this);
var options = { width: "resolve",
- closeOnSelect: !select_elt.is("[MULTIPLE]")
+ closeOnSelect: !select_elt.is("[MULTIPLE]"),
+ dropdownAutoWidth : true
};
return select_elt.select2( options );
}
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 366f5857055021b69fe623acd4101707c9fe569a client/galaxy/scripts/mvc/ui/ui-select.js
--- a/client/galaxy/scripts/mvc/ui/ui-select.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select.js
@@ -155,6 +155,8 @@
data : this.select_data,
containerCssClass : this.options.css,
placeholder : this.options.placeholder,
+ width : 'resolve',
+ dropdownAutoWidth : true
};
this.$el.select2(select_opt);
// select previous value (if exists)
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 366f5857055021b69fe623acd4101707c9fe569a static/scripts/galaxy.base.js
--- a/static/scripts/galaxy.base.js
+++ b/static/scripts/galaxy.base.js
@@ -237,7 +237,8 @@
$.fn.refresh_select2 = function() {
var select_elt = $(this);
var options = { width: "resolve",
- closeOnSelect: !select_elt.is("[MULTIPLE]")
+ closeOnSelect: !select_elt.is("[MULTIPLE]"),
+ dropdownAutoWidth : true
};
return select_elt.select2( options );
}
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 366f5857055021b69fe623acd4101707c9fe569a static/scripts/mvc/ui/ui-select.js
--- a/static/scripts/mvc/ui/ui-select.js
+++ b/static/scripts/mvc/ui/ui-select.js
@@ -155,6 +155,8 @@
data : this.select_data,
containerCssClass : this.options.css,
placeholder : this.options.placeholder,
+ width : 'resolve',
+ dropdownAutoWidth : true
};
this.$el.select2(select_opt);
// select previous value (if exists)
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 366f5857055021b69fe623acd4101707c9fe569a static/scripts/packed/galaxy.base.js
--- a/static/scripts/packed/galaxy.base.js
+++ b/static/scripts/packed/galaxy.base.js
@@ -1,1 +1,1 @@
-(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){var l=i.action||i;g.append($("<li></li>").append($("<a>").attr("href",i.url).html(j).click(l)))}else{g.append($("<li></li>").addClass("head").append($("<a href='#'></a>").html(j)))}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>").append(g).appendTo("body");var e=d.pageX-h.width()/2;e=Math.min(e,$(document).scrollLeft()+$(window).width()-$(h).width()-5);e=Math.max(e,$(document).scrollLeft()+5);h.css({top:d.pageY,left:e})},10);setTimeout(function(){var f=function(h){$(h).bind("click.close_popup",function(){$(".popmenu-wrapper").remove();h.unbind("click.close_popup")})};f($(window.document));f($(window.top.document));for(var e=window.top.frames.length;e--;){var g=$(window.top.frames[e].document);f(g)}},50);return false})}function make_popup_menus(a){a=a||document;$(a).find("div[popupmenu]").each(function(){var b={};var d=$(this);d.find("a").each(function(){var g=$(this),i=g.get(0),e=i.getAttribute("confirm"),f=i.getAttribute("href"),h=i.getAttribute("target");if(!f){b[g.text()]=null}else{b[g.text()]={url:f,action:function(){if(!e||confirm(e)){if(h){window.open(f,h);return false}else{g.click()}}}}}});var c=$(a).find("#"+d.attr("popupmenu"));c.find("a").bind("click",function(f){f.stopPropagation();return true});make_popupmenu(c,b);c.addClass("popup");d.remove()})}function naturalSort(j,h){var p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(d<o){return -1}else{if(d>o){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);i<c;i++){m=parseFloat(n[i])||n[i];f=parseFloat(e[i])||e[i];if(m<f){return -1}else{if(m>f){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={width:"resolve",closeOnSelect:!b.is("[MULTIPLE]")};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this).not("[multiple]");var d=e.find("option").length;if((d<a)||(d>c)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=("cur_text" in g?g.cur_text:a.text()),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}m.stopPropagation()})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).click(function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}jQuery.fn.preventDoubleSubmission=function(){$(this).on("submit",function(b){var a=$(this);if(a.data("submitted")===true){b.preventDefault()}else{a.data("submitted",true)}});return this};$(document).ready(function(){init_refresh_on_change();if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip()}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})});
\ No newline at end of file
+(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){var l=i.action||i;g.append($("<li></li>").append($("<a>").attr("href",i.url).html(j).click(l)))}else{g.append($("<li></li>").addClass("head").append($("<a href='#'></a>").html(j)))}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>").append(g).appendTo("body");var e=d.pageX-h.width()/2;e=Math.min(e,$(document).scrollLeft()+$(window).width()-$(h).width()-5);e=Math.max(e,$(document).scrollLeft()+5);h.css({top:d.pageY,left:e})},10);setTimeout(function(){var f=function(h){$(h).bind("click.close_popup",function(){$(".popmenu-wrapper").remove();h.unbind("click.close_popup")})};f($(window.document));f($(window.top.document));for(var e=window.top.frames.length;e--;){var g=$(window.top.frames[e].document);f(g)}},50);return false})}function make_popup_menus(a){a=a||document;$(a).find("div[popupmenu]").each(function(){var b={};var d=$(this);d.find("a").each(function(){var g=$(this),i=g.get(0),e=i.getAttribute("confirm"),f=i.getAttribute("href"),h=i.getAttribute("target");if(!f){b[g.text()]=null}else{b[g.text()]={url:f,action:function(){if(!e||confirm(e)){if(h){window.open(f,h);return false}else{g.click()}}}}}});var c=$(a).find("#"+d.attr("popupmenu"));c.find("a").bind("click",function(f){f.stopPropagation();return true});make_popupmenu(c,b);c.addClass("popup");d.remove()})}function naturalSort(j,h){var p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(d<o){return -1}else{if(d>o){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);i<c;i++){m=parseFloat(n[i])||n[i];f=parseFloat(e[i])||e[i];if(m<f){return -1}else{if(m>f){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={width:"resolve",closeOnSelect:!b.is("[MULTIPLE]"),dropdownAutoWidth:true};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this).not("[multiple]");var d=e.find("option").length;if((d<a)||(d>c)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=("cur_text" in g?g.cur_text:a.text()),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}m.stopPropagation()})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).click(function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}jQuery.fn.preventDoubleSubmission=function(){$(this).on("submit",function(b){var a=$(this);if(a.data("submitted")===true){b.preventDefault()}else{a.data("submitted",true)}});return this};$(document).ready(function(){init_refresh_on_change();if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip()}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})});
\ No newline at end of file
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 366f5857055021b69fe623acd4101707c9fe569a static/scripts/packed/mvc/ui/ui-select.js
--- a/static/scripts/packed/mvc/ui/ui-select.js
+++ b/static/scripts/packed/mvc/ui/ui-select.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:false,minimumInputLength:0,initialData:""},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(!this.options.multiple){if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){if(!this.options.multiple){var d=this._getValue();var c={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,};this.$el.select2(c);this._setValue(d)}else{var c={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(c)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:false,minimumInputLength:0,initialData:""},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(!this.options.multiple){if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){if(!this.options.multiple){var d=this._getValue();var c={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,width:"resolve",dropdownAutoWidth:true};this.$el.select2(c);this._setValue(d)}else{var c={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(c)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}});
\ No newline at end of file
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 366f5857055021b69fe623acd4101707c9fe569a static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1232,8 +1232,7 @@
.select2-offscreen,.select2-offscreen:focus{clip:rect(0 0 0 0) !important;width:1px !important;height:1px !important;border:0 !important;margin:0 !important;padding:0 !important;overflow:hidden !important;position:absolute !important;outline:0 !important;left:0px !important;top:0px !important}
.select2-display-none{display:none}
.select2-measure-scrollbar{position:absolute;top:-10000px;left:-10000px;width:100px;height:100px;overflow:scroll}
-@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.select2-container{min-width:256px}
-.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px}
+@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px}
.galaxy-frame .toggle{color:gold}
.galaxy-frame .frame-background{z-index:1000;position:absolute;display:none;top:0px;left:0px;height:100%;width:100%;opacity:0.6;background:#000;overflow:auto}
.galaxy-frame .frame-shadow{z-index:1001;position:absolute;display:none;top:0px;left:0px;opacity:0.5;background:#2c3143;border:1px solid #888}
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 366f5857055021b69fe623acd4101707c9fe569a static/style/src/less/base.less
--- a/static/style/src/less/base.less
+++ b/static/style/src/less/base.less
@@ -15,10 +15,6 @@
}
@import "select2.less";
-/* fix for zero width select2 - remove when fixed there */
-.select2-container {
- min-width: 256px;
-}
// galaxy sub-components
@import "frame.less";
https://bitbucket.org/galaxy/galaxy-central/commits/e6996e0ec636/
Changeset: e6996e0ec636
User: martenson
Date: 2014-09-18 18:48:50+00:00
Summary: tweaks to UI for library import, also added ext types and genome selection
Affected #: 6 files
diff -r 366f5857055021b69fe623acd4101707c9fe569a -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab client/galaxy/scripts/mvc/library/library-folderlist-view.js
--- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
@@ -1,4 +1,3 @@
-// dependencies
define([
"galaxy.masthead",
"utils/utils",
diff -r 366f5857055021b69fe623acd4101707c9fe569a -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -2,11 +2,15 @@
"galaxy.masthead",
"utils/utils",
"libs/toastr",
- "mvc/library/library-model"],
+ "mvc/library/library-model",
+ "mvc/ui/ui-select"
+ ],
function( mod_masthead,
- mod_utils,
- mod_toastr,
- mod_library_model ) {
+ mod_utils,
+ mod_toastr,
+ mod_library_model,
+ mod_select
+ ){
var FolderToolbarView = Backbone.View.extend({
el: '#center',
@@ -37,8 +41,28 @@
// user's histories
histories : null,
+ // genome select
+ select_genome : null,
+
+ // extension select
+ select_extension : null,
+
+ // extension types
+ list_extensions :[],
+
+ // datatype placeholder for extension auto-detection
+ auto: {
+ id : 'auto',
+ text : 'Auto-detect',
+ description : 'This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.'
+ },
+
+ // genomes
+ list_genomes : [],
+
initialize: function(options){
this.options = _.defaults( options || {}, this.defaults );
+ this.fetchExtAndGenomes();
this.render();
},
@@ -321,7 +345,7 @@
var template_modal = this.templateImportPathModal();
this.modal.show({
closing_events : true,
- title : 'Enter paths relative to Galaxy root',
+ title : 'Please enter paths to import',
body : template_modal({}),
buttons : {
'Import' : function() {that.importFromPathsClicked(that);},
@@ -332,9 +356,65 @@
Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
}
});
+ this.renderSelectBoxes();
},
/**
+ * Request all extensions and genomes from Galaxy
+ * and save them sorted in arrays.
+ */
+ fetchExtAndGenomes: function(){
+ var that = this;
+ mod_utils.get(galaxy_config.root + "api/datatypes?extension_only=False",
+ function(datatypes) {
+ for (key in datatypes) {
+ that.list_extensions.push({
+ id : datatypes[key].extension,
+ text : datatypes[key].extension,
+ description : datatypes[key].description,
+ description_url : datatypes[key].description_url
+ });
+ }
+ that.list_extensions.sort(function(a, b) {
+ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
+ });
+ that.list_extensions.unshift(that.auto);
+
+ });
+ mod_utils.get(galaxy_config.root + "api/genomes",
+ function(genomes) {
+ for (key in genomes) {
+ that.list_genomes.push({
+ id : genomes[key][1],
+ text : genomes[key][0]
+ });
+ }
+ that.list_genomes.sort(function(a, b) {
+ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
+ });
+ });
+ },
+
+ renderSelectBoxes: function(){
+ // This won't work properly unlesss we already have the data fetched.
+ // See this.fetchExtAndGenomes()
+ // TODO switch to common resources:
+ // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy…
+ var that = this;
+ this.select_genome = new mod_select.View( {
+ css: 'genome',
+ data: that.list_genomes,
+ container: Galaxy.modal.$el.find( '#genome' ),
+ value: '?'
+ } );
+ this.select_extension = new mod_select.View({
+ css: 'extension',
+ data: that.list_extensions,
+ container: Galaxy.modal.$el.find('#extension'),
+ value: 'auto'
+ });
+ },
+ /**
* Create modal for importing form user's directory
* on Galaxy. Bind jQuery events.
*/
@@ -343,18 +423,20 @@
this.modal = Galaxy.modal;
var template_modal = this.templateBrowserModal();
this.modal.show({
- closing_events : true,
- title : 'Select folders or files to import',
- body : template_modal({}),
- buttons : {
- 'Import' : function() {that.importFromUserdirClicked(that);},
- 'Close' : function() {Galaxy.modal.hide();}
- },
- closing_callback: function(){
- // TODO: should not trigger routes outside of the router
- Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
- }
- });
+ closing_events : true,
+ title : 'Please select folders or files',
+ body : template_modal({}),
+ buttons : {
+ 'Import' : function() {that.importFromUserdirClicked(that);},
+ 'Close' : function() {Galaxy.modal.hide();}
+ },
+ closing_callback: function(){
+ // TODO: should not trigger routes outside of the router
+ Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
+ }
+ });
+
+ this.renderSelectBoxes();
this.renderJstree({disabled_jstree_element: 'folders'});
$('input[type=radio]').change(function(event){
@@ -431,6 +513,8 @@
importFromPathsClicked: function(){
var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
+ var file_type = this.select_extension.value();
+ var dbkey = this.select_genome.value();
var paths = $('textarea#import_paths').val();
var valid_paths = [];
if (!paths){
@@ -445,7 +529,12 @@
}
};
this.initChainCallControl( { length: valid_paths.length, action: 'adding_datasets' } );
- this.chainCallImportingFolders(valid_paths, preserve_dirs, link_data, 'admin_path');
+ this.chainCallImportingFolders( { paths: valid_paths,
+ preserve_dirs: preserve_dirs,
+ link_data: link_data,
+ source: 'admin_path',
+ file_type: file_type,
+ dbkey: dbkey } );
}
},
@@ -494,6 +583,8 @@
var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' );
var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' );
+ var file_type = this.select_extension.value();
+ var dbkey = this.select_genome.value();
var selection_type = selected_nodes[0].type;
var paths = [];
if ( selected_nodes.length < 1 ){
@@ -507,9 +598,17 @@
}
this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } );
if ( selection_type === 'folder' ){
- this.chainCallImportingFolders( paths, preserve_dirs, link_data, 'userdir_folder' );
+
+ this.chainCallImportingFolders( { paths: paths,
+ preserve_dirs: preserve_dirs,
+ link_data: link_data,
+ source: 'userdir_folder',
+ file_type: file_type,
+ dbkey: dbkey } );
} else if ( selection_type === 'file' ){
- this.chainCallImportingUserdirFiles( paths );
+ this.chainCallImportingUserdirFiles( { paths : paths,
+ file_type: file_type,
+ dbkey: dbkey } );
}
}
},
@@ -600,9 +699,10 @@
* calling them in chain. Update the progress bar in between each.
* @param {array} paths paths relative to user folder on Galaxy
*/
- chainCallImportingUserdirFiles: function( paths ){
+ chainCallImportingUserdirFiles: function( options ){
+
var that = this;
- var popped_item = paths.pop();
+ var popped_item = options.paths.pop();
if ( typeof popped_item === "undefined" ) {
if ( this.options.chain_call_control.failed_number === 0 ){
mod_toastr.success( 'Selected files imported into the current folder' );
@@ -614,15 +714,17 @@
}
var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
'&source=userdir_file' +
- '&path=' + popped_item ) )
+ '&path=' + popped_item +
+ '&file_type=' + options.file_type +
+ '&dbkey=' + options.dbkey ) )
promise.done( function( response ){
that.updateProgress();
- that.chainCallImportingUserdirFiles( paths );
+ that.chainCallImportingUserdirFiles( options );
} )
.fail( function(){
that.options.chain_call_control.failed_number += 1;
that.updateProgress();
- that.chainCallImportingUserdirFiles( paths );
+ that.chainCallImportingUserdirFiles( options );
} );
},
@@ -635,10 +737,10 @@
* @param {str} source string representing what type of folder
* is the source of import
*/
- chainCallImportingFolders: function(paths, preserve_dirs, link_data, source){
- // need to check which paths to call
+ chainCallImportingFolders: function( options ){
+ // TODO need to check which paths to call
var that = this;
- var popped_item = paths.pop();
+ var popped_item = options.paths.pop();
if (typeof popped_item == "undefined") {
if (this.options.chain_call_control.failed_number === 0){
mod_toastr.success('Selected folders and their contents imported into the current folder.');
@@ -649,19 +751,31 @@
}
return true;
}
- var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id +
- '&source=' + source +
- '&path=' + popped_item +
- '&preserve_dirs=' + preserve_dirs +
- '&link_data=' + link_data))
+ var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
+ '&source=' + options.source +
+ '&path=' + popped_item +
+ '&preserve_dirs=' + options.preserve_dirs +
+ '&link_data=' + options.link_data +
+ '&file_type=' + options.file_type +
+ '&dbkey=' + options.dbkey ) )
promise.done(function(response){
that.updateProgress();
- that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+ that.chainCallImportingFolders( { paths: options.paths,
+ preserve_dirs: options.preserve_dirs,
+ link_data: options.link_data,
+ source: options.source,
+ file_type: options.file_type,
+ dbkey: options.dbkey } );
})
.fail(function(){
that.options.chain_call_control.failed_number += 1;
that.updateProgress();
- that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+ that.chainCallImportingFolders( { paths: options.paths,
+ preserve_dirs: options.preserve_dirs,
+ link_data: options.link_data,
+ source: options.source,
+ file_type: options.file_type,
+ dbkey: options.dbkey } );
});
},
@@ -1012,7 +1126,10 @@
var tmpl_array = [];
tmpl_array.push('<div id="file_browser_modal">');
+ tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
+ tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
+
tmpl_array.push('<div style="margin-bottom:1em;">');
tmpl_array.push('<label class="radio-inline">');
tmpl_array.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');
@@ -1020,22 +1137,25 @@
tmpl_array.push('<label class="radio-inline">');
tmpl_array.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');
tmpl_array.push('</label>');
-
+ tmpl_array.push('</div>');
+ tmpl_array.push('<div style="margin-bottom:1em;">');
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
tmpl_array.push('Preserve directory structure');
tmpl_array.push(' </label>');
-
tmpl_array.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
tmpl_array.push('Link files instead of copying');
tmpl_array.push(' </label>');
tmpl_array.push('</div>');
+ tmpl_array.push('<div id="jstree_browser">');
+ tmpl_array.push('</div>');
- tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
- tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
-
- tmpl_array.push('<div id="jstree_browser">');
+ tmpl_array.push('<hr />');
+ tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
+ tmpl_array.push('<div>');
+ tmpl_array.push('Type: <span id="extension" class="extension" />');
+ tmpl_array.push(' Genome: <span id="genome" class="genome" />');
tmpl_array.push('</div>');
tmpl_array.push('</div>');
@@ -1046,21 +1166,28 @@
var tmpl_array = [];
tmpl_array.push('<div id="file_browser_modal">');
+ tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
+ tmpl_array.push('<div style="margin-bottom: 0.5em;">');
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure">');
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
tmpl_array.push('Preserve directory structure');
tmpl_array.push(' </label>');
-
tmpl_array.push('<label class="checkbox-inline jstree-link-files">');
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
tmpl_array.push('Link files instead of copying');
tmpl_array.push(' </label>');
tmpl_array.push('</div>');
- tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
+ tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');
- tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');
+ tmpl_array.push('<hr />');
+ tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
+ tmpl_array.push('<div>');
+ tmpl_array.push('Type: <span id="extension" class="extension" />');
+ tmpl_array.push(' Genome: <span id="genome" class="genome" />');
+ tmpl_array.push('</div>');
+
tmpl_array.push('</div>');
return _.template(tmpl_array.join(''));
diff -r 366f5857055021b69fe623acd4101707c9fe569a -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab lib/galaxy/webapps/galaxy/api/lda_datasets.py
--- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
@@ -414,9 +414,9 @@
kwd[ 'space_to_tab' ] = 'False'
kwd[ 'to_posix_lines' ] = 'True'
- kwd[ 'dbkey' ] = '?'
