[galaxy-commits] commit/galaxy-central: guerler: ToolForm: Additional buttons, fixes and improvements, genome build selector, first commit for multiple dataset and collection selector

5 Sep 2014

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/be2c86442b3e/
Changeset:   be2c86442b3e
User:        guerler
Date:        2014-09-05 17:24:55
Summary:     ToolForm: Additional buttons, fixes and improvements, genome build selector, first commit for multiple dataset and collection selector
Affected #:  13 files

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/mvc/tools/tools-datasets.js

--- a/static/scripts/mvc/tools/tools-datasets.js
+++ b/static/scripts/mvc/tools/tools-datasets.js
@@ -6,7 +6,7 @@
             this.currHistoryContents = new HISTORY_CONTENTS.HistoryContents({});
             
             // identify current history id
-            this.currHistoryContents.historyId = "f597429621d6eb2b";//Galaxy.currHistoryPanel.model.id;
+            this.currHistoryContents.historyId = options.history_id;
             
             // make request
             var self = this;

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -40,7 +40,8 @@
             
             // initialize datasets
             this.datasets = new ToolDatasets({
-                success: function() {
+                history_id  : this.options.history_id,
+                success     : function() {
                     self._initializeToolForm();
                 }
             });
@@ -48,8 +49,40 @@
         
         // initialize tool form
         _initializeToolForm: function() {
+            // link this
+            var self = this;
+            
+            // create question button
+            var button_question = new Ui.ButtonIcon({
+                icon    : 'fa-question-circle',
+                title   : 'Question?',
+                tooltip : 'Ask a question about this tool (Biostar)',
+                onclick : function() {
+                    window.open(self.options.biostar_url + '/p/new/post/');
+                }
+            });
+            
+            // create search button
+            var button_search = new Ui.ButtonIcon({
+                icon    : 'fa-search',
+                title   : 'Search',
+                tooltip : 'Search help for this tool (Biostar)',
+                onclick : function() {
+                    window.open(self.options.biostar_url + '/t/' + self.options.id + '/');
+                }
+            });
+            
+            // create share button
+            var button_share = new Ui.ButtonIcon({
+                icon    : 'fa-share',
+                title   : 'Share',
+                tooltip : 'Share this tool',
+                onclick : function() {
+                    prompt('Copy to clipboard: Ctrl+C, Enter', galaxy_config.root + 'root?tool_id=' + self.options.id);
+                }
+            });
+            
             // fetch model and render form
-            var self = this;
             this.model.fetch({
                 error: function(response) {
                     console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.');
@@ -72,9 +105,20 @@
                                     console.log(self.tree.create(self));
                                 }
                             })
+                        },
+                        operations: {
+                            button_question: button_question,
+                            button_search: button_search,
+                            button_share: button_share
                         }
                     });
                     
+                    // configure button selection
+                    if(!self.options.biostar_url) {
+                        button_question.$el.hide();
+                        button_search.$el.hide();
+                    }
+                    
                     // create message
                     self.message = new Ui.Message();
                     self.portlet.append(self.message.$el);

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -1,5 +1,5 @@
-define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs'],
-    function(Utils, Table, Ui, Tabs) {
+define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'mvc/tools/tools-select-dataset'],
+    function(Utils, Table, Ui, Tabs, SelectDataset) {
 
     // create form view
     var View = Backbone.View.extend({
@@ -202,7 +202,7 @@
                 
                 // dataset column
                 case 'data_column':
-                    field = this._field_column(input_def);
+                    field = this._field_data_colum(input_def);
                     break;
                     
                 // conditional select field
@@ -229,11 +229,20 @@
                 case 'boolean':
                     field = this._field_boolean(input_def);
                     break;
-                    
-                // default
-                default:
+            }
+            
+            // pick a generic field if specific mapping failed
+            if (!field) {
+                if (input_def.options) {
+                    // assign select field
+                    field = this._field_select(input_def);
+                } else {
+                    // assign text field
                     field = this._field_text(input_def);
-                    console.debug('tools-form::_addRow() : Unmatched field type (' + field_type + ').');
+                }
+                
+                // log
+                console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').');
             }
             
             // set field value
@@ -319,28 +328,15 @@
             // get element id
             var id = input_def.id;
             
-            // get datasets
-            var datasets = this.app.datasets.filterType();
-            
-            // configure options fields
-            var options = [];
-            for (var i in datasets) {
-                options.push({
-                    label: datasets[i].get('name'),
-                    value: datasets[i].get('id')
-                });
-            }
-            
             // select field
-            return new Ui.Select.View({
+            return new SelectDataset.View(this.app, {
                 id          : 'field-' + id,
-                data        : options,
-                value       : options[0].value,
+                extensions  : input_def.extensions,
                 multiple    : input_def.multiple,
                 onchange    : function(value) {
                     // pick the first dataset if multiple might be selected
                     // TODO: iterate over all datasets and filter common/consistent columns
-                    if (input_def.multiple) {
+                    if (value instanceof Array) {
                         value = value[0];
                     }
                     
@@ -429,26 +425,22 @@
                     break;
             }
             
-            // force checkboxes if multiple has been selected
-            if (input_def.multiple) {
-                SelectClass = Ui.Checkbox;
-            }
-            
             // select field
             return new SelectClass.View({
                 id      : 'field-' + input_def.id,
-                data    : options
+                data    : options,
+                multiple: input_def.multiple
             });
         },
 
-        // column selection field
-        _field_column : function (input_def) {
+        // 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) {
             return new Ui.Input({
@@ -457,13 +449,20 @@
             });
         },
         
-        // integer field
+        // slider field
         _field_slider: function(input_def) {
+            // calculate step size
+            var step = 1;
+            if (input_def.type == 'float') {
+                step = (input_def.max - input_def.min) / 10000;
+            }
+            
+            // create slider
             return new Ui.Slider.View({
                 id      : 'field-' + input_def.id,
                 min     : input_def.min || 0,
                 max     : input_def.max || 1000,
-                decimal : input_def.type == 'float'
+                step    : step
             });
         },
         

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/mvc/tools/tools-select-dataset.js
--- /dev/null
+++ b/static/scripts/mvc/tools/tools-select-dataset.js
@@ -0,0 +1,109 @@
+// dependencies
+define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs'], function(Utils, Ui, Tabs) {
+
+var View = Backbone.View.extend({
+    // initialize
+    initialize : function(app, options) {
+        // link this
+        var self = this;
+    
+        // get datasets
+        var datasets = app.datasets.filterType();
+        
+        // configure options fields
+        var select_data = [];
+        for (var i in datasets) {
+            select_data.push({
+                label: datasets[i].get('name'),
+                value: datasets[i].get('id')
+            });
+        }
+        
+        // create select field
+        this.select = new Ui.Select.View({
+            data        : select_data,
+            value       : select_data[0].value,
+            onchange    : function() {
+                self.trigger('change');
+            }
+        });
+        
+        // create select field for multiple files
+        this.select_multiple = new Ui.Select.View({
+            multiple    : true,
+            data        : select_data,
+            value       : select_data[0].value,
+            onchange    : function() {
+                self.trigger('change');
+            }
+        });
+
+        
+        // create select field for multiple files
+        this.select_collection = new Ui.Select.View({
+            data        : select_data,
+            value       : select_data[0].value,
+            onchange    : function() {
+                self.trigger('change');
+            }
+        });
+                
+        // add change event. fires on trigger
+        this.on('change', function() {
+            if (options.onchange) {
+                options.onchange(self.value());
+            }
+        });
+        
+        // tabs
+        this.tabs = new Tabs.View();
+        
+        // add tab
+        this.tabs.add({
+            id      : 'single',
+            title   : 'Select a dataset',
+            $el     : this.select.$el
+        });
+        
+        // add tab
+        this.tabs.add({
+            id      : 'multiple',
+            title   : 'Select multiple datasets',
+            $el     : this.select_multiple.$el
+        });
+
+        // add tab
+        this.tabs.add({
+            id      : 'collection',
+            title   : 'Select a dataset collection',
+            $el     : this.select_collection.$el
+        });
+        
+        // add element
+        this.setElement(this.tabs.$el);
+    },
+    
+    // value
+    value : function (new_value) {
+        var current_tab = this.tabs.current();
+        switch(current_tab) {
+            case 'multiple' :
+                return this.select_multiple.value();
+            case 'collection' :
+                return this.select_collection.value();
+            default :
+                return this.select.value();
+        }
+    },
+    
+    // render
+    update: function(options) {
+        this.select.update(options);
+    }
+});
+
+return {
+    View: View
+}
+
+});