- kwd[ 'file_type' ] = 'auto'
-
+
+ kwd[ 'dbkey' ] = kwd.get( 'dbkey', '?' )
+ kwd[ 'file_type' ] = kwd.get( 'file_type', 'auto' )
kwd[' link_data_only' ] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files'
encoded_folder_id = kwd.get( 'encoded_folder_id', None )
if encoded_folder_id is not None:
@@ -473,9 +473,6 @@
trans, 'api', params, os.path.basename( file ), file, 'server_dir', library_bunch ) )
# user wants to import whole folder
if source == "userdir_folder":
- # import_folder_root = [next(part for part in path.split(os.path.sep) if part) for path in [os.path.splitdrive(path_to_root_import_folder)[1]]]
- # new_folder = self.folder_manager.create( trans, folder_id, import_folder_root[0] )
-
uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets(
trans, 'api', params, library_bunch, 200, '' )
uploaded_datasets = uploaded_datasets_bunch[0]
@@ -495,7 +492,6 @@
for ud in uploaded_datasets:
ud.path = os.path.abspath( ud.path )
abspath_datasets.append( ud )
-
json_file_path = upload_common.create_paramfile( trans, abspath_datasets )
data_list = [ ud.data for ud in abspath_datasets ]
job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=folder )
diff -r 366f5857055021b69fe623acd4101707c9fe569a -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab static/scripts/mvc/library/library-folderlist-view.js
--- a/static/scripts/mvc/library/library-folderlist-view.js
+++ b/static/scripts/mvc/library/library-folderlist-view.js
@@ -1,4 +1,3 @@
-// dependencies
define([
"galaxy.masthead",
"utils/utils",
diff -r 366f5857055021b69fe623acd4101707c9fe569a -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab static/scripts/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/mvc/library/library-foldertoolbar-view.js
@@ -2,11 +2,15 @@
"galaxy.masthead",
"utils/utils",
"libs/toastr",
- "mvc/library/library-model"],
+ "mvc/library/library-model",
+ "mvc/ui/ui-select"
+ ],
function( mod_masthead,
- mod_utils,
- mod_toastr,
- mod_library_model ) {
+ mod_utils,
+ mod_toastr,
+ mod_library_model,
+ mod_select
+ ){
var FolderToolbarView = Backbone.View.extend({
el: '#center',
@@ -37,8 +41,28 @@
// user's histories
histories : null,
+ // genome select
+ select_genome : null,
+
+ // extension select
+ select_extension : null,
+
+ // extension types
+ list_extensions :[],
+
+ // datatype placeholder for extension auto-detection
+ auto: {
+ id : 'auto',
+ text : 'Auto-detect',
+ description : 'This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.'
+ },
+
+ // genomes
+ list_genomes : [],
+
initialize: function(options){
this.options = _.defaults( options || {}, this.defaults );
+ this.fetchExtAndGenomes();
this.render();
},
@@ -321,7 +345,7 @@
var template_modal = this.templateImportPathModal();
this.modal.show({
closing_events : true,
- title : 'Enter paths relative to Galaxy root',
+ title : 'Please enter paths to import',
body : template_modal({}),
buttons : {
'Import' : function() {that.importFromPathsClicked(that);},
@@ -332,9 +356,65 @@
Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
}
});
+ this.renderSelectBoxes();
},
/**
+ * Request all extensions and genomes from Galaxy
+ * and save them sorted in arrays.
+ */
+ fetchExtAndGenomes: function(){
+ var that = this;
+ mod_utils.get(galaxy_config.root + "api/datatypes?extension_only=False",
+ function(datatypes) {
+ for (key in datatypes) {
+ that.list_extensions.push({
+ id : datatypes[key].extension,
+ text : datatypes[key].extension,
+ description : datatypes[key].description,
+ description_url : datatypes[key].description_url
+ });
+ }
+ that.list_extensions.sort(function(a, b) {
+ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
+ });
+ that.list_extensions.unshift(that.auto);
+
+ });
+ mod_utils.get(galaxy_config.root + "api/genomes",
+ function(genomes) {
+ for (key in genomes) {
+ that.list_genomes.push({
+ id : genomes[key][1],
+ text : genomes[key][0]
+ });
+ }
+ that.list_genomes.sort(function(a, b) {
+ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
+ });
+ });
+ },
+
+ renderSelectBoxes: function(){
+ // This won't work properly unlesss we already have the data fetched.
+ // See this.fetchExtAndGenomes()
+ // TODO switch to common resources:
+ // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy…
+ var that = this;
+ this.select_genome = new mod_select.View( {
+ css: 'genome',
+ data: that.list_genomes,
+ container: Galaxy.modal.$el.find( '#genome' ),
+ value: '?'
+ } );
+ this.select_extension = new mod_select.View({
+ css: 'extension',
+ data: that.list_extensions,
+ container: Galaxy.modal.$el.find('#extension'),
+ value: 'auto'
+ });
+ },
+ /**
* Create modal for importing form user's directory
* on Galaxy. Bind jQuery events.
*/
@@ -343,18 +423,20 @@
this.modal = Galaxy.modal;
var template_modal = this.templateBrowserModal();
this.modal.show({
- closing_events : true,
- title : 'Select folders or files to import',
- body : template_modal({}),
- buttons : {
- 'Import' : function() {that.importFromUserdirClicked(that);},
- 'Close' : function() {Galaxy.modal.hide();}
- },
- closing_callback: function(){
- // TODO: should not trigger routes outside of the router
- Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
- }
- });
+ closing_events : true,
+ title : 'Please select folders or files',
+ body : template_modal({}),
+ buttons : {
+ 'Import' : function() {that.importFromUserdirClicked(that);},
+ 'Close' : function() {Galaxy.modal.hide();}
+ },
+ closing_callback: function(){
+ // TODO: should not trigger routes outside of the router
+ Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
+ }
+ });
+
+ this.renderSelectBoxes();
this.renderJstree({disabled_jstree_element: 'folders'});
$('input[type=radio]').change(function(event){
@@ -431,6 +513,8 @@
importFromPathsClicked: function(){
var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
+ var file_type = this.select_extension.value();
+ var dbkey = this.select_genome.value();
var paths = $('textarea#import_paths').val();
var valid_paths = [];
if (!paths){
@@ -445,7 +529,12 @@
}
};
this.initChainCallControl( { length: valid_paths.length, action: 'adding_datasets' } );
- this.chainCallImportingFolders(valid_paths, preserve_dirs, link_data, 'admin_path');
+ this.chainCallImportingFolders( { paths: valid_paths,
+ preserve_dirs: preserve_dirs,
+ link_data: link_data,
+ source: 'admin_path',
+ file_type: file_type,
+ dbkey: dbkey } );
}
},
@@ -494,6 +583,8 @@
var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' );
var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' );
+ var file_type = this.select_extension.value();
+ var dbkey = this.select_genome.value();
var selection_type = selected_nodes[0].type;
var paths = [];
if ( selected_nodes.length < 1 ){
@@ -507,9 +598,17 @@
}
this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } );
if ( selection_type === 'folder' ){
- this.chainCallImportingFolders( paths, preserve_dirs, link_data, 'userdir_folder' );
+
+ this.chainCallImportingFolders( { paths: paths,
+ preserve_dirs: preserve_dirs,
+ link_data: link_data,
+ source: 'userdir_folder',
+ file_type: file_type,
+ dbkey: dbkey } );
} else if ( selection_type === 'file' ){
- this.chainCallImportingUserdirFiles( paths );
+ this.chainCallImportingUserdirFiles( { paths : paths,
+ file_type: file_type,
+ dbkey: dbkey } );
}
}
},
@@ -600,9 +699,10 @@
* calling them in chain. Update the progress bar in between each.
* @param {array} paths paths relative to user folder on Galaxy
*/
- chainCallImportingUserdirFiles: function( paths ){
+ chainCallImportingUserdirFiles: function( options ){
+
var that = this;
- var popped_item = paths.pop();
+ var popped_item = options.paths.pop();
if ( typeof popped_item === "undefined" ) {
if ( this.options.chain_call_control.failed_number === 0 ){
mod_toastr.success( 'Selected files imported into the current folder' );
@@ -614,15 +714,17 @@
}
var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
'&source=userdir_file' +
- '&path=' + popped_item ) )
+ '&path=' + popped_item +
+ '&file_type=' + options.file_type +
+ '&dbkey=' + options.dbkey ) )
promise.done( function( response ){
that.updateProgress();
- that.chainCallImportingUserdirFiles( paths );
+ that.chainCallImportingUserdirFiles( options );
} )
.fail( function(){
that.options.chain_call_control.failed_number += 1;
that.updateProgress();
- that.chainCallImportingUserdirFiles( paths );
+ that.chainCallImportingUserdirFiles( options );
} );
},
@@ -635,10 +737,10 @@
* @param {str} source string representing what type of folder
* is the source of import
*/
- chainCallImportingFolders: function(paths, preserve_dirs, link_data, source){
- // need to check which paths to call
+ chainCallImportingFolders: function( options ){
+ // TODO need to check which paths to call
var that = this;
- var popped_item = paths.pop();
+ var popped_item = options.paths.pop();
if (typeof popped_item == "undefined") {
if (this.options.chain_call_control.failed_number === 0){
mod_toastr.success('Selected folders and their contents imported into the current folder.');
@@ -649,19 +751,31 @@
}
return true;
}
- var promise = $.when($.post('/api/libraries/datasets?encoded_folder_id=' + that.id +
- '&source=' + source +
- '&path=' + popped_item +
- '&preserve_dirs=' + preserve_dirs +
- '&link_data=' + link_data))
+ var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
+ '&source=' + options.source +
+ '&path=' + popped_item +
+ '&preserve_dirs=' + options.preserve_dirs +
+ '&link_data=' + options.link_data +
+ '&file_type=' + options.file_type +
+ '&dbkey=' + options.dbkey ) )
promise.done(function(response){
that.updateProgress();
- that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+ that.chainCallImportingFolders( { paths: options.paths,
+ preserve_dirs: options.preserve_dirs,
+ link_data: options.link_data,
+ source: options.source,
+ file_type: options.file_type,
+ dbkey: options.dbkey } );
})
.fail(function(){
that.options.chain_call_control.failed_number += 1;
that.updateProgress();
- that.chainCallImportingFolders(paths, preserve_dirs, link_data, source);
+ that.chainCallImportingFolders( { paths: options.paths,
+ preserve_dirs: options.preserve_dirs,
+ link_data: options.link_data,
+ source: options.source,
+ file_type: options.file_type,
+ dbkey: options.dbkey } );
});
},
@@ -1012,7 +1126,10 @@
var tmpl_array = [];
tmpl_array.push('<div id="file_browser_modal">');
+ tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
+ tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
+
tmpl_array.push('<div style="margin-bottom:1em;">');
tmpl_array.push('<label class="radio-inline">');
tmpl_array.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');
@@ -1020,22 +1137,25 @@
tmpl_array.push('<label class="radio-inline">');
tmpl_array.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');
tmpl_array.push('</label>');
-
+ tmpl_array.push('</div>');
+ tmpl_array.push('<div style="margin-bottom:1em;">');
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
tmpl_array.push('Preserve directory structure');
tmpl_array.push(' </label>');
-
tmpl_array.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
tmpl_array.push('Link files instead of copying');
tmpl_array.push(' </label>');
tmpl_array.push('</div>');
+ tmpl_array.push('<div id="jstree_browser">');
+ tmpl_array.push('</div>');
- tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
- tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
-
- tmpl_array.push('<div id="jstree_browser">');
+ tmpl_array.push('<hr />');
+ tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
+ tmpl_array.push('<div>');
+ tmpl_array.push('Type: <span id="extension" class="extension" />');
+ tmpl_array.push(' Genome: <span id="genome" class="genome" />');
tmpl_array.push('</div>');
tmpl_array.push('</div>');
@@ -1046,21 +1166,28 @@
var tmpl_array = [];
tmpl_array.push('<div id="file_browser_modal">');
+ tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
+ tmpl_array.push('<div style="margin-bottom: 0.5em;">');
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure">');
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
tmpl_array.push('Preserve directory structure');
tmpl_array.push(' </label>');
-
tmpl_array.push('<label class="checkbox-inline jstree-link-files">');
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
tmpl_array.push('Link files instead of copying');
tmpl_array.push(' </label>');
tmpl_array.push('</div>');
- tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
+ tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');
- tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');
+ tmpl_array.push('<hr />');
+ tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
+ tmpl_array.push('<div>');
+ tmpl_array.push('Type: <span id="extension" class="extension" />');
+ tmpl_array.push(' Genome: <span id="genome" class="genome" />');
+ tmpl_array.push('</div>');
+
tmpl_array.push('</div>');
return _.template(tmpl_array.join(''));
diff -r 366f5857055021b69fe623acd4101707c9fe569a -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab static/scripts/packed/mvc/library/library-foldertoolbar-view.js
--- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){g.is_admin=Galaxy.currUser.isAdmin();g.is_anonym=Galaxy.currUser.isAnonymous();if(g.user_library_import_dir!==null||g.allow_library_path_paste!==false||g.library_import_dir!==null){g.mutiple_add_dataset_options=true}}this.$el.html(h(g))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(h){h.preventDefault();h.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created.");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})}else{e.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(h){var g=h.templateBulkImportInModal();h.modal=Galaxy.modal;h.modal.show({closing_events:true,title:"Import into History",body:g({histories:h.histories.models}),buttons:{Import:function(){h.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var j=$("select[name=dataset_import_bulk] option:selected").val();var m=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=j;var g=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});var l=[];for(var h=g.length-1;h>=0;h--){var f=g[h];var k=new c.HistoryItem();k.url=k.urlRoot+j+"/contents";k.content=f;k.source="library";l.push(k)}this.initChainCallControl({length:l.length,action:"to_history",history_name:m});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+j);this.chainCallImportingIntoHistory(l,m)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon.")}else{e.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesFromHistory();var h=f.options.full_path[f.options.full_path.length-1][1];f.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+h,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(i){f.fetchAndDisplayHistoryContents(i.target.value)})}else{e.error("An error ocurred.")}})},importFilesFromPathModal:function(){var g=this;this.modal=Galaxy.modal;var f=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Enter paths relative to Galaxy root",body:f({}),buttons:{Import:function(){g.importFromPathsClicked(g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+g.id,{trigger:true})}})},importFilesFromUserdirModal:function(){var g=this;this.modal=Galaxy.modal;var f=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Select folders or files to import",body:f({}),buttons:{Import:function(){g.importFromUserdirClicked(g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+g.id,{trigger:true})}});this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(h){if(h.target.value==="jstree-disable-folders"){g.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(h.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(f){var h=this;this.options=_.extend(this.options,f);var g=this.options.disabled_jstree_element;this.jstree=new c.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+g;this.jstree.fetch({success:function(j,i){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(k){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:j},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},importFromPathsClicked:function(){var f=this.modal.$el.find(".preserve-checkbox").is(":checked");var k=this.modal.$el.find(".link-checkbox").is(":checked");var j=$("textarea#import_paths").val();var h=[];if(!j){e.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");j=j.split("\n");for(var g=j.length-1;g>=0;g--){trimmed=j[g].trim();if(trimmed.length!==0){h.push(trimmed)}}this.initChainCallControl({length:h.length,action:"adding_datasets"});this.chainCallImportingFolders(h,f,k,"admin_path")}},initChainCallControl:function(f){var g;switch(f.action){case"adding_datasets":g=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(g({folder_name:this.options.folder_name}));break;case"deleting_datasets":g=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(g());break;case"to_history":g=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(g({history_name:f.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/f.length;this.options.chain_call_control.total_number=f.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(k){var g=$("#jstree_browser").jstree().get_selected(true);var f=this.modal.$el.find(".preserve-checkbox").is(":checked");var m=this.modal.$el.find(".link-checkbox").is(":checked");var j=g[0].type;var l=[];if(g.length<1){e.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var h=g.length-1;h>=0;h--){if(g[h].li_attr.full_path!==undefined){l.push(g[h].li_attr.full_path)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders(l,f,m,"userdir_folder")}else{if(j==="file"){this.chainCallImportingUserdirFiles(l)}}}},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var k=this.modal.$el.find("#selected_history_content").find(":checked");var f=[];var j=[];if(k.length<1){e.info("You must select some datasets first.")}else{this.modal.disableButton("Add");k.each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.initChainCallControl({length:j.length,action:"adding_datasets"});this.chainCallAddingHdas(j)}},chainCallImportingIntoHistory:function(g,j){var f=this;var h=g.pop();if(typeof h=="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCallImportingIntoHistory(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallImportingIntoHistory(g,j)})},chainCallImportingUserdirFiles:function(i){var f=this;var g=i.pop();if(typeof g==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{e.error("An error occured.")