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/mvc/ui/ui-slider.js
--- a/static/scripts/mvc/ui/ui-slider.js
+++ b/static/scripts/mvc/ui/ui-slider.js
@@ -8,8 +8,7 @@
         value   : '',
         min     : 1,
         max     : 100,
-        step    : 0.1,
-        decimal : false
+        step    : 1
     },
     
     // initialize
@@ -29,11 +28,6 @@
         // backup integer field
         this.$text = this.$el.find('#text');
         
-        // set step size
-        if (!this.options.decimal) {
-            this.options.step = 1;
-        }
-        
         // load slider plugin
         this.$slider.slider(this.options);
         
@@ -46,7 +40,7 @@
         this.$text.on('keydown', function (event) {
             var v = event.which;
             if (!(v == 13 || v == 8 || v == 37 || v == 39 || v == 189 || (v >= 48 && v <= 57)
-                || (self.options.decimal && $(this).val().indexOf('.') == -1) && v == 190)) {
+                || (self.options.step != 1 && $(this).val().indexOf('.') == -1) && v == 190)) {
                 event.preventDefault();
             }
         });

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/mvc/ui/ui-tabs.js
--- a/static/scripts/mvc/ui/ui-tabs.js
+++ b/static/scripts/mvc/ui/ui-tabs.js
@@ -71,6 +71,11 @@
         return _.size(this.list);
     },
     
+    // front
+    current: function() {
+        return this.$el.find('.tab-pane.active').attr('id');
+    },
+    
     // append
     add: function(options) {
         // self

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/packed/mvc/tools/tools-datasets.js
--- a/static/scripts/packed/mvc/tools/tools-datasets.js
+++ b/static/scripts/packed/mvc/tools/tools-datasets.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-contents"],function(a){return Backbone.Model.extend({initialize:function(c){this.currHistoryContents=new a.HistoryContents({});this.currHistoryContents.historyId="f597429621d6eb2b";var b=this;var d=this.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request failed.")})},filterType:function(b){return this.currHistoryContents.filter(function(c){var d=c.get("history_content_type");var e=c.get("file_ext");return d==="dataset"})},filter:function(b){return _.first(this.currHistoryContents.filter(function(c){return c.get("id")===b}))}})});
\ No newline at end of file
+define(["mvc/history/history-contents"],function(a){return Backbone.Model.extend({initialize:function(c){this.currHistoryContents=new a.HistoryContents({});this.currHistoryContents.historyId=c.history_id;var b=this;var d=this.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request failed.")})},filterType:function(b){return this.currHistoryContents.filter(function(c){var d=c.get("history_content_type");var e=c.get("file_ext");return d==="dataset"})},filter:function(b){return _.first(this.currHistoryContents.filter(function(c){return c.get("id")===b}))}})});
\ No newline at end of file