}return true}var h=$.when($.post("/api/libraries/datasets?encoded_folder_id="+f.id+"&source=userdir_file&path="+g));h.done(function(j){f.updateProgress();f.chainCallImportingUserdirFiles(i)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallImportingUserdirFiles(i)})},chainCallImportingFolders:function(k,f,l,i){var g=this;var h=k.pop();if(typeof h=="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{e.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+g.id+"&source="+i+"&path="+h+"&preserve_dirs="+f+"&link_data="+l));j.done(function(m){g.updateProgress();g.chainCallImportingFolders(k,f,l,i)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingFolders(k,f,l,i)})},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h=="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You must select at least one dataset for deletion.")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},showLibInfo:function(){var g=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var f=null;var h=this;if(Galaxy.libraries.libraryListView!==null){f=Galaxy.libraries.libraryListView.collection.get(g);this.showLibInfoModal(f)}else{f=new c.Library({id:g});f.fetch({success:function(){h.showLibInfoModal(f)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred.")}}})}},showLibInfoModal:function(f){var g=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:g({library:f}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(f){switch(f.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();e.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateBrowserModal:function(){var f=[];f.push('<div id="file_browser_modal">');f.push('<div style="margin-bottom:1em;">');f.push('<label class="radio-inline">');f.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');f.push("</label>");f.push('<label class="radio-inline">');f.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');f.push("</label>");f.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');f.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');f.push("Preserve directory structure");f.push(" </label>");f.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');f.push(' <input class="link-checkbox" type="checkbox" value="link_files">');f.push("Link files instead of copying");f.push(" </label>");f.push("</div>");f.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');f.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');f.push('<div id="jstree_browser">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateImportPathModal:function(){var f=[];f.push('<div id="file_browser_modal">');f.push('<label class="checkbox-inline jstree-preserve-structure">');f.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');f.push("Preserve directory structure");f.push(" </label>");f.push('<label class="checkbox-inline jstree-link-files">');f.push(' <input class="link-checkbox" type="checkbox" value="link_files">');f.push("Link files instead of copying");f.push(" </label>");f.push("</div>");f.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');f.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Paths separated by newline"></textarea>');f.push("</div>");return _.template(f.join(""))},templateAddFilesFromHistory:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push("<br/>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("<strong>Choose the datasets to import:</strong>");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/1cf25d3a5cdc/
Changeset: 1cf25d3a5cdc
User: martenson
Date: 2014-09-18 18:49:20+00:00
Summary: Merge
Affected #: 22 files
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
--- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
@@ -257,12 +257,26 @@
// ......................................................................... events
/** event map */
events : _.extend( _.clone( _super.prototype.events ), {
- 'click .undelete-link' : function( ev ){ this.model.undelete(); return false; },
- 'click .purge-link' : '_confirmPurge'
+ 'click .undelete-link' : '_clickUndeleteLink',
+ 'click .purge-link' : '_clickPurgeLink',
+
+ 'click .edit-btn' : function( ev ){ this.trigger( 'edit', this, ev ); },
+ 'click .delete-btn' : function( ev ){ this.trigger( 'delete', this, ev ); },
+ 'click .rerun-btn' : function( ev ){ this.trigger( 'rerun', this, ev ); },
+ 'click .report-err-btn' : function( ev ){ this.trigger( 'report-err', this, ev ); },
+ 'click .visualization-btn' : function( ev ){ this.trigger( 'visualize', this, ev ); },
+ 'click .dbkey a' : function( ev ){ this.trigger( 'edit', this, ev ); }
}),
- /** listener for item purge */
- _confirmPurge : function _confirmPurge( ev ){
+
+ /** listener for item undelete (in the messages section) */
+ _clickUndeleteLink : function( ev ){
+ this.model.undelete();
+ return false;
+ },
+
+ /** listener for item purge (in the messages section) */
+ _clickPurgeLink : function( ev ){
//TODO: confirm dialog
this.model.purge();
return false;
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 client/galaxy/scripts/mvc/dataset/dataset-li.js
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -314,6 +314,13 @@
},
// ......................................................................... misc
+ events : _.extend( _.clone( _super.prototype.events ), {
+ 'click .display-btn' : function( ev ){ this.trigger( 'display', this, ev ); },
+ 'click .params-btn' : function( ev ){ this.trigger( 'params', this, ev ); },
+ 'click .download-btn' : function( ev ){ this.trigger( 'download', this, ev ); }
+ }),
+
+ // ......................................................................... misc
/** String representation */
toString : function(){
var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 client/galaxy/scripts/mvc/history/history-panel-edit-current.js
--- a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js
+++ b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js
@@ -14,7 +14,13 @@
/** should the tags editor be shown or hidden initially? */
tagsEditorShown : false,
/** should the annotation editor be shown or hidden initially? */
- annotationEditorShown : false
+ annotationEditorShown : false,
+ ///** what is the currently focused content (dataset or collection) in the current history?
+ // * (the history panel will highlight and scroll to the focused content view)
+ // */
+ //focusedContentId : null
+ /** Current scroll position */
+ scrollPosition : 0
},
toString : function(){
return 'HistoryPanelPrefs(' + JSON.stringify( this.toJSON() ) + ')';
@@ -70,6 +76,20 @@
/** sub-views that will overlay this panel (collections) */
this.panelStack = [];
+
+ /** id of currently focused content */
+ this.currentContentId = attributes.currentContentId || null;
+ //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value
+ },
+
+ /** Override to cache the current scroll position with a listener */
+ _setUpListeners : function(){
+ _super.prototype._setUpListeners.call( this );
+
+ var panel = this;
+ this.$scrollContainer().on( 'scroll', function( ev ){
+ panel.preferences.set( 'scrollPosition', $( this ).scrollTop() );
+ });
},
// ------------------------------------------------------------------------ loading history/item models
@@ -243,11 +263,34 @@
});
},
+ /** Override to scroll to cached position (in prefs) after swapping */
+ _swapNewRender : function( $newRender ){
+ _super.prototype._swapNewRender.call( this, $newRender );
+ var panel = this;
+
+ _.delay( function(){
+ var pos = panel.preferences.get( 'scrollPosition' );
+ if( pos ){
+ panel.scrollTo( pos );
+ }
+ }, 10 );
+ //TODO: is this enough of a delay on larger histories?
+
+ return this;
+ },
+
// ------------------------------------------------------------------------ sub-views
// reverse HID order
- /** Override to reverse order of views - newest contents on top */
+ /** Override to reverse order of views - newest contents on top
+ * and add the current-content highlight class to currentContentId's view
+ */
_attachItems : function( $whereTo ){
+ var panel = this;
this.$list( $whereTo ).append( this.views.reverse().map( function( view ){
+ // add current content
+ if( panel.currentContentId && view.model.id === panel.currentContentId ){
+ view.$el.addClass( 'current-content' );
+ }
return view.$el;
}));
return this;
@@ -298,9 +341,26 @@
view.on( 'collapsed:drilldown', function( v, drilldown ){
this._collapseDrilldownPanel( drilldown );
}, this );
+
+ // when content is manipulated, make it the current-content
+ view.on( 'display edit params rerun report-err visualize', function( v, ev ){
+ this.setCurrentContent( v );
+ }, this );
+
return this;
},
+ /** display 'current content': add a visible highlight and store the id of a content item */
+ setCurrentContent : function( view ){
+ this.$( '.history-content.current-content' ).removeClass( 'current-content' );
+ if( view ){
+ view.$el.addClass( 'current-content' );
+ this.currentContentId = view.model.id;
+ } else {
+ this.currentContentId = null;
+ }
+ },
+
/** Handle drill down by hiding this panels list and controls and showing the sub-panel */
_expandDrilldownPanel : function( drilldown ){
this.panelStack.push( drilldown );
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 client/galaxy/scripts/mvc/list/list-panel.js
--- a/client/galaxy/scripts/mvc/list/list-panel.js
+++ b/client/galaxy/scripts/mvc/list/list-panel.js
@@ -679,28 +679,28 @@
},
/** set the current scroll position of the panel in its parent */
- scrollTo : function( pos ){
- this.$scrollContainer().scrollTop( pos );
+ scrollTo : function( pos, speed ){
+ speed = speed || 0;
+ this.$scrollContainer().animate({ scrollTop: pos }, speed );
return this;
},
/** Scrolls the panel to the top. */
- scrollToTop : function(){
- this.$scrollContainer().scrollTop( 0 );
- return this;
+ scrollToTop : function( speed ){
+ return this.scrollTo( 0, speed );
},
/** */
- scrollToItem : function( view ){
+ scrollToItem : function( view, speed ){
if( !view ){ return this; }
- var itemTop = view.$el.offset().top;
- this.$scrollContainer().scrollTop( itemTop );
- return this;
+ //var itemTop = view.$el.offset().top;
+ var itemTop = view.$el.position().top;
+ return this.scrollTo( itemTop, speed );
},
/** Scrolls the panel to show the content with the given id. */
- scrollToId : function( id ){
- return this.scrollToItem( this.viewFromModelId( id ) );
+ scrollToId : function( id, speed ){
+ return this.scrollToItem( this.viewFromModelId( id ), speed );
},
// ------------------------------------------------------------------------ panel events
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 client/galaxy/scripts/mvc/tools/tools-repeat.js
--- a/client/galaxy/scripts/mvc/tools/tools-repeat.js
+++ b/client/galaxy/scripts/mvc/tools/tools-repeat.js
@@ -85,7 +85,7 @@
// append content
portlet.append(options.$el);
- // append section row class
+ // tag as section row
portlet.$el.addClass('section-row');
// append to dom
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 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
@@ -141,16 +141,11 @@
cls : 'ui-table-plain'
});
- // create input field wrapper
- var input_element = new InputElement({
- label : '',
- help : input_def.help,
- $el : sub_section.$el,
- highlight : true
- });
+ // displays as grouped subsection
+ sub_section.$el.addClass('ui-table-form-section');
// create table row
- this.table.add(input_element.$el);
+ this.table.add(sub_section.$el);
// append to table
this.table.append(sub_section_id);
@@ -234,7 +229,7 @@
$el : repeat.$el,
highlight : true
});
-
+
// create table row
this.table.add(input_element.$el);
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 lib/galaxy/visualization/registry.py
--- a/lib/galaxy/visualization/registry.py
+++ b/lib/galaxy/visualization/registry.py
@@ -159,7 +159,7 @@
# config file is required, otherwise skip this visualization
plugin[ 'config_file' ] = os.path.join( plugin_path, 'config', ( plugin.name + '.xml' ) )
config = self.config_parser.parse_file( plugin.config_file )
-
+
if not config:
return None
plugin[ 'config' ] = config
@@ -390,14 +390,9 @@
Parse the given XML file for visualizations data.
:returns: visualization config dictionary
"""
- try:
- xml_tree = galaxy.util.parse_xml( xml_filepath )
- visualization = self.parse_visualization( xml_tree.getroot() )
- return visualization
- # skip vis' with parsing errors - don't shutdown the startup
- except ParsingException, parse_exc:
- log.exception( 'Skipped visualization config "%s" due to parsing errors', xml_filepath )
- return None
+ xml_tree = galaxy.util.parse_xml( xml_filepath )
+ visualization = self.parse_visualization( xml_tree.getroot() )
+ return visualization
def parse_visualization( self, xml_tree ):
"""
@@ -406,16 +401,16 @@
"""
returned = {}
- # allow manually turning off a vis by checking for a disabled property
- if 'disabled' in xml_tree.attrib:
-#TODO: differentiate between disabled and failed to parse, log.warn only on failure, log.info otherwise
- return None
-
# a text display name for end user links
returned[ 'name' ] = xml_tree.attrib.get( 'name', None )
if not returned[ 'name' ]:
raise ParsingException( 'visualization needs a name attribute' )
+ # allow manually turning off a vis by checking for a disabled property
+ if 'disabled' in xml_tree.attrib:
+ log.info( '%s, plugin disabled: %s. Skipping...', self, returned[ 'name' ] )
+ return None
+
# record the embeddable flag - defaults to false
# this is a design by contract promise that the visualization can be rendered inside another page
# often by rendering only a DOM fragment. Since this is an advanced feature that requires a bit more
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 lib/galaxy/web/base/pluginframework.py
--- a/lib/galaxy/web/base/pluginframework.py
+++ b/lib/galaxy/web/base/pluginframework.py
@@ -118,15 +118,14 @@
for plugin_path in self.find_plugins():
try:
plugin = self.load_plugin( plugin_path )
- if not plugin:
- log.warn( '%s, plugin load failed or disabled: %s. Skipping...', self, plugin_path )
+
+ if plugin and plugin.name not in self.plugins:
+ self.plugins[ plugin.name ] = plugin
+ log.info( '%s, loaded plugin: %s', self, plugin.name )
#NOTE: prevent silent, implicit overwrite here (two plugins in two diff directories)
#TODO: overwriting may be desired
- elif plugin.name in self.plugins:
+ elif plugin and plugin.name in self.plugins:
log.warn( '%s, plugin with name already exists: %s. Skipping...', self, plugin.name )
- else:
- self.plugins[ plugin.name ] = plugin
- log.info( '%s, loaded plugin: %s', self, plugin.name )
except Exception, exc:
if not self.skip_bad_plugins:
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/mvc/dataset/dataset-li-edit.js
--- a/static/scripts/mvc/dataset/dataset-li-edit.js
+++ b/static/scripts/mvc/dataset/dataset-li-edit.js
@@ -257,12 +257,26 @@
// ......................................................................... events
/** event map */
events : _.extend( _.clone( _super.prototype.events ), {
- 'click .undelete-link' : function( ev ){ this.model.undelete(); return false; },
- 'click .purge-link' : '_confirmPurge'
+ 'click .undelete-link' : '_clickUndeleteLink',
+ 'click .purge-link' : '_clickPurgeLink',
+
+ 'click .edit-btn' : function( ev ){ this.trigger( 'edit', this, ev ); },
+ 'click .delete-btn' : function( ev ){ this.trigger( 'delete', this, ev ); },
+ 'click .rerun-btn' : function( ev ){ this.trigger( 'rerun', this, ev ); },
+ 'click .report-err-btn' : function( ev ){ this.trigger( 'report-err', this, ev ); },
+ 'click .visualization-btn' : function( ev ){ this.trigger( 'visualize', this, ev ); },
+ 'click .dbkey a' : function( ev ){ this.trigger( 'edit', this, ev ); }
}),
- /** listener for item purge */
- _confirmPurge : function _confirmPurge( ev ){
+
+ /** listener for item undelete (in the messages section) */
+ _clickUndeleteLink : function( ev ){
+ this.model.undelete();
+ return false;
+ },
+
+ /** listener for item purge (in the messages section) */
+ _clickPurgeLink : function( ev ){
//TODO: confirm dialog
this.model.purge();
return false;
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/mvc/dataset/dataset-li.js
--- a/static/scripts/mvc/dataset/dataset-li.js
+++ b/static/scripts/mvc/dataset/dataset-li.js
@@ -314,6 +314,13 @@
},
// ......................................................................... misc
+ events : _.extend( _.clone( _super.prototype.events ), {
+ 'click .display-btn' : function( ev ){ this.trigger( 'display', this, ev ); },
+ 'click .params-btn' : function( ev ){ this.trigger( 'params', this, ev ); },
+ 'click .download-btn' : function( ev ){ this.trigger( 'download', this, ev ); }
+ }),
+
+ // ......................................................................... misc
/** String representation */
toString : function(){
var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/mvc/history/history-panel-edit-current.js
--- a/static/scripts/mvc/history/history-panel-edit-current.js
+++ b/static/scripts/mvc/history/history-panel-edit-current.js
@@ -14,7 +14,13 @@
/** should the tags editor be shown or hidden initially? */
tagsEditorShown : false,
/** should the annotation editor be shown or hidden initially? */
- annotationEditorShown : false
+ annotationEditorShown : false,
+ ///** what is the currently focused content (dataset or collection) in the current history?
+ // * (the history panel will highlight and scroll to the focused content view)
+ // */
+ //focusedContentId : null
+ /** Current scroll position */
+ scrollPosition : 0
},
toString : function(){
return 'HistoryPanelPrefs(' + JSON.stringify( this.toJSON() ) + ')';
@@ -70,6 +76,20 @@
/** sub-views that will overlay this panel (collections) */
this.panelStack = [];
+
+ /** id of currently focused content */
+ this.currentContentId = attributes.currentContentId || null;
+ //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value
+ },
+
+ /** Override to cache the current scroll position with a listener */
+ _setUpListeners : function(){
+ _super.prototype._setUpListeners.call( this );
+
+ var panel = this;
+ this.$scrollContainer().on( 'scroll', function( ev ){
+ panel.preferences.set( 'scrollPosition', $( this ).scrollTop() );
+ });
},
// ------------------------------------------------------------------------ loading history/item models
@@ -243,11 +263,34 @@
});
},
+ /** Override to scroll to cached position (in prefs) after swapping */
+ _swapNewRender : function( $newRender ){
+ _super.prototype._swapNewRender.call( this, $newRender );
+ var panel = this;
+
+ _.delay( function(){
+ var pos = panel.preferences.get( 'scrollPosition' );
+ if( pos ){
+ panel.scrollTo( pos );
+ }
+ }, 10 );
+ //TODO: is this enough of a delay on larger histories?
+
+ return this;
+ },
+
// ------------------------------------------------------------------------ sub-views
// reverse HID order
- /** Override to reverse order of views - newest contents on top */
+ /** Override to reverse order of views - newest contents on top
+ * and add the current-content highlight class to currentContentId's view
+ */
_attachItems : function( $whereTo ){
+ var panel = this;
this.$list( $whereTo ).append( this.views.reverse().map( function( view ){
+ // add current content
+ if( panel.currentContentId && view.model.id === panel.currentContentId ){
+ view.$el.addClass( 'current-content' );
+ }
return view.$el;
}));
return this;
@@ -298,9 +341,26 @@
view.on( 'collapsed:drilldown', function( v, drilldown ){
this._collapseDrilldownPanel( drilldown );
}, this );
+
+ // when content is manipulated, make it the current-content
+ view.on( 'display edit params rerun report-err visualize', function( v, ev ){
+ this.setCurrentContent( v );
+ }, this );
+
return this;
},
+ /** display 'current content': add a visible highlight and store the id of a content item */
+ setCurrentContent : function( view ){
+ this.$( '.history-content.current-content' ).removeClass( 'current-content' );
+ if( view ){
+ view.$el.addClass( 'current-content' );
+ this.currentContentId = view.model.id;
+ } else {
+ this.currentContentId = null;
+ }
+ },
+
/** Handle drill down by hiding this panels list and controls and showing the sub-panel */
_expandDrilldownPanel : function( drilldown ){
this.panelStack.push( drilldown );
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/mvc/list/list-panel.js
--- a/static/scripts/mvc/list/list-panel.js
+++ b/static/scripts/mvc/list/list-panel.js
@@ -679,28 +679,28 @@
},
/** set the current scroll position of the panel in its parent */
- scrollTo : function( pos ){
- this.$scrollContainer().scrollTop( pos );
+ scrollTo : function( pos, speed ){
+ speed = speed || 0;
+ this.$scrollContainer().animate({ scrollTop: pos }, speed );
return this;
},
/** Scrolls the panel to the top. */
- scrollToTop : function(){
- this.$scrollContainer().scrollTop( 0 );
- return this;
+ scrollToTop : function( speed ){
+ return this.scrollTo( 0, speed );
},
/** */
- scrollToItem : function( view ){
+ scrollToItem : function( view, speed ){
if( !view ){ return this; }
- var itemTop = view.$el.offset().top;
- this.$scrollContainer().scrollTop( itemTop );
- return this;
+ //var itemTop = view.$el.offset().top;
+ var itemTop = view.$el.position().top;
+ return this.scrollTo( itemTop, speed );
},
/** Scrolls the panel to show the content with the given id. */
- scrollToId : function( id ){
- return this.scrollToItem( this.viewFromModelId( id ) );
+ scrollToId : function( id, speed ){
+ return this.scrollToItem( this.viewFromModelId( id ), speed );
},
// ------------------------------------------------------------------------ panel events
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/mvc/tools/tools-repeat.js
--- a/static/scripts/mvc/tools/tools-repeat.js
+++ b/static/scripts/mvc/tools/tools-repeat.js
@@ -85,7 +85,7 @@
// append content
portlet.append(options.$el);
- // append section row class
+ // tag as section row
portlet.$el.addClass('section-row');
// append to dom
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -141,16 +141,11 @@
cls : 'ui-table-plain'
});
- // create input field wrapper
- var input_element = new InputElement({
- label : '',
- help : input_def.help,
- $el : sub_section.$el,
- highlight : true
- });
+ // displays as grouped subsection
+ sub_section.$el.addClass('ui-table-form-section');
// create table row
- this.table.add(input_element.$el);
+ this.table.add(sub_section.$el);
// append to table
this.table.append(sub_section_id);
@@ -234,7 +229,7 @@
$el : repeat.$el,
highlight : true
});
-
+
// create table row
this.table.add(input_element.$el);
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/packed/mvc/dataset/dataset-li-edit.js
--- a/static/scripts/packed/mvc/dataset/dataset-li-edit.js
+++ b/static/scripts/packed/mvc/dataset/dataset-li-edit.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","mvc/base-mvc","utils/localization"],function(g,d,e,a,h,b){var f=d.DatasetListItemView;var i=f.extend({initialize:function(j){f.prototype.initialize.call(this,j);this.hasUser=j.hasUser;this.purgeAllowed=j.purgeAllowed||false;this.tagsEditorShown=j.tagsEditorShown||false;this.annotationEditorShown=j.annotationEditorShown||false},_renderPrimaryActions:function(){var j=f.prototype._renderPrimaryActions.call(this);if(this.model.get("state")===g.NOT_VIEWABLE){return j}return f.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if((this.model.get("state")===g.DISCARDED)||(!this.model.get("accessible"))){return null}var l=this.model.get("purged"),j=this.model.get("deleted"),k={title:b("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};if(j||l){k.disabled=true;if(l){k.title=b("Cannot edit attributes of datasets removed from disk")}else{if(j){k.title=b("Undelete dataset to edit attributes")}}}else{if(_.contains([g.UPLOAD,g.NEW],this.model.get("state"))){k.disabled=true;k.title=b("This dataset is not yet editable")}}return faIconButton(k)},_renderDeleteButton:function(){if((!this.model.get("accessible"))){return null}var j=this,k=this.model.isDeletedOrPurged();return faIconButton({title:!k?b("Delete"):b("Dataset is already deleted"),disabled:k,faIcon:"fa-times",classes:"delete-btn",onclick:function(){j.$el.find(".icon-btn.delete-btn").trigger("mouseout");j.model["delete"]()}})},_renderDetails:function(){var j=f.prototype._renderDetails.call(this),k=this.model.get("state");if(!this.model.isDeletedOrPurged()&&_.contains([g.OK,g.FAILED_METADATA],k)){this._renderTags(j);this._renderAnnotation(j);this._makeDbkeyEditLink(j)}this._setUpBehaviors(j);return j},_renderSecondaryActions:function(){var j=f.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case g.UPLOAD:case g.NEW:case g.NOT_VIEWABLE:return j;case g.ERROR:j.unshift(this._renderErrButton());return j.concat([this._renderRerunButton()]);case g.OK:case g.FAILED_METADATA:return j.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return j.concat([this._renderRerunButton()])},_renderErrButton:function(){return faIconButton({title:b("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){return faIconButton({title:b("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_renderVisualizationsButton:function(){var j=this.model.get("visualizations");if((this.model.isDeletedOrPurged())||(!this.hasUser)||(!this.model.hasData())||(_.isEmpty(j))){return null}if(!_.isObject(j[0])){this.warn("Visualizations have been switched off");return null}var k=$(this.templates.visualizations(j,this));this._addScratchBookFn(k.find(".visualization-link").addBack(".visualization-link"));return k},_addScratchBookFn:function(j){j.click(function(k){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")});k.preventDefault();k.stopPropagation()}})},_renderTags:function(j){if(!this.hasUser){return}var k=this;this.tagsEditor=new e.TagsEditor({model:this.model,el:j.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.tagsEditorShown=true},onhide:function(){k.tagsEditorShown=false},$activator:faIconButton({title:b("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){if(!this.hasUser){return}var k=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:j.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.annotationEditorShown=true},onhide:function(){k.annotationEditorShown=false},$activator:faIconButton({title:b("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},_makeDbkeyEditLink:function(j){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var k=$('<a class="value">?</a>').attr("href",this.model.urls.edit).attr("target",this.linkTarget);j.find(".dbkey .value").replaceWith(k)}},events:_.extend(_.clone(f.prototype.events),{"click .undelete-link":function(j){this.model.undelete();return false},"click .purge-link":"_confirmPurge"}),_confirmPurge:function c(j){this.model.purge();return false},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"HDAEditView("+j+")"}});i.prototype.templates=(function(){var k=_.extend({},f.prototype.templates.warnings,{failed_metadata:h.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','<div class="failed_metadata-warning warningmessagesmall">',b("An error occurred setting the metadata for this dataset"),'<br /><a href="<%= dataset.urls.edit %>" target="<%= view.linkTarget %>">',b("Set it manually or retry auto-detection"),"</a>","</div>","<% } %>"],"dataset"),deleted:h.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',b("This dataset has been deleted"),'<br /><a class="undelete-link" href="javascript:void(0);">',b("Undelete it"),"</a>","<% if( view.purgeAllowed ){ %>",'<br /><a class="purge-link" href="javascript:void(0);">',b("Permanently remove it from disk"),"</a>","<% } %>","</div>","<% } %>"],"dataset")});var j=h.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'<a class="visualization-btn visualization-link icon-btn" href="<%= visualizations[0].href %>"',' target="<%= visualizations[0].target %>" title="',b("Visualize in"),' <%= visualizations[0].html %>">','<span class="fa fa-bar-chart-o"></span>',"</a>","<% } else { %>",'<div class="visualizations-dropdown dropdown">','<a class="visualization-btn icon-btn" data-toggle="dropdown" title="',b("Visualize"),'">','<span class="fa fa-bar-chart-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu">',"<% _.each( visualizations, function( visualization ){ %>",'<li><a class="visualization-link" href="<%= visualization.href %>"',' target="<%= visualization.target %>">',"<%= visualization.html %>","</a></li>","<% }); %>","</ul>","</div>","<% } %>"],"visualizations");return _.extend({},f.prototype.templates,{warnings:k,visualizations:j})}());return{DatasetListItemEdit:i}});
\ No newline at end of file
+define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","mvc/base-mvc","utils/localization"],function(b,h,g,e,c,d){var f=h.DatasetListItemView;var a=f.extend({initialize:function(i){f.prototype.initialize.call(this,i);this.hasUser=i.hasUser;this.purgeAllowed=i.purgeAllowed||false;this.tagsEditorShown=i.tagsEditorShown||false;this.annotationEditorShown=i.annotationEditorShown||false},_renderPrimaryActions:function(){var i=f.prototype._renderPrimaryActions.call(this);if(this.model.get("state")===b.NOT_VIEWABLE){return i}return f.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if((this.model.get("state")===b.DISCARDED)||(!this.model.get("accessible"))){return null}var k=this.model.get("purged"),i=this.model.get("deleted"),j={title:d("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};if(i||k){j.disabled=true;if(k){j.title=d("Cannot edit attributes of datasets removed from disk")}else{if(i){j.title=d("Undelete dataset to edit attributes")}}}else{if(_.contains([b.UPLOAD,b.NEW],this.model.get("state"))){j.disabled=true;j.title=d("This dataset is not yet editable")}}return faIconButton(j)},_renderDeleteButton:function(){if((!this.model.get("accessible"))){return null}var i=this,j=this.model.isDeletedOrPurged();return faIconButton({title:!j?d("Delete"):d("Dataset is already deleted"),disabled:j,faIcon:"fa-times",classes:"delete-btn",onclick:function(){i.$el.find(".icon-btn.delete-btn").trigger("mouseout");i.model["delete"]()}})},_renderDetails:function(){var i=f.prototype._renderDetails.call(this),j=this.model.get("state");if(!this.model.isDeletedOrPurged()&&_.contains([b.OK,b.FAILED_METADATA],j)){this._renderTags(i);this._renderAnnotation(i);this._makeDbkeyEditLink(i)}this._setUpBehaviors(i);return i},_renderSecondaryActions:function(){var i=f.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case b.UPLOAD:case b.NEW:case b.NOT_VIEWABLE:return i;case b.ERROR:i.unshift(this._renderErrButton());return i.concat([this._renderRerunButton()]);case b.OK:case b.FAILED_METADATA:return i.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return i.concat([this._renderRerunButton()])},_renderErrButton:function(){return faIconButton({title:d("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){return faIconButton({title:d("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_renderVisualizationsButton:function(){var i=this.model.get("visualizations");if((this.model.isDeletedOrPurged())||(!this.hasUser)||(!this.model.hasData())||(_.isEmpty(i))){return null}if(!_.isObject(i[0])){this.warn("Visualizations have been switched off");return null}var j=$(this.templates.visualizations(i,this));this._addScratchBookFn(j.find(".visualization-link").addBack(".visualization-link"));return j},_addScratchBookFn:function(i){i.click(function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")});j.preventDefault();j.stopPropagation()}})},_renderTags:function(i){if(!this.hasUser){return}var j=this;this.tagsEditor=new g.TagsEditor({model:this.model,el:i.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.tagsEditorShown=true},onhide:function(){j.tagsEditorShown=false},$activator:faIconButton({title:d("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(i){if(!this.hasUser){return}var j=this;this.annotationEditor=new e.AnnotationEditor({model:this.model,el:i.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.annotationEditorShown=true},onhide:function(){j.annotationEditorShown=false},$activator:faIconButton({title:d("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},_makeDbkeyEditLink:function(i){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var j=$('<a class="value">?</a>').attr("href",this.model.urls.edit).attr("target",this.linkTarget);i.find(".dbkey .value").replaceWith(j)}},events:_.extend(_.clone(f.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(i){this.trigger("edit",this,i)},"click .delete-btn":function(i){this.trigger("delete",this,i)},"click .rerun-btn":function(i){this.trigger("rerun",this,i)},"click .report-err-btn":function(i){this.trigger("report-err",this,i)},"click .visualization-btn":function(i){this.trigger("visualize",this,i)},"click .dbkey a":function(i){this.trigger("edit",this,i)}}),_clickUndeleteLink:function(i){this.model.undelete();return false},_clickPurgeLink:function(i){this.model.purge();return false},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"HDAEditView("+i+")"}});a.prototype.templates=(function(){var j=_.extend({},f.prototype.templates.warnings,{failed_metadata:c.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','<div class="failed_metadata-warning warningmessagesmall">',d("An error occurred setting the metadata for this dataset"),'<br /><a href="<%= dataset.urls.edit %>" target="<%= view.linkTarget %>">',d("Set it manually or retry auto-detection"),"</a>","</div>","<% } %>"],"dataset"),deleted:c.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',d("This dataset has been deleted"),'<br /><a class="undelete-link" href="javascript:void(0);">',d("Undelete it"),"</a>","<% if( view.purgeAllowed ){ %>",'<br /><a class="purge-link" href="javascript:void(0);">',d("Permanently remove it from disk"),"</a>","<% } %>","</div>","<% } %>"],"dataset")});var i=c.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'<a class="visualization-btn visualization-link icon-btn" href="<%= visualizations[0].href %>"',' target="<%= visualizations[0].target %>" title="',d("Visualize in"),' <%= visualizations[0].html %>">','<span class="fa fa-bar-chart-o"></span>',"</a>","<% } else { %>",'<div class="visualizations-dropdown dropdown">','<a class="visualization-btn icon-btn" data-toggle="dropdown" title="',d("Visualize"),'">','<span class="fa fa-bar-chart-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu">',"<% _.each( visualizations, function( visualization ){ %>",'<li><a class="visualization-link" href="<%= visualization.href %>"',' target="<%= visualization.target %>">',"<%= visualization.html %>","</a></li>","<% }); %>","</ul>","</div>","<% } %>"],"visualizations");return _.extend({},f.prototype.templates,{warnings:j,visualizations:i})}());return{DatasetListItemEdit:a}});
\ No newline at end of file
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/packed/mvc/dataset/dataset-li.js
--- a/static/scripts/packed/mvc/dataset/dataset-li.js
+++ b/static/scripts/packed/mvc/dataset/dataset-li.js
@@ -1,1 +1,1 @@