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,k,i,a,f,d,h,j,c){var e=Backbone.Model.extend({initialize:function(l){this.url=galaxy_config.root+"api/tools/"+l.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(m){var l=this;this.options=m;this.model=new e({id:m.id});this.tree=new c(this);this.field_list={};this.input_list={};this.datasets=new h({success:function(){l._initializeToolForm()}})},_initializeToolForm:function(){var l=this;this.model.fetch({error:function(m){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){l.inputs=l.model.get("inputs");l.portlet=new g.View({icon:"fa-wrench",title:"<b>"+l.model.get("name")+"</b> "+l.model.get("description"),buttons:{execute:new k.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){console.log(l.tree.create(l))}})}});l.message=new k.Message();l.portlet.append(l.message.$el);$(l.main_el).append(l.portlet.$el);if(l.options.help!=""){$(l.main_el).append(d.help(l.options.help))}if(l.options.citations){$(l.main_el).append(d.citations());var m=new i.ToolCitationCollection();m.tool_id=l.options.id;var n=new a.CitationListView({collection:m});n.render();m.fetch()}l.setElement(l.portlet.content());l.section=new j.View(l,{inputs:l.model.get("inputs")});l.portlet.append(l.section.$el);l.refresh()}})},refresh:function(){this.tree.refresh();for(var l in this.field_list){this.field_list[l].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")}});return{View:b}});
\ No newline at end of file
+define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,k,i,a,f,d,h,j,c){var e=Backbone.Model.extend({initialize:function(l){this.url=galaxy_config.root+"api/tools/"+l.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(m){var l=this;this.options=m;this.model=new e({id:m.id});this.tree=new c(this);this.field_list={};this.input_list={};this.datasets=new h({history_id:this.options.history_id,success:function(){l._initializeToolForm()}})},_initializeToolForm:function(){var m=this;var n=new k.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(m.options.biostar_url+"/p/new/post/")}});var o=new k.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(m.options.biostar_url+"/t/"+m.options.id+"/")}});var l=new k.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+m.options.id)}});this.model.fetch({error:function(p){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){m.inputs=m.model.get("inputs");m.portlet=new g.View({icon:"fa-wrench",title:"<b>"+m.model.get("name")+"</b> "+m.model.get("description"),buttons:{execute:new k.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){console.log(m.tree.create(m))}})},operations:{button_question:n,button_search:o,button_share:l}});if(!m.options.biostar_url){n.$el.hide();o.$el.hide()}m.message=new k.Message();m.portlet.append(m.message.$el);$(m.main_el).append(m.portlet.$el);if(m.options.help!=""){$(m.main_el).append(d.help(m.options.help))}if(m.options.citations){$(m.main_el).append(d.citations());var p=new i.ToolCitationCollection();p.tool_id=m.options.id;var q=new a.CitationListView({collection:p});q.render();p.fetch()}m.setElement(m.portlet.content());m.section=new j.View(m,{inputs:m.model.get("inputs")});m.portlet.append(m.section.$el);m.refresh()}})},refresh:function(){this.tree.refresh();for(var l in this.field_list){this.field_list[l].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")}});return{View:b}});
\ No newline at end of file