-define(["mvc/list/list-item","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(d,a,b,c){var f=d.ListItemView;var e=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);f.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this);this.model.on("change",function(h,g){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},_fetchModelDetails:function(){var g=this;if(g.model.inReadyState()&&!g.model.hasDetails()){return g.model.fetch({silent:true})}return jQuery.when()},remove:function(h,i){var g=this;h=h||this.fxSpeed;this.$el.fadeOut(h,function(){Backbone.View.prototype.remove.call(g);if(i){i.call(g)}})},render:function(g){return f.prototype.render.call(this,g)},_swapNewRender:function(g){f.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var i=this.model.get("state");if((i===a.NOT_VIEWABLE)||(i===a.DISCARDED)||(!this.model.get("accessible"))){return null}var h={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){h.disabled=true;h.title=c("Cannot display datasets removed from disk")}else{if(i===a.UPLOAD){h.disabled=true;h.title=c("This dataset must finish uploading before it can be viewed")}else{if(i===a.NEW){h.disabled=true;h.title=c("This dataset is not yet viewable")}else{h.title=c("View data");h.href=this.model.urls.display;var g=this;h.onclick=function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+g.model.get("name"),type:"other",content:function(k){require(["mvc/data"],function(l){var m=new l.TabularDataset({id:g.model.get("id")});$.when(m.fetch()).then(function(){l.createTabularDatasetChunkedView({model:m,parent_elt:k,embedded:true,height:"100%"})})})}});j.preventDefault()}}}}}h.faIcon="fa-eye";return faIconButton(h)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var g=f.prototype._renderDetails.call(this);g.find(".actions .left").empty().append(this._renderSecondaryActions());g.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());g.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(g);return g},_renderSummary:function(){var g=this.model.toJSON(),h=this.templates.summaries[g.state];h=h||this.templates.summaries.unknown;return h(g,this)},_renderDetailMessages:function(){var g=this,i=$('<div class="detail-messages"></div>'),h=g.model.toJSON();_.each(g.templates.detailMessages,function(j){i.append($(j(h,g)))});return i},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var g=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+g.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(h){return['<li><a href="',g.meta_download+h.file_type,'">',c("Download")," ",h.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+g+")"}});e.prototype.templates=(function(){var i=_.extend({},f.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var j=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var h=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var k={};k[a.OK]=k[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");k[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");k[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");k[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");k[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");k[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");k[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");k[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");k[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");k[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");k[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");k.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var l={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var g=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:i,details:j,noAccess:h,summaries:k,detailMessages:l,displayApplications:g})}());return{DatasetListItemView:e}});
\ No newline at end of file
+define(["mvc/list/list-item","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(d,a,b,c){var f=d.ListItemView;var e=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);f.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this);this.model.on("change",function(h,g){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},_fetchModelDetails:function(){var g=this;if(g.model.inReadyState()&&!g.model.hasDetails()){return g.model.fetch({silent:true})}return jQuery.when()},remove:function(h,i){var g=this;h=h||this.fxSpeed;this.$el.fadeOut(h,function(){Backbone.View.prototype.remove.call(g);if(i){i.call(g)}})},render:function(g){return f.prototype.render.call(this,g)},_swapNewRender:function(g){f.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var i=this.model.get("state");if((i===a.NOT_VIEWABLE)||(i===a.DISCARDED)||(!this.model.get("accessible"))){return null}var h={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){h.disabled=true;h.title=c("Cannot display datasets removed from disk")}else{if(i===a.UPLOAD){h.disabled=true;h.title=c("This dataset must finish uploading before it can be viewed")}else{if(i===a.NEW){h.disabled=true;h.title=c("This dataset is not yet viewable")}else{h.title=c("View data");h.href=this.model.urls.display;var g=this;h.onclick=function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+g.model.get("name"),type:"other",content:function(k){require(["mvc/data"],function(l){var m=new l.TabularDataset({id:g.model.get("id")});$.when(m.fetch()).then(function(){l.createTabularDatasetChunkedView({model:m,parent_elt:k,embedded:true,height:"100%"})})})}});j.preventDefault()}}}}}h.faIcon="fa-eye";return faIconButton(h)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var g=f.prototype._renderDetails.call(this);g.find(".actions .left").empty().append(this._renderSecondaryActions());g.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());g.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(g);return g},_renderSummary:function(){var g=this.model.toJSON(),h=this.templates.summaries[g.state];h=h||this.templates.summaries.unknown;return h(g,this)},_renderDetailMessages:function(){var g=this,i=$('<div class="detail-messages"></div>'),h=g.model.toJSON();_.each(g.templates.detailMessages,function(j){i.append($(j(h,g)))});return i},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var g=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+g.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(h){return['<li><a href="',g.meta_download+h.file_type,'">',c("Download")," ",h.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(g){this.trigger("display",this,g)},"click .params-btn":function(g){this.trigger("params",this,g)},"click .download-btn":function(g){this.trigger("download",this,g)}}),toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+g+")"}});e.prototype.templates=(function(){var i=_.extend({},f.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var j=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var h=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var k={};k[a.OK]=k[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");k[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");k[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");k[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");k[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");k[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");k[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");k[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");k[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");k[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");k[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");k.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var l={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var g=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:i,details:j,noAccess:h,summaries:k,detailMessages:l,displayApplications:g})}());return{DatasetListItemView:e}});
\ No newline at end of file
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/packed/mvc/history/history-panel-edit-current.js
--- a/static/scripts/packed/mvc/history/history-panel-edit-current.js
+++ b/static/scripts/packed/mvc/history/history-panel-edit-current.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[]},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_attachItems:function(j){this.$list(j).append(this.views.reverse().map(function(k){return k.$el}));return this},addItemView:function(o,p,n){this.log(this+".addItemView:",o);var l=this;if(!l._filterItem(o)){return undefined}if(l.panelStack.length){return this._collapseDrilldownPanel()}var k=l._createItemView(o);l.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);return this},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}});
\ No newline at end of file
+define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){j.preferences.set("scrollPosition",$(this).scrollTop())})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){var j=this;this.$list(k).append(this.views.reverse().map(function(l){if(j.currentContentId&&l.model.id===j.currentContentId){l.$el.addClass("current-content")}return l.$el}));return this},addItemView:function(o,p,n){this.log(this+".addItemView:",o);var l=this;if(!l._filterItem(o)){return undefined}if(l.panelStack.length){return this._collapseDrilldownPanel()}var k=l._createItemView(o);l.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}});
\ No newline at end of file
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/packed/mvc/list/list-panel.js
--- a/static/scripts/packed/mvc/list/list-panel.js
+++ b/static/scripts/packed/mvc/list/list-panel.js
@@ -1,1 +1,1 @@
-define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(f){this.$scrollContainer().scrollTop(f);return this},scrollToTop:function(){this.$scrollContainer().scrollTop(0);return this},scrollToItem:function(f){if(!f){return this}var g=f.$el.offset().top;this.$scrollContainer().scrollTop(g);return this},scrollToId:function(f){return this.scrollToItem(this.viewFromModelId(f))},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}});
\ No newline at end of file
+define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}});
\ No newline at end of file
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-dataset"],function(d,a,g,c,b){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn()},reset:function(){this.$el.find(".ui-table-form-error").hide()},_template:function(h){var i;if(h.highlight){i=$('<div class="ui-table-element ui-table-form-section"/>')}else{i=$('<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 n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});var m=new e({label:"",help:h.help,$el:n.$el,highlight:true});this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el,highlight:true});this.table.add(n.$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(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_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.RadioButton;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_data_colum:function(h){return new g.Select.View({id:"field-"+h.id,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){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||0,max:h.max||1000,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.$el.find(".ui-table-form-error").fadeIn()},reset:function(){this.$el.find(".ui-table-form-error").hide()},_template:function(h){var i;if(h.highlight){i=$('<div class="ui-table-element ui-table-form-section"/>')}else{i=$('<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 m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$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-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el,highlight:true});this.table.add(n.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$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(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_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.RadioButton;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_data_colum:function(h){return new g.Select.View({id:"field-"+h.id,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){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||0,max:h.max||1000,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 e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1285,9 +1285,9 @@
.ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px}
.ui-radiobutton label{height:23px;line-height:1em}
.ui-table tbody{cursor:pointer}
-.ui-table-plain tbody td{padding:5px 0px 5px 5px !important;border:none !important}
+.ui-table-plain tbody td{padding:5px 0px 5px 0px !important;border:none !important}
.ui-table-plain tbody{cursor:auto !important}
-.ui-table-form-section{border-left:solid 3px #ebd9b2;border-radius:5px;padding-left:5px}
+.ui-table-form-section{border-left:solid 3px #ebd9b2;border-radius:5px !important;padding-left:10px}
.ui-table-form-title-strong{font-weight:bold;padding-bottom:5px}
.ui-table-form-info{clear:both !important}
.ui-table-form-separator{font-weight:bold;font-size:0.9em}
@@ -1307,7 +1307,7 @@
.ui-portlet .no-scroll{height:calc(100% - 80px)}
.ui-portlet-repeat{border:none;border-left:solid 3px #ebd9b2;border-radius:5px}.ui-portlet-repeat .portlet-header{background:#ebd9b2;border-radius:3px;border-bottom-left-radius:0px;padding:1px 0px 0px 2px}
.ui-portlet-repeat .portlet-title{padding-top:1px}
-.ui-portlet-repeat .portlet-content{padding:0px}.ui-portlet-repeat .portlet-content .content{padding:0px;padding-left:5px}
+.ui-portlet-repeat .portlet-content{padding:0px}.ui-portlet-repeat .portlet-content .content{padding:0px;padding-left:10px}
.ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer}
.ui-popover .popover-title{padding:4px 10px}
.ui-select,.ui-select-multiple{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}
@@ -1953,6 +1953,9 @@
.history-panel .controls .list-actions .list-action-popup-btn{float:right}
.history-panel .list-item.history-content{border-width:1px 0px 0px 0px}.history-panel .list-item.history-content:last-child{border-width:1px 0px 1px 0px}
.history-panel .empty-message{margin:0px 10px 0px 10px}
+.history-panel .dataset-collection .subtitle{margin-top:2px;font-size:90%;color:#777}
+.history-panel .dataset-collection-panel .controls{padding:0px}
+.history-panel .dataset-collection-panel .list-items{margin-top:0px}
.annotated-history-panel .controls{margin:0px}.annotated-history-panel .controls .name{font-size:150%;margin-bottom:4px}
.annotated-history-panel .controls .subtitle{color:black}.annotated-history-panel .controls .subtitle:not(:empty){margin:0px 0px 0px 4px}
.annotated-history-panel .controls .messages:not(:empty){margin-top:16px}
@@ -1964,9 +1967,8 @@
.annotated-history-panel table.list-items>tbody>tr>td:nth-child(2){padding:8px 16px 8px 16px;white-space:pre-wrap}
.annotated-history-panel table.list-items>tbody>tr>td>.list-item{border:0px}
.annotated-history-panel .empty-message{margin-top:8px}
-.history-panel .dataset-collection .subtitle{margin-top:2px;font-size:90%;color:#777}
-.history-panel .dataset-collection-panel .controls{padding:0px}
-.history-panel .dataset-collection-panel .list-items{margin-top:0px}
+.current-history-panel .list-item.history-content.current-content{border:2px solid black;border-bottom-width:2px}.current-history-panel .list-item.history-content.current-content .title-bar{padding:5px 8px 6px 6px}
+.current-history-panel .list-item.history-content.current-content .details{padding:0px 8px 5px 6px}
body.historyPage{background:#dfe5f9;color:#000;margin:5px;border:0;padding:0}
div.historyLinks{margin:5px 5px}
div.historyItem{margin:0 -5px;padding:8px 10px;border-top:solid #bfbfbf 1px;border-right:none;word-wrap:break-word;background:#eee}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat}
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/style/src/less/history.less
--- a/static/style/src/less/history.less
+++ b/static/style/src/less/history.less
@@ -488,6 +488,27 @@
}
}
+
+// ---------------------------------------------------------------------------- collections nested in histories
+.history-panel {
+ .dataset-collection {
+ .subtitle {
+ margin-top: 2px;
+ font-size: 90%;
+ color: #777;
+ }
+ }
+ .dataset-collection-panel {
+ .controls {
+ padding: 0px;
+ }
+ .list-items {
+ margin-top: 0px;
+ }
+ }
+}
+
+
// ---------------------------------------------------------------------------- annotated-history-panel
.annotated-history-panel {
.controls {
@@ -566,21 +587,31 @@
}
-// ---------------------------------------------------------------------------- collections nested in histories
-.history-panel {
- .dataset-collection {
- .subtitle {
- margin-top: 2px;
- font-size: 90%;
- color: #777;
+// ---------------------------------------------------------------------------- current-history-panel
+.current-history-panel {
+ .list-item.history-content.current-content {
+ //border-top: 2px solid black;
+ //border-right: 1px solid black;
+ //border-bottom: 2px solid black;
+ //border-left: 1px solid black;
+
+ //.title-bar {
+ // border-color: black;
+ // background: black;
+ // color: white;
+ //}
+
+ //position: relative;
+ //margin-left: -24px;
+ //z-index: 1000;
+
+ border: 2px solid black;
+ border-bottom-width: 2px;
+ .title-bar {
+ padding: 5px 8px 6px 6px;
}
- }
- .dataset-collection-panel {
- .controls {
- padding: 0px;
- }
- .list-items {
- margin-top: 0px;
+ .details {
+ padding: 0px 8px 5px 6px;
}
}
}
diff -r e6996e0ec636bd3dd8e9b11c608b999c3c2a50ab -r 1cf25d3a5cdc2f256e5519532d73c3c8e48faa48 static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -62,7 +62,7 @@
&:extend(.grid);
tbody td {
- padding: 5px 0px 5px 5px !important;
+ padding: 5px 0px 5px 0px !important;
border: none !important;
}
@@ -73,8 +73,8 @@
.ui-table-form-section {
border-left: solid 3px @form-heading-bg;
- border-radius: 5px;
- padding-left: 5px;
+ border-radius: 5px !important;
+ padding-left: 10px;
}
.ui-table-form-title-strong {
@@ -239,7 +239,7 @@
padding: 0px;
.content {
padding : 0px;
- padding-left: 5px;
+ padding-left: 10px;
}
}
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Visualizations registry: do not warn when a plugin is set to 'disabled' - use info
by commits-noreply＠bitbucket.org 18 Sep '14
by commits-noreply＠bitbucket.org 18 Sep '14
18 Sep '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ec017c724b83/
Changeset: ec017c724b83
User: carlfeberhard
Date: 2014-09-18 18:44:51+00:00
Summary: Visualizations registry: do not warn when a plugin is set to 'disabled' - use info
Affected #: 2 files
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r ec017c724b8326279c7c5b8856cce3c98b9cb61a lib/galaxy/visualization/registry.py
--- a/lib/galaxy/visualization/registry.py
+++ b/lib/galaxy/visualization/registry.py
@@ -159,7 +159,7 @@
# config file is required, otherwise skip this visualization
plugin[ 'config_file' ] = os.path.join( plugin_path, 'config', ( plugin.name + '.xml' ) )
config = self.config_parser.parse_file( plugin.config_file )
-
+
if not config:
return None
plugin[ 'config' ] = config
@@ -390,14 +390,9 @@
Parse the given XML file for visualizations data.