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 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/ui/ui-tabs"],function(c,b,e,a){var d=Backbone.View.extend({initialize:function(g,f){this.app=g;this.inputs=f.inputs;f.cls_tr="section-row";this.table=new b.View(f);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var f in this.inputs){this._add(this.inputs[f])}},_add:function(h){var g=this;var f=jQuery.extend(true,{},h);f.id=c.uuid();this.app.input_list[f.id]=f;var i=f.type;switch(i){case"conditional":this._addConditional(f);break;case"repeat":this._addRepeat(f);break;default:this._addRow(i,f)}},_addConditional:function(f){f.label=f.test_param.label;f.value=f.test_param.value;this._addRow("conditional",f);for(var h in f.cases){var g=f.id+"-section-"+h;var j=new d(this.app,{inputs:f.cases[h].inputs,cls:"ui-table-plain"});this.table.add("");this.table.add(j.$el);this.table.append(g)}},_addRepeat:function(f){var g=this;var k=new a.View({title_new:"Add "+f.title,max:f.max,onnew:function(){var i=f.id+"-section-"+c.uuid();var m=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:i,title:f.title,$el:m.$el,ondel:function(){k.del(i);k.retitle(f.title);g.app.refresh()}});k.retitle(f.title);k.show(i);g.app.refresh()}});for(var j=0;j<f.min;j++){var h=f.id+"-section-"+c.uuid();var l=new d(g.app,{inputs:f.inputs,cls:"ui-table-plain"});k.add({id:h,title:f.title,$el:l.$el})}k.retitle(f.title);this.table.add("");this.table.add(k.$el);this.table.append(f.id)},_addRow:function(h,f){var j=f.id;var g=null;switch(h){case"text":g=this._field_text(f);break;case"select":g=this._field_select(f);break;case"data":g=this._field_data(f);break;case"data_column":g=this._field_column(f);break;case"conditional":g=this._field_conditional(f);break;case"hidden":g=this._field_hidden(f);break;case"integer":g=this._field_slider(f);break;case"float":g=this._field_slider(f);break;case"boolean":g=this._field_boolean(f);break;default:g=this._field_text(f);console.debug("tools-form::_addRow() : Unmatched field type ("+h+").")}if(f.value!==undefined){g.value(f.value)}this.app.field_list[j]=g;var i=$("<div/>");i.append(g.$el);if(f.help){i.append('<div class="ui-table-form-info">'+f.help+"</div>")}this.table.add('<span class="ui-table-form-title">'+f.label+"</span>","20%");this.table.add(i);this.table.append(j)},_field_conditional:function(f){var g=this;var h=[];for(var j in f.test_param.options){var k=f.test_param.options[j];h.push({label:k[0],value:k[1]})}return new e.Select.View({id:"field-"+f.id,data:h,onchange:function(s){for(var q in f.cases){var m=f.cases[q];var p=f.id+"-section-"+q;var l=g.table.get(p);var o=false;for(var n in m.inputs){var r=m.inputs[n].type;if(r&&r!=="hidden"){o=true;break}}if(m.value==s&&o){l.fadeIn("fast")}else{l.hide()}}}})},_field_data:function(f){var g=this;var l=f.id;var k=this.app.datasets.filterType();var h=[];for(var j in k){h.push({label:k[j].get("name"),value:k[j].get("id")})}return new e.Select.View({id:"field-"+l,data:h,value:h[0].value,onchange:function(u){var s=g.app.tree.findReferences(l,"data_column");var n=g.app.datasets.filter(u);if(n&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+u+".");var w=n.get("metadata_column_types");if(!w){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+u+".")}for(var p in s){var q=g.app.input_list[s[p]];var r=g.app.field_list[s[p]];if(!q||!r){console.debug("tool-form::field_data() - FAILED: Column not found.")}var o=q.numerical;var m=[];for(var v in w){var t=w[v];if(t=="int"||t=="float"||!o){m.push({label:"Column: "+(parseInt(v)+1)+" ["+w[v]+"]",value:v})}}if(r){r.update(m);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(f){var g=[];for(var h in f.options){var j=f.options[h];g.push({label:j[0],value:j[1]})}var k=e.Select;switch(f.display){case"checkboxes":k=e.Checkbox;break;case"radio":k=e.RadioButton;break}if(f.multiple){k=e.Checkbox}return new k.View({id:"field-"+f.id,data:g})},_field_column:function(f){return new e.Select.View({id:"field-"+f.id,multiple:f.multiple})},_field_text:function(f){return new e.Input({id:"field-"+f.id,area:f.area})},_field_slider:function(f){return new e.Slider.View({id:"field-"+f.id,min:f.min||0,max:f.max||1000,decimal:f.type=="float"})},_field_hidden:function(f){return new e.Hidden({id:"field-"+f.id})},_field_boolean:function(f){return new e.RadioButton.View({id:"field-"+f.id,data:[{label:"Yes",value:true},{label:"No",value:false}]})}});return{View:d}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-select-dataset"],function(d,b,f,a,c){var e=Backbone.View.extend({initialize:function(h,g){this.app=h;this.inputs=g.inputs;g.cls_tr="section-row";this.table=new b.View(g);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var g in this.inputs){this._add(this.inputs[g])}},_add:function(i){var h=this;var g=jQuery.extend(true,{},i);g.id=d.uuid();this.app.input_list[g.id]=g;var j=g.type;switch(j){case"conditional":this._addConditional(g);break;case"repeat":this._addRepeat(g);break;default:this._addRow(j,g)}},_addConditional:function(g){g.label=g.test_param.label;g.value=g.test_param.value;this._addRow("conditional",g);for(var j in g.cases){var h=g.id+"-section-"+j;var k=new e(this.app,{inputs:g.cases[j].inputs,cls:"ui-table-plain"});this.table.add("");this.table.add(k.$el);this.table.append(h)}},_addRepeat:function(g){var h=this;var l=new a.View({title_new:"Add "+g.title,max:g.max,onnew:function(){var i=g.id+"-section-"+d.uuid();var n=new e(h.app,{inputs:g.inputs,cls:"ui-table-plain"});l.add({id:i,title:g.title,$el:n.$el,ondel:function(){l.del(i);l.retitle(g.title);h.app.refresh()}});l.retitle(g.title);l.show(i);h.app.refresh()}});for(var k=0;k<g.min;k++){var j=g.id+"-section-"+d.uuid();var m=new e(h.app,{inputs:g.inputs,cls:"ui-table-plain"});l.add({id:j,title:g.title,$el:m.$el})}l.retitle(g.title);this.table.add("");this.table.add(l.$el);this.table.append(g.id)},_addRow:function(i,g){var k=g.id;var h=null;switch(i){case"text":h=this._field_text(g);break;case"select":h=this._field_select(g);break;case"data":h=this._field_data(g);break;case"data_column":h=this._field_data_colum(g);break;case"conditional":h=this._field_conditional(g);break;case"hidden":h=this._field_hidden(g);break;case"integer":h=this._field_slider(g);break;case"float":h=this._field_slider(g);break;case"boolean":h=this._field_boolean(g);break}if(!h){if(g.options){h=this._field_select(g)}else{h=this._field_text(g)}console.debug("tools-form::_addRow() : Auto matched field type ("+i+").")}if(g.value!==undefined){h.value(g.value)}this.app.field_list[k]=h;var j=$("<div/>");j.append(h.$el);if(g.help){j.append('<div class="ui-table-form-info">'+g.help+"</div>")}this.table.add('<span class="ui-table-form-title">'+g.label+"</span>","20%");this.table.add(j);this.table.append(k)},_field_conditional:function(g){var h=this;var j=[];for(var k in g.test_param.options){var l=g.test_param.options[k];j.push({label:l[0],value:l[1]})}return new f.Select.View({id:"field-"+g.id,data:j,onchange:function(t){for(var r in g.cases){var n=g.cases[r];var q=g.id+"-section-"+r;var m=h.table.get(q);var p=false;for(var o in n.inputs){var s=n.inputs[o].type;if(s&&s!=="hidden"){p=true;break}}if(n.value==t&&p){m.fadeIn("fast")}else{m.hide()}}}})},_field_data:function(g){var h=this;var i=g.id;return new c.View(this.app,{id:"field-"+i,extensions:g.extensions,multiple:g.multiple,onchange:function(r){if(r instanceof Array){r=r[0]}var p=h.app.tree.findReferences(i,"data_column");var k=h.app.datasets.filter(r);if(k&&p.length>0){console.debug("tool-form::field_data() - Selected dataset "+r+".");var t=k.get("metadata_column_types");if(!t){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+r+".")}for(var m in p){var n=h.app.input_list[p[m]];var o=h.app.field_list[p[m]];if(!n||!o){console.debug("tool-form::field_data() - FAILED: Column not found.")}var l=n.numerical;var j=[];for(var s in t){var q=t[s];if(q=="int"||q=="float"||!l){j.push({label:"Column: "+(parseInt(s)+1)+" ["+t[s]+"]",value:s})}}if(o){o.update(j);if(!o.exists(o.value())){o.value(o.first())}}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+r+".")}}})},_field_select:function(g){var h=[];for(var j in g.options){var k=g.options[j];h.push({label:k[0],value:k[1]})}var l=f.Select;switch(g.display){case"checkboxes":l=f.Checkbox;break;case"radio":l=f.RadioButton;break}return new l.View({id:"field-"+g.id,data:h,multiple:g.multiple})},_field_data_colum:function(g){return new f.Select.View({id:"field-"+g.id,multiple:g.multiple})},_field_text:function(g){return new f.Input({id:"field-"+g.id,area:g.area})},_field_slider:function(g){var h=1;if(g.type=="float"){h=(g.max-g.min)/10000}return new f.Slider.View({id:"field-"+g.id,min:g.min||0,max:g.max||1000,step:h})},_field_hidden:function(g){return new f.Hidden({id:"field-"+g.id})},_field_boolean:function(g){return new f.RadioButton.View({id:"field-"+g.id,data:[{label:"Yes",value:true},{label:"No",value:false}]})}});return{View:e}});
\ No newline at end of file