:returns: visualization config dictionary
"""
- try:
- xml_tree = galaxy.util.parse_xml( xml_filepath )
- visualization = self.parse_visualization( xml_tree.getroot() )
- return visualization
- # skip vis' with parsing errors - don't shutdown the startup
- except ParsingException, parse_exc:
- log.exception( 'Skipped visualization config "%s" due to parsing errors', xml_filepath )
- return None
+ xml_tree = galaxy.util.parse_xml( xml_filepath )
+ visualization = self.parse_visualization( xml_tree.getroot() )
+ return visualization
def parse_visualization( self, xml_tree ):
"""
@@ -406,16 +401,16 @@
"""
returned = {}
- # allow manually turning off a vis by checking for a disabled property
- if 'disabled' in xml_tree.attrib:
-#TODO: differentiate between disabled and failed to parse, log.warn only on failure, log.info otherwise
- return None
-
# a text display name for end user links
returned[ 'name' ] = xml_tree.attrib.get( 'name', None )
if not returned[ 'name' ]:
raise ParsingException( 'visualization needs a name attribute' )
+ # allow manually turning off a vis by checking for a disabled property
+ if 'disabled' in xml_tree.attrib:
+ log.info( '%s, plugin disabled: %s. Skipping...', self, returned[ 'name' ] )
+ return None
+
# record the embeddable flag - defaults to false
# this is a design by contract promise that the visualization can be rendered inside another page
# often by rendering only a DOM fragment. Since this is an advanced feature that requires a bit more
diff -r 5b745b6649d29bd576cccfd0466cb1f5950838aa -r ec017c724b8326279c7c5b8856cce3c98b9cb61a lib/galaxy/web/base/pluginframework.py
--- a/lib/galaxy/web/base/pluginframework.py
+++ b/lib/galaxy/web/base/pluginframework.py
@@ -118,15 +118,14 @@
for plugin_path in self.find_plugins():
try:
plugin = self.load_plugin( plugin_path )
- if not plugin:
- log.warn( '%s, plugin load failed or disabled: %s. Skipping...', self, plugin_path )
+
+ if plugin and plugin.name not in self.plugins:
+ self.plugins[ plugin.name ] = plugin
+ log.info( '%s, loaded plugin: %s', self, plugin.name )
#NOTE: prevent silent, implicit overwrite here (two plugins in two diff directories)
#TODO: overwriting may be desired
- elif plugin.name in self.plugins:
+ elif plugin and plugin.name in self.plugins:
log.warn( '%s, plugin with name already exists: %s. Skipping...', self, plugin.name )
- else:
- self.plugins[ plugin.name ] = plugin
- log.info( '%s, loaded plugin: %s', self, plugin.name )
except Exception, exc:
if not self.skip_bad_plugins:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Fix subsection creation
by commits-noreply＠bitbucket.org 18 Sep '14
by commits-noreply＠bitbucket.org 18 Sep '14
18 Sep '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5b745b6649d2/
Changeset: 5b745b6649d2
User: guerler
Date: 2014-09-18 18:07:44+00:00
Summary: ToolForm: Fix subsection creation
Affected #: 7 files
diff -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 -r 5b745b6649d29bd576cccfd0466cb1f5950838aa client/galaxy/scripts/mvc/tools/tools-repeat.js
--- a/client/galaxy/scripts/mvc/tools/tools-repeat.js
+++ b/client/galaxy/scripts/mvc/tools/tools-repeat.js
@@ -85,7 +85,7 @@
// append content
portlet.append(options.$el);
- // append section row class
+ // tag as section row
portlet.$el.addClass('section-row');
// append to dom
diff -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 -r 5b745b6649d29bd576cccfd0466cb1f5950838aa 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
@@ -141,16 +141,11 @@
cls : 'ui-table-plain'
});
- // create input field wrapper
- var input_element = new InputElement({
- label : '',
- help : input_def.help,
- $el : sub_section.$el,
- highlight : true
- });
+ // displays as grouped subsection
+ sub_section.$el.addClass('ui-table-form-section');
// create table row
- this.table.add(input_element.$el);
+ this.table.add(sub_section.$el);
// append to table
this.table.append(sub_section_id);
@@ -234,7 +229,7 @@
$el : repeat.$el,
highlight : true
});
-
+
// create table row
this.table.add(input_element.$el);
diff -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 -r 5b745b6649d29bd576cccfd0466cb1f5950838aa static/scripts/mvc/tools/tools-repeat.js
--- a/static/scripts/mvc/tools/tools-repeat.js
+++ b/static/scripts/mvc/tools/tools-repeat.js
@@ -85,7 +85,7 @@
// append content
portlet.append(options.$el);
- // append section row class
+ // tag as section row
portlet.$el.addClass('section-row');
// append to dom
diff -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 -r 5b745b6649d29bd576cccfd0466cb1f5950838aa static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -141,16 +141,11 @@
cls : 'ui-table-plain'
});
- // create input field wrapper
- var input_element = new InputElement({
- label : '',
- help : input_def.help,
- $el : sub_section.$el,
- highlight : true
- });
+ // displays as grouped subsection
+ sub_section.$el.addClass('ui-table-form-section');
// create table row
- this.table.add(input_element.$el);
+ this.table.add(sub_section.$el);
// append to table
this.table.append(sub_section_id);
@@ -234,7 +229,7 @@
$el : repeat.$el,
highlight : true
});
-
+
// create table row
this.table.add(input_element.$el);
diff -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 -r 5b745b6649d29bd576cccfd0466cb1f5950838aa static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-dataset"],function(d,a,g,c,b){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn()},reset:function(){this.$el.find(".ui-table-form-error").hide()},_template:function(h){var i;if(h.highlight){i=$('<div class="ui-table-element ui-table-form-section"/>')}else{i=$('<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 n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});var m=new e({label:"",help:h.help,$el:n.$el,highlight:true});this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el,highlight:true});this.table.add(n.$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(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_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.RadioButton;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_data_colum:function(h){return new g.Select.View({id:"field-"+h.id,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){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||0,max:h.max||1000,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.$el.find(".ui-table-form-error").fadeIn()},reset:function(){this.$el.find(".ui-table-form-error").hide()},_template:function(h){var i;if(h.highlight){i=$('<div class="ui-table-element ui-table-form-section"/>')}else{i=$('<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 m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+d.uuid();var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:p.$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-"+d.uuid();var o=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:o.$el})}m.retitle(h.title);var n=new e({label:h.title,help:h.help,$el:m.$el,highlight:true});this.table.add(n.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$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(u){if(u instanceof Array){u=u[0]}var s=i.app.tree.references(j,"data_column");var m=i.app.datasets.filter(u);if(m&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=m.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var o in s){var q=i.app.input_list[s[o]];var r=i.app.field_list[s[o]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=q.numerical;var l=[];for(var v in w){var t=w[v];var k=(parseInt(v)+1);var p="Text";if(t=="int"||t=="float"){p="Number"}if(t=="int"||t=="float"||!n){l.push({label:"Column: "+k+" ["+p+"]",value:k})}}if(r){r.update(l);if(!r.exists(r.value())){r.value(r.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+u+".")}}})},_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.RadioButton;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_data_colum:function(h){return new g.Select.View({id:"field-"+h.id,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){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||0,max:h.max||1000,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 025d227c0c1325f38a76aff4dc264c749f24e4e7 -r 5b745b6649d29bd576cccfd0466cb1f5950838aa static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1286,9 +1286,9 @@
.ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px}
.ui-radiobutton label{height:23px;line-height:1em}
.ui-table tbody{cursor:pointer}
-.ui-table-plain tbody td{padding:5px 0px 5px 5px !important;border:none !important}
+.ui-table-plain tbody td{padding:5px 0px 5px 0px !important;border:none !important}
.ui-table-plain tbody{cursor:auto !important}
-.ui-table-form-section{border-left:solid 3px #ebd9b2;border-radius:5px;padding-left:5px}
+.ui-table-form-section{border-left:solid 3px #ebd9b2;border-radius:5px !important;padding-left:10px}
.ui-table-form-title-strong{font-weight:bold;padding-bottom:5px}
.ui-table-form-info{clear:both !important}
.ui-table-form-separator{font-weight:bold;font-size:0.9em}
@@ -1308,7 +1308,7 @@
.ui-portlet .no-scroll{height:calc(100% - 80px)}
.ui-portlet-repeat{border:none;border-left:solid 3px #ebd9b2;border-radius:5px}.ui-portlet-repeat .portlet-header{background:#ebd9b2;border-radius:3px;border-bottom-left-radius:0px;padding:1px 0px 0px 2px}
.ui-portlet-repeat .portlet-title{padding-top:1px}
-.ui-portlet-repeat .portlet-content{padding:0px}.ui-portlet-repeat .portlet-content .content{padding:0px;padding-left:5px}
+.ui-portlet-repeat .portlet-content{padding:0px}.ui-portlet-repeat .portlet-content .content{padding:0px;padding-left:10px}
.ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer}
.ui-popover .popover-title{padding:4px 10px}
.ui-select,.ui-select-multiple{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}
diff -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 -r 5b745b6649d29bd576cccfd0466cb1f5950838aa static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -62,7 +62,7 @@
&:extend(.grid);
tbody td {
- padding: 5px 0px 5px 5px !important;
+ padding: 5px 0px 5px 0px !important;
border: none !important;
}
@@ -73,8 +73,8 @@
.ui-table-form-section {
border-left: solid 3px @form-heading-bg;
- border-radius: 5px;
- padding-left: 5px;
+ border-radius: 5px !important;
+ padding-left: 10px;
}
.ui-table-form-title-strong {
@@ -239,7 +239,7 @@
padding: 0px;
.content {
padding : 0px;
- padding-left: 5px;
+ padding-left: 10px;
}
}
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: History panel, current: highlight focused/active/current item, set active item on 'display, edit, rerun, info/params, visualize, report-error', cache scroll position in sessionstorage and re-render at same, allow list-panel.scrollTo to be animated and given a speed
by commits-noreply＠bitbucket.org 18 Sep '14
by commits-noreply＠bitbucket.org 18 Sep '14
18 Sep '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/025d227c0c13/
Changeset: 025d227c0c13
User: carlfeberhard
Date: 2014-09-18 16:33:52+00:00
Summary: History panel, current: highlight focused/active/current item, set active item on 'display,edit,rerun,info/params,visualize,report-error', cache scroll position in sessionstorage and re-render at same, allow list-panel.scrollTo to be animated and given a speed
Affected #: 14 files
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
--- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
@@ -257,12 +257,26 @@
// ......................................................................... events
/** event map */
events : _.extend( _.clone( _super.prototype.events ), {
- 'click .undelete-link' : function( ev ){ this.model.undelete(); return false; },
- 'click .purge-link' : '_confirmPurge'
+ 'click .undelete-link' : '_clickUndeleteLink',
+ 'click .purge-link' : '_clickPurgeLink',
+
+ 'click .edit-btn' : function( ev ){ this.trigger( 'edit', this, ev ); },
+ 'click .delete-btn' : function( ev ){ this.trigger( 'delete', this, ev ); },
+ 'click .rerun-btn' : function( ev ){ this.trigger( 'rerun', this, ev ); },
+ 'click .report-err-btn' : function( ev ){ this.trigger( 'report-err', this, ev ); },
+ 'click .visualization-btn' : function( ev ){ this.trigger( 'visualize', this, ev ); },
+ 'click .dbkey a' : function( ev ){ this.trigger( 'edit', this, ev ); }
}),
- /** listener for item purge */
- _confirmPurge : function _confirmPurge( ev ){
+
+ /** listener for item undelete (in the messages section) */
+ _clickUndeleteLink : function( ev ){
+ this.model.undelete();
+ return false;
+ },
+
+ /** listener for item purge (in the messages section) */
+ _clickPurgeLink : function( ev ){
//TODO: confirm dialog
this.model.purge();
return false;
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 client/galaxy/scripts/mvc/dataset/dataset-li.js
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -314,6 +314,13 @@
},
// ......................................................................... misc
+ events : _.extend( _.clone( _super.prototype.events ), {
+ 'click .display-btn' : function( ev ){ this.trigger( 'display', this, ev ); },
+ 'click .params-btn' : function( ev ){ this.trigger( 'params', this, ev ); },
+ 'click .download-btn' : function( ev ){ this.trigger( 'download', this, ev ); }
+ }),
+
+ // ......................................................................... misc
/** String representation */
toString : function(){
var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 client/galaxy/scripts/mvc/history/history-panel-edit-current.js
--- a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js
+++ b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js
@@ -14,7 +14,13 @@
/** should the tags editor be shown or hidden initially? */
tagsEditorShown : false,
/** should the annotation editor be shown or hidden initially? */
- annotationEditorShown : false
+ annotationEditorShown : false,
+ ///** what is the currently focused content (dataset or collection) in the current history?
+ // * (the history panel will highlight and scroll to the focused content view)
+ // */
+ //focusedContentId : null
+ /** Current scroll position */
+ scrollPosition : 0
},
toString : function(){
return 'HistoryPanelPrefs(' + JSON.stringify( this.toJSON() ) + ')';
@@ -70,6 +76,20 @@
/** sub-views that will overlay this panel (collections) */
this.panelStack = [];
+
+ /** id of currently focused content */
+ this.currentContentId = attributes.currentContentId || null;
+ //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value
+ },
+
+ /** Override to cache the current scroll position with a listener */
+ _setUpListeners : function(){
+ _super.prototype._setUpListeners.call( this );
+
+ var panel = this;
+ this.$scrollContainer().on( 'scroll', function( ev ){
+ panel.preferences.set( 'scrollPosition', $( this ).scrollTop() );
+ });
},
// ------------------------------------------------------------------------ loading history/item models
@@ -243,11 +263,34 @@
});
},
+ /** Override to scroll to cached position (in prefs) after swapping */
+ _swapNewRender : function( $newRender ){
+ _super.prototype._swapNewRender.call( this, $newRender );
+ var panel = this;
+
+ _.delay( function(){
+ var pos = panel.preferences.get( 'scrollPosition' );
+ if( pos ){
+ panel.scrollTo( pos );
+ }
+ }, 10 );
+ //TODO: is this enough of a delay on larger histories?
+
+ return this;
+ },
+
// ------------------------------------------------------------------------ sub-views
// reverse HID order
- /** Override to reverse order of views - newest contents on top */
+ /** Override to reverse order of views - newest contents on top
+ * and add the current-content highlight class to currentContentId's view
+ */
_attachItems : function( $whereTo ){
+ var panel = this;
this.$list( $whereTo ).append( this.views.reverse().map( function( view ){
+ // add current content
+ if( panel.currentContentId && view.model.id === panel.currentContentId ){
+ view.$el.addClass( 'current-content' );
+ }
return view.$el;
}));
return this;
@@ -298,9 +341,26 @@
view.on( 'collapsed:drilldown', function( v, drilldown ){
this._collapseDrilldownPanel( drilldown );
}, this );
+
+ // when content is manipulated, make it the current-content
+ view.on( 'display edit params rerun report-err visualize', function( v, ev ){
+ this.setCurrentContent( v );
+ }, this );
+
return this;
},
+ /** display 'current content': add a visible highlight and store the id of a content item */
+ setCurrentContent : function( view ){
+ this.$( '.history-content.current-content' ).removeClass( 'current-content' );
+ if( view ){
+ view.$el.addClass( 'current-content' );
+ this.currentContentId = view.model.id;
+ } else {
+ this.currentContentId = null;
+ }
+ },
+
/** Handle drill down by hiding this panels list and controls and showing the sub-panel */
_expandDrilldownPanel : function( drilldown ){
this.panelStack.push( drilldown );
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 client/galaxy/scripts/mvc/list/list-panel.js
--- a/client/galaxy/scripts/mvc/list/list-panel.js
+++ b/client/galaxy/scripts/mvc/list/list-panel.js
@@ -679,28 +679,28 @@
},
/** set the current scroll position of the panel in its parent */
- scrollTo : function( pos ){
- this.$scrollContainer().scrollTop( pos );
+ scrollTo : function( pos, speed ){
+ speed = speed || 0;
+ this.$scrollContainer().animate({ scrollTop: pos }, speed );
return this;
},
/** Scrolls the panel to the top. */
- scrollToTop : function(){
- this.$scrollContainer().scrollTop( 0 );
- return this;
+ scrollToTop : function( speed ){
+ return this.scrollTo( 0, speed );
},
/** */
- scrollToItem : function( view ){
+ scrollToItem : function( view, speed ){
if( !view ){ return this; }
- var itemTop = view.$el.offset().top;
- this.$scrollContainer().scrollTop( itemTop );
- return this;
+ //var itemTop = view.$el.offset().top;
+ var itemTop = view.$el.position().top;
+ return this.scrollTo( itemTop, speed );
},
/** Scrolls the panel to show the content with the given id. */
- scrollToId : function( id ){
- return this.scrollToItem( this.viewFromModelId( id ) );
+ scrollToId : function( id, speed ){
+ return this.scrollToItem( this.viewFromModelId( id ), speed );
},
// ------------------------------------------------------------------------ panel events
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/scripts/mvc/dataset/dataset-li-edit.js
--- a/static/scripts/mvc/dataset/dataset-li-edit.js
+++ b/static/scripts/mvc/dataset/dataset-li-edit.js
@@ -257,12 +257,26 @@
// ......................................................................... events
/** event map */
events : _.extend( _.clone( _super.prototype.events ), {
- 'click .undelete-link' : function( ev ){ this.model.undelete(); return false; },
- 'click .purge-link' : '_confirmPurge'
+ 'click .undelete-link' : '_clickUndeleteLink',
+ 'click .purge-link' : '_clickPurgeLink',
+
+ 'click .edit-btn' : function( ev ){ this.trigger( 'edit', this, ev ); },
+ 'click .delete-btn' : function( ev ){ this.trigger( 'delete', this, ev ); },
+ 'click .rerun-btn' : function( ev ){ this.trigger( 'rerun', this, ev ); },
+ 'click .report-err-btn' : function( ev ){ this.trigger( 'report-err', this, ev ); },
+ 'click .visualization-btn' : function( ev ){ this.trigger( 'visualize', this, ev ); },
+ 'click .dbkey a' : function( ev ){ this.trigger( 'edit', this, ev ); }
}),
- /** listener for item purge */
- _confirmPurge : function _confirmPurge( ev ){
+
+ /** listener for item undelete (in the messages section) */
+ _clickUndeleteLink : function( ev ){
+ this.model.undelete();
+ return false;
+ },
+
+ /** listener for item purge (in the messages section) */
+ _clickPurgeLink : function( ev ){
//TODO: confirm dialog
this.model.purge();
return false;
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/scripts/mvc/dataset/dataset-li.js
--- a/static/scripts/mvc/dataset/dataset-li.js
+++ b/static/scripts/mvc/dataset/dataset-li.js
@@ -314,6 +314,13 @@
},
// ......................................................................... misc
+ events : _.extend( _.clone( _super.prototype.events ), {
+ 'click .display-btn' : function( ev ){ this.trigger( 'display', this, ev ); },
+ 'click .params-btn' : function( ev ){ this.trigger( 'params', this, ev ); },
+ 'click .download-btn' : function( ev ){ this.trigger( 'download', this, ev ); }
+ }),
+
+ // ......................................................................... misc
/** String representation */
toString : function(){
var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/scripts/mvc/history/history-panel-edit-current.js
--- a/static/scripts/mvc/history/history-panel-edit-current.js
+++ b/static/scripts/mvc/history/history-panel-edit-current.js
@@ -14,7 +14,13 @@
/** should the tags editor be shown or hidden initially? */
tagsEditorShown : false,
/** should the annotation editor be shown or hidden initially? */
- annotationEditorShown : false
+ annotationEditorShown : false,
+ ///** what is the currently focused content (dataset or collection) in the current history?
+ // * (the history panel will highlight and scroll to the focused content view)
+ // */
+ //focusedContentId : null
+ /** Current scroll position */
+ scrollPosition : 0
},
toString : function(){
return 'HistoryPanelPrefs(' + JSON.stringify( this.toJSON() ) + ')';
@@ -70,6 +76,20 @@
/** sub-views that will overlay this panel (collections) */
this.panelStack = [];
+
+ /** id of currently focused content */
+ this.currentContentId = attributes.currentContentId || null;
+ //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value
+ },
+
+ /** Override to cache the current scroll position with a listener */
+ _setUpListeners : function(){
+ _super.prototype._setUpListeners.call( this );
+
+ var panel = this;
+ this.$scrollContainer().on( 'scroll', function( ev ){
+ panel.preferences.set( 'scrollPosition', $( this ).scrollTop() );
+ });
},
// ------------------------------------------------------------------------ loading history/item models
@@ -243,11 +263,34 @@
});
},
+ /** Override to scroll to cached position (in prefs) after swapping */
+ _swapNewRender : function( $newRender ){
+ _super.prototype._swapNewRender.call( this, $newRender );
+ var panel = this;
+
+ _.delay( function(){
+ var pos = panel.preferences.get( 'scrollPosition' );
+ if( pos ){
+ panel.scrollTo( pos );
+ }
+ }, 10 );
+ //TODO: is this enough of a delay on larger histories?