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/packed/mvc/tools/tools-select-dataset.js
--- /dev/null
+++ b/static/scripts/packed/mvc/tools/tools-select-dataset.js
@@ -0,0 +1,1 @@
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(b,d,a){var c=Backbone.View.extend({initialize:function(k,f){var e=this;var h=k.datasets.filterType();var j=[];for(var g in h){j.push({label:h[g].get("name"),value:h[g].get("id")})}this.select=new d.Select.View({data:j,value:j[0].value,onchange:function(){e.trigger("change")}});this.select_multiple=new d.Select.View({multiple:true,data:j,value:j[0].value,onchange:function(){e.trigger("change")}});this.select_collection=new d.Select.View({data:j,value:j[0].value,onchange:function(){e.trigger("change")}});this.on("change",function(){if(f.onchange){f.onchange(e.value())}});this.tabs=new a.View();this.tabs.add({id:"single",title:"Select a dataset",$el:this.select.$el});this.tabs.add({id:"multiple",title:"Select multiple datasets",$el:this.select_multiple.$el});this.tabs.add({id:"collection",title:"Select a dataset collection",$el:this.select_collection.$el});this.setElement(this.tabs.$el)},value:function(e){var f=this.tabs.current();switch(f){case"multiple":return this.select_multiple.value();case"collection":return this.select_collection.value();default:return this.select.value()}},update:function(e){this.select.update(e)}});return{View:c}});
\ No newline at end of file

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/packed/mvc/ui/ui-slider.js
--- a/static/scripts/packed/mvc/ui/ui-slider.js
+++ b/static/scripts/packed/mvc/ui/ui-slider.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:1,max:100,step:0.1,decimal:false},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$slider=this.$el.find("#slider");this.$text=this.$el.find("#text");if(!this.options.decimal){this.options.step=1}this.$slider.slider(this.options);this.$text.on("change",function(){c.value($(this).val())});this.$text.on("keydown",function(f){var e=f.which;if(!(e==13||e==8||e==37||e==39||e==189||(e>=48&&e<=57)||(c.options.decimal&&$(this).val().indexOf(".")==-1)&&e==190)){f.preventDefault()}});this.$slider.on("slide",function(e,f){c.value(f.value)})},value:function(c){if(c!==undefined){c=Math.max(Math.min(c,this.options.max),this.options.min);if(this.options.onchange){this.options.onchange(c)}this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" style=""><input id="text" type="text" class="ui-input" style="width: 50px; float: left"/><div id="slider" style="width: calc(100% - 60px); float: left; top: 8px; left: 10px;"/></div>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:1,max:100,step:1},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$slider=this.$el.find("#slider");this.$text=this.$el.find("#text");this.$slider.slider(this.options);this.$text.on("change",function(){c.value($(this).val())});this.$text.on("keydown",function(f){var e=f.which;if(!(e==13||e==8||e==37||e==39||e==189||(e>=48&&e<=57)||(c.options.step!=1&&$(this).val().indexOf(".")==-1)&&e==190)){f.preventDefault()}});this.$slider.on("slide",function(e,f){c.value(f.value)})},value:function(c){if(c!==undefined){c=Math.max(Math.min(c,this.options.max),this.options.min);if(this.options.onchange){this.options.onchange(c)}this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" style=""><input id="text" type="text" class="ui-input" style="width: 50px; float: left"/><div id="slider" style="width: calc(100% - 60px); float: left; top: 8px; left: 10px;"/></div>'}});return{View:b}});
\ No newline at end of file