+
+ return this;
+ },
+
// ------------------------------------------------------------------------ sub-views
// reverse HID order
- /** Override to reverse order of views - newest contents on top */
+ /** Override to reverse order of views - newest contents on top
+ * and add the current-content highlight class to currentContentId's view
+ */
_attachItems : function( $whereTo ){
+ var panel = this;
this.$list( $whereTo ).append( this.views.reverse().map( function( view ){
+ // add current content
+ if( panel.currentContentId && view.model.id === panel.currentContentId ){
+ view.$el.addClass( 'current-content' );
+ }
return view.$el;
}));
return this;
@@ -298,9 +341,26 @@
view.on( 'collapsed:drilldown', function( v, drilldown ){
this._collapseDrilldownPanel( drilldown );
}, this );
+
+ // when content is manipulated, make it the current-content
+ view.on( 'display edit params rerun report-err visualize', function( v, ev ){
+ this.setCurrentContent( v );
+ }, this );
+
return this;
},
+ /** display 'current content': add a visible highlight and store the id of a content item */
+ setCurrentContent : function( view ){
+ this.$( '.history-content.current-content' ).removeClass( 'current-content' );
+ if( view ){
+ view.$el.addClass( 'current-content' );
+ this.currentContentId = view.model.id;
+ } else {
+ this.currentContentId = null;
+ }
+ },
+
/** Handle drill down by hiding this panels list and controls and showing the sub-panel */
_expandDrilldownPanel : function( drilldown ){
this.panelStack.push( drilldown );
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/scripts/mvc/list/list-panel.js
--- a/static/scripts/mvc/list/list-panel.js
+++ b/static/scripts/mvc/list/list-panel.js
@@ -679,28 +679,28 @@
},
/** set the current scroll position of the panel in its parent */
- scrollTo : function( pos ){
- this.$scrollContainer().scrollTop( pos );
+ scrollTo : function( pos, speed ){
+ speed = speed || 0;
+ this.$scrollContainer().animate({ scrollTop: pos }, speed );
return this;
},
/** Scrolls the panel to the top. */
- scrollToTop : function(){
- this.$scrollContainer().scrollTop( 0 );
- return this;
+ scrollToTop : function( speed ){
+ return this.scrollTo( 0, speed );
},
/** */
- scrollToItem : function( view ){
+ scrollToItem : function( view, speed ){
if( !view ){ return this; }
- var itemTop = view.$el.offset().top;
- this.$scrollContainer().scrollTop( itemTop );
- return this;
+ //var itemTop = view.$el.offset().top;
+ var itemTop = view.$el.position().top;
+ return this.scrollTo( itemTop, speed );
},
/** Scrolls the panel to show the content with the given id. */
- scrollToId : function( id ){
- return this.scrollToItem( this.viewFromModelId( id ) );
+ scrollToId : function( id, speed ){
+ return this.scrollToItem( this.viewFromModelId( id ), speed );
},
// ------------------------------------------------------------------------ panel events
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/scripts/packed/mvc/dataset/dataset-li-edit.js
--- a/static/scripts/packed/mvc/dataset/dataset-li-edit.js
+++ b/static/scripts/packed/mvc/dataset/dataset-li-edit.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","mvc/base-mvc","utils/localization"],function(g,d,e,a,h,b){var f=d.DatasetListItemView;var i=f.extend({initialize:function(j){f.prototype.initialize.call(this,j);this.hasUser=j.hasUser;this.purgeAllowed=j.purgeAllowed||false;this.tagsEditorShown=j.tagsEditorShown||false;this.annotationEditorShown=j.annotationEditorShown||false},_renderPrimaryActions:function(){var j=f.prototype._renderPrimaryActions.call(this);if(this.model.get("state")===g.NOT_VIEWABLE){return j}return f.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if((this.model.get("state")===g.DISCARDED)||(!this.model.get("accessible"))){return null}var l=this.model.get("purged"),j=this.model.get("deleted"),k={title:b("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};if(j||l){k.disabled=true;if(l){k.title=b("Cannot edit attributes of datasets removed from disk")}else{if(j){k.title=b("Undelete dataset to edit attributes")}}}else{if(_.contains([g.UPLOAD,g.NEW],this.model.get("state"))){k.disabled=true;k.title=b("This dataset is not yet editable")}}return faIconButton(k)},_renderDeleteButton:function(){if((!this.model.get("accessible"))){return null}var j=this,k=this.model.isDeletedOrPurged();return faIconButton({title:!k?b("Delete"):b("Dataset is already deleted"),disabled:k,faIcon:"fa-times",classes:"delete-btn",onclick:function(){j.$el.find(".icon-btn.delete-btn").trigger("mouseout");j.model["delete"]()}})},_renderDetails:function(){var j=f.prototype._renderDetails.call(this),k=this.model.get("state");if(!this.model.isDeletedOrPurged()&&_.contains([g.OK,g.FAILED_METADATA],k)){this._renderTags(j);this._renderAnnotation(j);this._makeDbkeyEditLink(j)}this._setUpBehaviors(j);return j},_renderSecondaryActions:function(){var j=f.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case g.UPLOAD:case g.NEW:case g.NOT_VIEWABLE:return j;case g.ERROR:j.unshift(this._renderErrButton());return j.concat([this._renderRerunButton()]);case g.OK:case g.FAILED_METADATA:return j.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return j.concat([this._renderRerunButton()])},_renderErrButton:function(){return faIconButton({title:b("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){return faIconButton({title:b("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_renderVisualizationsButton:function(){var j=this.model.get("visualizations");if((this.model.isDeletedOrPurged())||(!this.hasUser)||(!this.model.hasData())||(_.isEmpty(j))){return null}if(!_.isObject(j[0])){this.warn("Visualizations have been switched off");return null}var k=$(this.templates.visualizations(j,this));this._addScratchBookFn(k.find(".visualization-link").addBack(".visualization-link"));return k},_addScratchBookFn:function(j){j.click(function(k){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")});k.preventDefault();k.stopPropagation()}})},_renderTags:function(j){if(!this.hasUser){return}var k=this;this.tagsEditor=new e.TagsEditor({model:this.model,el:j.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.tagsEditorShown=true},onhide:function(){k.tagsEditorShown=false},$activator:faIconButton({title:b("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){if(!this.hasUser){return}var k=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:j.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.annotationEditorShown=true},onhide:function(){k.annotationEditorShown=false},$activator:faIconButton({title:b("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},_makeDbkeyEditLink:function(j){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var k=$('<a class="value">?</a>').attr("href",this.model.urls.edit).attr("target",this.linkTarget);j.find(".dbkey .value").replaceWith(k)}},events:_.extend(_.clone(f.prototype.events),{"click .undelete-link":function(j){this.model.undelete();return false},"click .purge-link":"_confirmPurge"}),_confirmPurge:function c(j){this.model.purge();return false},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"HDAEditView("+j+")"}});i.prototype.templates=(function(){var k=_.extend({},f.prototype.templates.warnings,{failed_metadata:h.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','<div class="failed_metadata-warning warningmessagesmall">',b("An error occurred setting the metadata for this dataset"),'<br /><a href="<%= dataset.urls.edit %>" target="<%= view.linkTarget %>">',b("Set it manually or retry auto-detection"),"</a>","</div>","<% } %>"],"dataset"),deleted:h.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',b("This dataset has been deleted"),'<br /><a class="undelete-link" href="javascript:void(0);">',b("Undelete it"),"</a>","<% if( view.purgeAllowed ){ %>",'<br /><a class="purge-link" href="javascript:void(0);">',b("Permanently remove it from disk"),"</a>","<% } %>","</div>","<% } %>"],"dataset")});var j=h.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'<a class="visualization-btn visualization-link icon-btn" href="<%= visualizations[0].href %>"',' target="<%= visualizations[0].target %>" title="',b("Visualize in"),' <%= visualizations[0].html %>">','<span class="fa fa-bar-chart-o"></span>',"</a>","<% } else { %>",'<div class="visualizations-dropdown dropdown">','<a class="visualization-btn icon-btn" data-toggle="dropdown" title="',b("Visualize"),'">','<span class="fa fa-bar-chart-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu">',"<% _.each( visualizations, function( visualization ){ %>",'<li><a class="visualization-link" href="<%= visualization.href %>"',' target="<%= visualization.target %>">',"<%= visualization.html %>","</a></li>","<% }); %>","</ul>","</div>","<% } %>"],"visualizations");return _.extend({},f.prototype.templates,{warnings:k,visualizations:j})}());return{DatasetListItemEdit:i}});
\ No newline at end of file
+define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","mvc/base-mvc","utils/localization"],function(b,h,g,e,c,d){var f=h.DatasetListItemView;var a=f.extend({initialize:function(i){f.prototype.initialize.call(this,i);this.hasUser=i.hasUser;this.purgeAllowed=i.purgeAllowed||false;this.tagsEditorShown=i.tagsEditorShown||false;this.annotationEditorShown=i.annotationEditorShown||false},_renderPrimaryActions:function(){var i=f.prototype._renderPrimaryActions.call(this);if(this.model.get("state")===b.NOT_VIEWABLE){return i}return f.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if((this.model.get("state")===b.DISCARDED)||(!this.model.get("accessible"))){return null}var k=this.model.get("purged"),i=this.model.get("deleted"),j={title:d("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};if(i||k){j.disabled=true;if(k){j.title=d("Cannot edit attributes of datasets removed from disk")}else{if(i){j.title=d("Undelete dataset to edit attributes")}}}else{if(_.contains([b.UPLOAD,b.NEW],this.model.get("state"))){j.disabled=true;j.title=d("This dataset is not yet editable")}}return faIconButton(j)},_renderDeleteButton:function(){if((!this.model.get("accessible"))){return null}var i=this,j=this.model.isDeletedOrPurged();return faIconButton({title:!j?d("Delete"):d("Dataset is already deleted"),disabled:j,faIcon:"fa-times",classes:"delete-btn",onclick:function(){i.$el.find(".icon-btn.delete-btn").trigger("mouseout");i.model["delete"]()}})},_renderDetails:function(){var i=f.prototype._renderDetails.call(this),j=this.model.get("state");if(!this.model.isDeletedOrPurged()&&_.contains([b.OK,b.FAILED_METADATA],j)){this._renderTags(i);this._renderAnnotation(i);this._makeDbkeyEditLink(i)}this._setUpBehaviors(i);return i},_renderSecondaryActions:function(){var i=f.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case b.UPLOAD:case b.NEW:case b.NOT_VIEWABLE:return i;case b.ERROR:i.unshift(this._renderErrButton());return i.concat([this._renderRerunButton()]);case b.OK:case b.FAILED_METADATA:return i.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return i.concat([this._renderRerunButton()])},_renderErrButton:function(){return faIconButton({title:d("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){return faIconButton({title:d("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_renderVisualizationsButton:function(){var i=this.model.get("visualizations");if((this.model.isDeletedOrPurged())||(!this.hasUser)||(!this.model.hasData())||(_.isEmpty(i))){return null}if(!_.isObject(i[0])){this.warn("Visualizations have been switched off");return null}var j=$(this.templates.visualizations(i,this));this._addScratchBookFn(j.find(".visualization-link").addBack(".visualization-link"));return j},_addScratchBookFn:function(i){i.click(function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")});j.preventDefault();j.stopPropagation()}})},_renderTags:function(i){if(!this.hasUser){return}var j=this;this.tagsEditor=new g.TagsEditor({model:this.model,el:i.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.tagsEditorShown=true},onhide:function(){j.tagsEditorShown=false},$activator:faIconButton({title:d("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(i){if(!this.hasUser){return}var j=this;this.annotationEditor=new e.AnnotationEditor({model:this.model,el:i.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.annotationEditorShown=true},onhide:function(){j.annotationEditorShown=false},$activator:faIconButton({title:d("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},_makeDbkeyEditLink:function(i){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var j=$('<a class="value">?</a>').attr("href",this.model.urls.edit).attr("target",this.linkTarget);i.find(".dbkey .value").replaceWith(j)}},events:_.extend(_.clone(f.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(i){this.trigger("edit",this,i)},"click .delete-btn":function(i){this.trigger("delete",this,i)},"click .rerun-btn":function(i){this.trigger("rerun",this,i)},"click .report-err-btn":function(i){this.trigger("report-err",this,i)},"click .visualization-btn":function(i){this.trigger("visualize",this,i)},"click .dbkey a":function(i){this.trigger("edit",this,i)}}),_clickUndeleteLink:function(i){this.model.undelete();return false},_clickPurgeLink:function(i){this.model.purge();return false},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"HDAEditView("+i+")"}});a.prototype.templates=(function(){var j=_.extend({},f.prototype.templates.warnings,{failed_metadata:c.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','<div class="failed_metadata-warning warningmessagesmall">',d("An error occurred setting the metadata for this dataset"),'<br /><a href="<%= dataset.urls.edit %>" target="<%= view.linkTarget %>">',d("Set it manually or retry auto-detection"),"</a>","</div>","<% } %>"],"dataset"),deleted:c.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',d("This dataset has been deleted"),'<br /><a class="undelete-link" href="javascript:void(0);">',d("Undelete it"),"</a>","<% if( view.purgeAllowed ){ %>",'<br /><a class="purge-link" href="javascript:void(0);">',d("Permanently remove it from disk"),"</a>","<% } %>","</div>","<% } %>"],"dataset")});var i=c.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'<a class="visualization-btn visualization-link icon-btn" href="<%= visualizations[0].href %>"',' target="<%= visualizations[0].target %>" title="',d("Visualize in"),' <%= visualizations[0].html %>">','<span class="fa fa-bar-chart-o"></span>',"</a>","<% } else { %>",'<div class="visualizations-dropdown dropdown">','<a class="visualization-btn icon-btn" data-toggle="dropdown" title="',d("Visualize"),'">','<span class="fa fa-bar-chart-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu">',"<% _.each( visualizations, function( visualization ){ %>",'<li><a class="visualization-link" href="<%= visualization.href %>"',' target="<%= visualization.target %>">',"<%= visualization.html %>","</a></li>","<% }); %>","</ul>","</div>","<% } %>"],"visualizations");return _.extend({},f.prototype.templates,{warnings:j,visualizations:i})}());return{DatasetListItemEdit:a}});
\ No newline at end of file
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/scripts/packed/mvc/dataset/dataset-li.js
--- a/static/scripts/packed/mvc/dataset/dataset-li.js
+++ b/static/scripts/packed/mvc/dataset/dataset-li.js
@@ -1,1 +1,1 @@
-define(["mvc/list/list-item","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(d,a,b,c){var f=d.ListItemView;var e=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);f.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this);this.model.on("change",function(h,g){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},_fetchModelDetails:function(){var g=this;if(g.model.inReadyState()&&!g.model.hasDetails()){return g.model.fetch({silent:true})}return jQuery.when()},remove:function(h,i){var g=this;h=h||this.fxSpeed;this.$el.fadeOut(h,function(){Backbone.View.prototype.remove.call(g);if(i){i.call(g)}})},render:function(g){return f.prototype.render.call(this,g)},_swapNewRender:function(g){f.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var i=this.model.get("state");if((i===a.NOT_VIEWABLE)||(i===a.DISCARDED)||(!this.model.get("accessible"))){return null}var h={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){h.disabled=true;h.title=c("Cannot display datasets removed from disk")}else{if(i===a.UPLOAD){h.disabled=true;h.title=c("This dataset must finish uploading before it can be viewed")}else{if(i===a.NEW){h.disabled=true;h.title=c("This dataset is not yet viewable")}else{h.title=c("View data");h.href=this.model.urls.display;var g=this;h.onclick=function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+g.model.get("name"),type:"other",content:function(k){require(["mvc/data"],function(l){var m=new l.TabularDataset({id:g.model.get("id")});$.when(m.fetch()).then(function(){l.createTabularDatasetChunkedView({model:m,parent_elt:k,embedded:true,height:"100%"})})})}});j.preventDefault()}}}}}h.faIcon="fa-eye";return faIconButton(h)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var g=f.prototype._renderDetails.call(this);g.find(".actions .left").empty().append(this._renderSecondaryActions());g.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());g.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(g);return g},_renderSummary:function(){var g=this.model.toJSON(),h=this.templates.summaries[g.state];h=h||this.templates.summaries.unknown;return h(g,this)},_renderDetailMessages:function(){var g=this,i=$('<div class="detail-messages"></div>'),h=g.model.toJSON();_.each(g.templates.detailMessages,function(j){i.append($(j(h,g)))});return i},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var g=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+g.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(h){return['<li><a href="',g.meta_download+h.file_type,'">',c("Download")," ",h.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+g+")"}});e.prototype.templates=(function(){var i=_.extend({},f.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var j=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var h=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var k={};k[a.OK]=k[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");k[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");k[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");k[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");k[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");k[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");k[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");k[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");k[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");k[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");k[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");k.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var l={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var g=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:i,details:j,noAccess:h,summaries:k,detailMessages:l,displayApplications:g})}());return{DatasetListItemView:e}});
\ No newline at end of file