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 static/scripts/packed/mvc/ui/ui-tabs.js
--- a/static/scripts/packed/mvc/ui/ui-tabs.js
+++ b/static/scripts/packed/mvc/ui/ui-tabs.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,min:null,max:null},initialize:function(e){this.visible=false;this.$nav=null;this.$content=null;this.first_tab=null;this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.find(".operations").append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom",container:d.$el});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},size:function(){return _.size(this.list)},add:function(f){var e=this;var h=f.id;var g=$(this._template_tab(f));var d=$(this._template_tab_content(f));this.list[h]=f.ondel?true:false;if(this.options.onnew){this.$nav.find("#new-tab").before(g)}else{this.$nav.append(g)}d.append(f.$el);this.$content.append(d);if(this.size()==1){g.addClass("active");d.addClass("active");this.first_tab=h}if(this.options.max&&this.size()>=this.options.max){this.$el.find("#new-tab").hide()}if(f.ondel){var c=g.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom",container:e.$el});c.on("click",function(){c.tooltip("destroy");e.$el.find(".tooltip").remove();f.ondel();return false})}g.on("click",function(i){i.preventDefault();if(f.onclick){f.onclick()}else{e.show(h)}})},del:function(c){this.$el.find("#tab-"+c).remove();this.$el.find("#"+c).remove();if(this.first_tab==c){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}if(this.list[c]){delete this.list[c]}if(this.size()<this.options.max){this.$el.find("#new-tab").show()}},delRemovable:function(){for(var c in this.list){this.del(c)}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.$el.find(".tab-element").removeClass("active");this.$el.find(".tab-pane").removeClass("active");this.$el.find("#tab-"+c).addClass("active");this.$el.find("#"+c).addClass("active")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.$el.find("#tab-title-text-"+e);if(d){c.html(d)}return c.html()},retitle:function(d){var c=0;for(var e in this.list){this.title(e,++c+": "+d)}},_template:function(c){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(c){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="tab-'+d.id+'" class="tab-element"><a id="tab-title-link-'+d.id+'" title="" href="#'+d.id+'" data-original-title=""><span id="tab-title-text-'+d.id+'" class="tab-title-text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="'+c.id+'" class="tab-pane"/>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,min:null,max:null},initialize:function(e){this.visible=false;this.$nav=null;this.$content=null;this.first_tab=null;this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.find(".operations").append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom",container:d.$el});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(f){var e=this;var h=f.id;var g=$(this._template_tab(f));var d=$(this._template_tab_content(f));this.list[h]=f.ondel?true:false;if(this.options.onnew){this.$nav.find("#new-tab").before(g)}else{this.$nav.append(g)}d.append(f.$el);this.$content.append(d);if(this.size()==1){g.addClass("active");d.addClass("active");this.first_tab=h}if(this.options.max&&this.size()>=this.options.max){this.$el.find("#new-tab").hide()}if(f.ondel){var c=g.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom",container:e.$el});c.on("click",function(){c.tooltip("destroy");e.$el.find(".tooltip").remove();f.ondel();return false})}g.on("click",function(i){i.preventDefault();if(f.onclick){f.onclick()}else{e.show(h)}})},del:function(c){this.$el.find("#tab-"+c).remove();this.$el.find("#"+c).remove();if(this.first_tab==c){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}if(this.list[c]){delete this.list[c]}if(this.size()<this.options.max){this.$el.find("#new-tab").show()}},delRemovable:function(){for(var c in this.list){this.del(c)}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.$el.find(".tab-element").removeClass("active");this.$el.find(".tab-pane").removeClass("active");this.$el.find("#tab-"+c).addClass("active");this.$el.find("#"+c).addClass("active")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.$el.find("#tab-title-text-"+e);if(d){c.html(d)}return c.html()},retitle:function(d){var c=0;for(var e in this.list){this.title(e,++c+": "+d)}},_template:function(c){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(c){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="tab-'+d.id+'" class="tab-element"><a id="tab-title-link-'+d.id+'" title="" href="#'+d.id+'" data-original-title=""><span id="tab-title-text-'+d.id+'" class="tab-title-text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="'+c.id+'" class="tab-pane"/>'}});return{View:b}});
\ No newline at end of file

diff -r 0df64c45db90ca84e763c34919ebe9304d96f202 -r be2c86442b3e28407d7b845a90420c3feb3fe859 templates/webapps/galaxy/tool_form.api.mako
--- a/templates/webapps/galaxy/tool_form.api.mako
+++ b/templates/webapps/galaxy/tool_form.api.mako
@@ -24,9 +24,11 @@
 
     # form configuration
     self.form_config = {
-        'id'        : tool.id,
-        'help'      : tool_help,
-        'citations' : tool_citations
+        'id'            : tool.id,
+        'help'          : tool_help,
+        'citations'     : tool_citations,
+        'biostar_url'   : trans.app.config.biostar_url,
+        'history_id'    : trans.security.encode_id( trans.history.id )
     }
 %>
 ${h.js( "libs/bibtex", "libs/jquery/jquery-ui" )}

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

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[galaxy-commits] commit/galaxy-central: guerler: ToolForm: Additional buttons, fixes and improvements, genome build selector, first commit for multiple dataset and collection selector

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