+define(["mvc/list/list-item","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(d,a,b,c){var f=d.ListItemView;var e=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);f.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this);this.model.on("change",function(h,g){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},_fetchModelDetails:function(){var g=this;if(g.model.inReadyState()&&!g.model.hasDetails()){return g.model.fetch({silent:true})}return jQuery.when()},remove:function(h,i){var g=this;h=h||this.fxSpeed;this.$el.fadeOut(h,function(){Backbone.View.prototype.remove.call(g);if(i){i.call(g)}})},render:function(g){return f.prototype.render.call(this,g)},_swapNewRender:function(g){f.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var i=this.model.get("state");if((i===a.NOT_VIEWABLE)||(i===a.DISCARDED)||(!this.model.get("accessible"))){return null}var h={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){h.disabled=true;h.title=c("Cannot display datasets removed from disk")}else{if(i===a.UPLOAD){h.disabled=true;h.title=c("This dataset must finish uploading before it can be viewed")}else{if(i===a.NEW){h.disabled=true;h.title=c("This dataset is not yet viewable")}else{h.title=c("View data");h.href=this.model.urls.display;var g=this;h.onclick=function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+g.model.get("name"),type:"other",content:function(k){require(["mvc/data"],function(l){var m=new l.TabularDataset({id:g.model.get("id")});$.when(m.fetch()).then(function(){l.createTabularDatasetChunkedView({model:m,parent_elt:k,embedded:true,height:"100%"})})})}});j.preventDefault()}}}}}h.faIcon="fa-eye";return faIconButton(h)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var g=f.prototype._renderDetails.call(this);g.find(".actions .left").empty().append(this._renderSecondaryActions());g.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());g.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(g);return g},_renderSummary:function(){var g=this.model.toJSON(),h=this.templates.summaries[g.state];h=h||this.templates.summaries.unknown;return h(g,this)},_renderDetailMessages:function(){var g=this,i=$('<div class="detail-messages"></div>'),h=g.model.toJSON();_.each(g.templates.detailMessages,function(j){i.append($(j(h,g)))});return i},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var g=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+g.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(h){return['<li><a href="',g.meta_download+h.file_type,'">',c("Download")," ",h.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(g){this.trigger("display",this,g)},"click .params-btn":function(g){this.trigger("params",this,g)},"click .download-btn":function(g){this.trigger("download",this,g)}}),toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+g+")"}});e.prototype.templates=(function(){var i=_.extend({},f.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var j=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var h=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var k={};k[a.OK]=k[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");k[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");k[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");k[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");k[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");k[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");k[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");k[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");k[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");k[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");k[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");k.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var l={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var g=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:i,details:j,noAccess:h,summaries:k,detailMessages:l,displayApplications:g})}());return{DatasetListItemView:e}});
\ No newline at end of file
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/scripts/packed/mvc/history/history-panel-edit-current.js
--- a/static/scripts/packed/mvc/history/history-panel-edit-current.js
+++ b/static/scripts/packed/mvc/history/history-panel-edit-current.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[]},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_attachItems:function(j){this.$list(j).append(this.views.reverse().map(function(k){return k.$el}));return this},addItemView:function(o,p,n){this.log(this+".addItemView:",o);var l=this;if(!l._filterItem(o)){return undefined}if(l.panelStack.length){return this._collapseDrilldownPanel()}var k=l._createItemView(o);l.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);return this},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}});
\ No newline at end of file
+define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){j.preferences.set("scrollPosition",$(this).scrollTop())})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){var j=this;this.$list(k).append(this.views.reverse().map(function(l){if(j.currentContentId&&l.model.id===j.currentContentId){l.$el.addClass("current-content")}return l.$el}));return this},addItemView:function(o,p,n){this.log(this+".addItemView:",o);var l=this;if(!l._filterItem(o)){return undefined}if(l.panelStack.length){return this._collapseDrilldownPanel()}var k=l._createItemView(o);l.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}});
\ No newline at end of file
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/scripts/packed/mvc/list/list-panel.js
--- a/static/scripts/packed/mvc/list/list-panel.js
+++ b/static/scripts/packed/mvc/list/list-panel.js
@@ -1,1 +1,1 @@
-define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(f){this.$scrollContainer().scrollTop(f);return this},scrollToTop:function(){this.$scrollContainer().scrollTop(0);return this},scrollToItem:function(f){if(!f){return this}var g=f.$el.offset().top;this.$scrollContainer().scrollTop(g);return this},scrollToId:function(f){return this.scrollToItem(this.viewFromModelId(f))},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}});
\ No newline at end of file
+define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}});
\ No newline at end of file
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1954,6 +1954,9 @@
.history-panel .controls .list-actions .list-action-popup-btn{float:right}
.history-panel .list-item.history-content{border-width:1px 0px 0px 0px}.history-panel .list-item.history-content:last-child{border-width:1px 0px 1px 0px}
.history-panel .empty-message{margin:0px 10px 0px 10px}
+.history-panel .dataset-collection .subtitle{margin-top:2px;font-size:90%;color:#777}
+.history-panel .dataset-collection-panel .controls{padding:0px}
+.history-panel .dataset-collection-panel .list-items{margin-top:0px}
.annotated-history-panel .controls{margin:0px}.annotated-history-panel .controls .name{font-size:150%;margin-bottom:4px}
.annotated-history-panel .controls .subtitle{color:black}.annotated-history-panel .controls .subtitle:not(:empty){margin:0px 0px 0px 4px}
.annotated-history-panel .controls .messages:not(:empty){margin-top:16px}
@@ -1965,9 +1968,8 @@
.annotated-history-panel table.list-items>tbody>tr>td:nth-child(2){padding:8px 16px 8px 16px;white-space:pre-wrap}
.annotated-history-panel table.list-items>tbody>tr>td>.list-item{border:0px}
.annotated-history-panel .empty-message{margin-top:8px}
-.history-panel .dataset-collection .subtitle{margin-top:2px;font-size:90%;color:#777}
-.history-panel .dataset-collection-panel .controls{padding:0px}
-.history-panel .dataset-collection-panel .list-items{margin-top:0px}
+.current-history-panel .list-item.history-content.current-content{border:2px solid black;border-bottom-width:2px}.current-history-panel .list-item.history-content.current-content .title-bar{padding:5px 8px 6px 6px}
+.current-history-panel .list-item.history-content.current-content .details{padding:0px 8px 5px 6px}
body.historyPage{background:#dfe5f9;color:#000;margin:5px;border:0;padding:0}
div.historyLinks{margin:5px 5px}
div.historyItem{margin:0 -5px;padding:8px 10px;border-top:solid #bfbfbf 1px;border-right:none;word-wrap:break-word;background:#eee}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat}
diff -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 -r 025d227c0c1325f38a76aff4dc264c749f24e4e7 static/style/src/less/history.less
--- a/static/style/src/less/history.less
+++ b/static/style/src/less/history.less
@@ -488,6 +488,27 @@
}
}
+
+// ---------------------------------------------------------------------------- collections nested in histories
+.history-panel {
+ .dataset-collection {
+ .subtitle {
+ margin-top: 2px;
+ font-size: 90%;
+ color: #777;
+ }
+ }
+ .dataset-collection-panel {
+ .controls {
+ padding: 0px;
+ }
+ .list-items {
+ margin-top: 0px;
+ }
+ }
+}
+
+
// ---------------------------------------------------------------------------- annotated-history-panel
.annotated-history-panel {
.controls {
@@ -566,21 +587,31 @@
}
-// ---------------------------------------------------------------------------- collections nested in histories
-.history-panel {
- .dataset-collection {
- .subtitle {
- margin-top: 2px;
- font-size: 90%;
- color: #777;
+// ---------------------------------------------------------------------------- current-history-panel
+.current-history-panel {
+ .list-item.history-content.current-content {
+ //border-top: 2px solid black;
+ //border-right: 1px solid black;
+ //border-bottom: 2px solid black;
+ //border-left: 1px solid black;
+
+ //.title-bar {
+ // border-color: black;
+ // background: black;
+ // color: white;
+ //}
+
+ //position: relative;
+ //margin-left: -24px;
+ //z-index: 1000;
+
+ border: 2px solid black;
+ border-bottom-width: 2px;
+ .title-bar {
+ padding: 5px 8px 6px 6px;
}
- }
- .dataset-collection-panel {
- .controls {
- padding: 0px;
- }
- .list-items {
- margin-top: 0px;
+ .details {
+ padding: 0px 8px 5px 6px;
}
}
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxyproject/ansible-galaxy] 0ed236: Align variable field names between galaxy_mutable_...
by GitHub 18 Sep '14
by GitHub 18 Sep '14
18 Sep '14
Branch: refs/heads/master
Home: https://github.com/galaxyproject/ansible-galaxy
Commit: 0ed236dbf8da954d0a7e27d611476cbe22521457
https://github.com/galaxyproject/ansible-galaxy/commit/0ed236dbf8da954d0a7e…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2014-09-18 (Thu, 18 Sep 2014)
Changed paths:
M tasks/static_setup.yml
Log Message:
-----------
Align variable field names between galaxy_mutable_configs, galaxy_config_files and galaxy_config_templates variables
Commit: 3c8a55e99dc2bf098c8b4a6500107800aba07605
https://github.com/galaxyproject/ansible-galaxy/commit/3c8a55e99dc2bf098c8b…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2014-09-18 (Thu, 18 Sep 2014)
Changed paths:
M tasks/eggs.yml
Log Message:
-----------
Explicitly use venv python (as it's done in other tasks)
Compare: https://github.com/galaxyproject/ansible-galaxy/compare/289dc4eabe17...3c8a…
1
0
commit/galaxy-central: carlfeberhard: Client build: remove potentially confusing copy of pack_scripts.py from client/galaxy/scripts; remove unused packed
by commits-noreply＠bitbucket.org 18 Sep '14
by commits-noreply＠bitbucket.org 18 Sep '14
18 Sep '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/66abf553f05e/
Changeset: 66abf553f05e
User: carlfeberhard
Date: 2014-09-18 14:00:11+00:00
Summary: Client build: remove potentially confusing copy of pack_scripts.py from client/galaxy/scripts; remove unused packed
Affected #: 3 files
diff -r bd682aec7471f0e76423ae13eee6fd829cf1eaf8 -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 client/galaxy/scripts/pack_scripts.py
--- a/client/galaxy/scripts/pack_scripts.py
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/usr/bin/env python
-
-import sys, os
-
-from glob import glob
-from subprocess import call
-from shutil import copyfile
-from os import path
-
-# Scripts that should not be packed -- just copied
-do_not_pack = set()
-
-cmd = "java -jar ../../scripts/yuicompressor.jar --charset utf-8 --type js %(fname)s -o packed/%(fname)s"
-# cmd = "java -jar ../../scripts/compiler.jar --compilation_level SIMPLE_OPTIMIZATIONS --js %(fname)s --js_output_file packed/%(fname)s"
-
-# If specific scripts specified on command line, just pack them, otherwise pack
-# all.
-
-def recursive_glob( pattern, excluded_dirs ):
- """
- Returns all items that match pattern in root and subdirectories.
- """
-
- a_dir, a_pattern = path.split( pattern )
-
- # Skip excluded dirs.
- if a_dir in excluded_dirs:
- return []
-
- # Search current dir.
- # print a_dir, a_pattern
- rval = glob( pattern )
- for item in glob( path.join( a_dir, "*" ) ):
- if path.isdir( item ):
- rval.extend( recursive_glob( path.join( item, a_pattern ), excluded_dirs ) )
-
- return rval
-
-# Get files to pack.
-if len( sys.argv ) > 1:
- to_pack = sys.argv[1:]
-else:
- to_pack = recursive_glob( "*.js", [ "packed" ] )
-
-
-for fname in to_pack:
- d = dict( fname=fname )
- packed_fname = path.join( 'packed', fname )
-
- # Only copy if full version is newer than packed version.
- if path.exists( packed_fname ) and ( path.getmtime( fname ) < path.getmtime( packed_fname ) ):
- print "Packed is current: %s" % fname
- continue
-
- print "%(fname)s --> packed/%(fname)s" % d
-
- # Create destination dir if necessary.
- dir, name = os.path.split( packed_fname )
- if not path.exists( dir ):
- print "Creating needed directory %s" % dir
- os.makedirs( dir )
-
- # Copy/pack.
- if fname in do_not_pack:
- copyfile( fname, path.join( packed_fname ) )
- else:
- out = call( cmd % d, shell=True )
diff -r bd682aec7471f0e76423ae13eee6fd829cf1eaf8 -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 static/scripts/packed/mvc/visualization/scatterplotControlForm.js
--- a/static/scripts/packed/mvc/visualization/scatterplotControlForm.js
+++ /dev/null
@@ -1,1 +0,0 @@
-var ScatterplotControlForm=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_config.root+"static/images/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find("[title]").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column_with_stats",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]};
\ No newline at end of file
diff -r bd682aec7471f0e76423ae13eee6fd829cf1eaf8 -r 66abf553f05ebf5fa00fda6800b2a7bb95d3b559 static/scripts/packed/mvc/visualizations/scatterplotControlForm.js
--- a/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js
+++ /dev/null
@@ -1,1 +0,0 @@
-var ScatterplotControlForm=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_config.root+"static/images/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find("[title]").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column_with_stats",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]};
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/aa867e3d2bd9/
Changeset: aa867e3d2bd9
User: jmchilton
Date: 2014-09-18 13:50:52+00:00
Summary: More complete testing of workflow import and export.
Test some new aspects of step description inputs.
Affected #: 3 files
diff -r 76be361f50b29515226f94bd2a2e01f0d9ff413b -r aa867e3d2bd96b38eed23bc4bcacfa77345b017e test/api/test_workflow_1.ga
--- a/test/api/test_workflow_1.ga
+++ b/test/api/test_workflow_1.ga
@@ -5,12 +5,12 @@
"name": "TestWorkflow1",
"steps": {
"0": {
- "annotation": "",
+ "annotation": "input1 description",
"id": 0,
"input_connections": {},
"inputs": [
{
- "description": "",
+ "description": "input1 description",
"name": "WorkflowInput1"
}
],
diff -r 76be361f50b29515226f94bd2a2e01f0d9ff413b -r aa867e3d2bd96b38eed23bc4bcacfa77345b017e test/api/test_workflow_with_runtime_input.ga
--- /dev/null
+++ b/test/api/test_workflow_with_runtime_input.ga
@@ -0,0 +1,66 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "test_workflow_with_runtime_input",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 248.49653673171997,
+ "top": 154.98959398269653
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": []
+ },
+ "1": {
+ "annotation": "",
+ "id": 1,
+ "input_connections": {
+ "input": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Select random lines",
+ "name": "num_lines"
+ }
+ ],
+ "name": "Select random lines",
+ "outputs": [
+ {
+ "name": "out_file1",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "left": 514.0208587646484,
+ "top": 116.01736450195312
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "random_lines1",
+ "tool_state": "{\"input\": \"null\", \"seed_source\": \"{\\\"__current_case__\\\": 0, \\\"seed_source_selector\\\": \\\"no_seed\\\"}\", \"__rerun_remap_job_id__\": null, \"num_lines\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}",
+ "tool_version": "2.0.1",
+ "type": "tool",
+ "user_outputs": []
+ }
+ },
+ "uuid": "ebb0e189-e1ae-4f08-a0aa-97d8674f9f76"
+}
\ No newline at end of file
diff -r 76be361f50b29515226f94bd2a2e01f0d9ff413b -r aa867e3d2bd96b38eed23bc4bcacfa77345b017e test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -105,6 +105,17 @@
assert len( downloaded_workflow[ "steps" ] ) == 3
first_input = downloaded_workflow[ "steps" ][ "0" ][ "inputs" ][ 0 ]
assert first_input[ "name" ] == "WorkflowInput1"
+ assert first_input[ "description" ] == "input1 description"
+
+ def test_import_export_with_runtime_inputs( self ):
+ workflow = self.workflow_populator.load_workflow_from_resource( name="test_workflow_with_runtime_input" )
+ workflow_id = self.workflow_populator.create_workflow( workflow )
+ download_response = self._get( "workflows/%s/download" % workflow_id )
+ downloaded_workflow = download_response.json()
+ assert len( downloaded_workflow[ "steps" ] ) == 2
+ runtime_input = downloaded_workflow[ "steps" ][ "1" ][ "inputs" ][ 0 ]
+ assert runtime_input[ "description" ].startswith( "runtime parameter for tool" )
+ assert runtime_input[ "name" ] == "num_lines"
@skip_without_tool( "cat1" )
def test_run_workflow_by_index( self ):
https://bitbucket.org/galaxy/galaxy-central/commits/bd682aec7471/
Changeset: bd682aec7471
User: jmchilton
Date: 2014-09-18 13:50:52+00:00
Summary: Refactor logic for generating dictified runtime inputs for workflow steps into workflow module.
Continuing the pattern - this is one less place where consumers of workflows modules need to explicitly dispatch on type and should make it easier and clear what needs to be defined when adding new workflow modules. This also reduces the cyclomatic complexity of the large _workflow_to_dict method.
Previous commit provides test coverage verifying this doesn't modify the behavior of workflow extraction.
Affected #: 2 files
diff -r aa867e3d2bd96b38eed23bc4bcacfa77345b017e -r bd682aec7471f0e76423ae13eee6fd829cf1eaf8 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -41,7 +41,7 @@
from galaxy.managers import tags
from galaxy.managers import base as managers_base
from galaxy.datatypes.metadata import FileParameter
-from galaxy.tools.parameters import RuntimeValue, visit_input_values
+from galaxy.tools.parameters import visit_input_values
from galaxy.tools.parameters.basic import DataToolParameter
from galaxy.tools.parameters.basic import DataCollectionToolParameter
from galaxy.util.json import dumps
@@ -1738,25 +1738,7 @@
action_arguments = pja.action_arguments )
step_dict[ 'post_job_actions' ] = pja_dict
# Data inputs
- step_dict['inputs'] = []
- if module.type == "data_input":
- # Get input dataset name; default to 'Input Dataset'
- name = module.state.get( 'name', 'Input Dataset')
- step_dict['inputs'].append( { "name" : name, "description" : annotation_str } )
- elif module.type == "data_collection_input":
- name = module.state.get( 'name', 'Input Dataset Collection' )
- step_dict['inputs'].append( { "name" : name, "description" : annotation_str } )
- else:
- # Step is a tool and may have runtime inputs.
- for name, val in module.state.inputs.items():
- input_type = type( val )
- if input_type == RuntimeValue:
- step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } )
- elif input_type == dict:
- # Input type is described by a dict, e.g. indexed parameters.
- for partval in val.values():
- if type( partval ) == RuntimeValue:
- step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } )
+ step_dict['inputs'] = module.get_runtime_input_dicts( annotation_str )
# User outputs
step_dict['user_outputs'] = []
"""
diff -r aa867e3d2bd96b38eed23bc4bcacfa77345b017e -r bd682aec7471f0e76423ae13eee6fd829cf1eaf8 lib/galaxy/workflow/modules.py
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -98,11 +98,16 @@
return None
def get_data_inputs( self ):
+ """ Get configure time data input descriptions. """
return []
def get_data_outputs( self ):
return []
+ def get_runtime_input_dicts( self, step_annotation ):
+ """ Get runtime inputs (inputs and parameters) as simple dictionary. """
+ return []
+
def get_config_form( self ):
""" Render form that is embedded in workflow editor for modifying the
step state of a node.
@@ -194,6 +199,10 @@
"""
raise TypeError( "Abstract method" )
+ def get_runtime_input_dicts( self, step_annotation ):
+ name = self.state.get( "name", self.default_name )
+ return [ dict( name=name, description=step_annotation ) ]
+
def recover_state( self, state, **kwds ):
""" Recover state `dict` from simple dictionary describing configuration
state (potentially from persisted step state).
@@ -529,6 +538,20 @@
data_outputs.append( dict( name=name, extensions=formats ) )
return data_outputs
+ def get_runtime_input_dicts( self, step_annotation ):
+ # Step is a tool and may have runtime inputs.
+ input_dicts = []
+ for name, val in self.state.inputs.items():
+ input_type = type( val )
+ if input_type == RuntimeValue:
+ input_dicts.append( { "name": name, "description": "runtime parameter for tool %s" % self.get_name() } )
+ elif input_type == dict:
+ # Input type is described by a dict, e.g. indexed parameters.
+ for partval in val.values():
+ if type( partval ) == RuntimeValue:
+ input_dicts.append( { "name": name, "description": "runtime parameter for tool %s" % self.get_name() } )
+ return input_dicts
+
def get_post_job_actions( self ):
return self.post_job_actions
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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