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commit/galaxy-central: guerler: Merge
by commits-noreply＠bitbucket.org 13 Feb '14

13 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/784f02de9eff/ Changeset: 784f02de9eff User: guerler Date: 2014-02-13 17:27:25 Summary: Merge Affected #: 1 file diff -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 -r 784f02de9effb43eafa84b5253af62091e6f2f36 lib/galaxy/webapps/reports/controllers/jobs.py --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -29,7 +29,7 @@ return job.tool_id class CreateTimeColumn( grids.DateTimeColumn ): def get_value( self, trans, grid, job ): - return job.create_time.isoformat() + return job.create_time.strftime("%b %d, %Y, %H:%M:%S") class UserColumn( grids.GridColumn ): def get_value( self, trans, grid, job ): if job.user: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Reports: Fix time format in grids
by commits-noreply＠bitbucket.org 13 Feb '14

13 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3691fd3e12ef/ Changeset: 3691fd3e12ef Branch: stable User: guerler Date: 2014-02-13 17:19:54 Summary: Reports: Fix time format in grids Affected #: 1 file diff -r b463c73f334811d4c48298c40de9ac489261c32d -r 3691fd3e12ef8160ae993cef5ebd51ddeee95da1 lib/galaxy/webapps/reports/controllers/jobs.py --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -29,7 +29,7 @@ return job.tool_id class CreateTimeColumn( grids.DateTimeColumn ): def get_value( self, trans, grid, job ): - return job.create_time + return job.create_time.strftime("%b %d, %Y, %H:%M:%S") class UserColumn( grids.GridColumn ): def get_value( self, trans, grid, job ): if job.user: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Ui: Apply naming convention
by commits-noreply＠bitbucket.org 13 Feb '14

13 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/75a8d88ba728/ Changeset: 75a8d88ba728 User: guerler Date: 2014-02-13 10:21:06 Summary: Ui: Apply naming convention Affected #: 12 files diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/ui/popover.js --- a/static/scripts/mvc/ui/popover.js +++ /dev/null @@ -1,169 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -var View = Backbone.View.extend({ - - // default options - optionsDefault: { - with_close : true, - container : 'body', - title : null, - placement : 'top' - }, - - // visibility flag - visible: false, - - // initialize - initialize: function (options) { - - // link this - var self = this; - - // update options - this.options = _.defaults(options, this.optionsDefault); - - // set element - this.setElement(this._template(this.options)); - - // attach popover to parent - this.options.container.parent().append(this.$el); - - // attach close - if (this.options.with_close) { - this.$el.find('#close').on('click', function() { self.hide(); }); - } - - // generate unique id - this.uuid = Utils.uuid(); - - // add event to hide if click is outside of popup - var self = this; - $('body').on('mousedown.' + this.uuid, function(e) { self._hide(e) }); - }, - - // title - title: function(val) { - if (val !== undefined) { - this.$el.find('.popover-title-label').html(val); - } - }, - - // show - show: function () { - // show popover - this.$el.show(); - this.visible = true; - - // calculate position - var position = this._get_placement(this.options.placement); - - // set position - this.$el.css(position); - }, - - // calculate position and error - _get_placement: function(placement) { - // get popover dimensions - var width = this._get_width(this.$el); - var height = this.$el.height(); - - // get container details - var $container = this.options.container; - var container_width = this._get_width($container); - var container_height = this._get_height($container); - var container_position = $container.position(); - - // initialize position - var top = 0; - var left = 0; - - // calculate position - if (placement == 'top' || placement == 'bottom') { - left = container_position.left - width + (container_width + width) / 2; - if (placement == 'top') { - top = container_position.top - height - 5; - } else { - top = container_position.top + container_height + 5; - } - } - - // return - return {top: top, left: left}; - }, - - // width - _get_width: function($el) { - return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('padding-right')) - }, - - // heigth - _get_height: function($el) { - return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom')) - }, - - // hide - hide: function () { - this.$el.hide(); - this.visible = false; - }, - - // append - append: function($el) { - this.$el.find('.popover-content').append($el); - }, - - // empty - empty: function($el) { - this.$el.find('.popover-content').empty(); - }, - - // remove - remove: function() { - // remove event handler - $('body').off('mousedown.' + this.uuid); - - // remove element from dom - this.$el.remove(); - }, - - // remove - _hide : function(e) { - //the 'is' for buttons that trigger popups - //the 'has' for icons within a button that triggers a popup - if (!$(this.options.container).is(e.target) && - !$(this.el).is(e.target) && - $(this.el).has(e.target).length === 0) { - this.hide(); - } - }, - - // template - _template: function(options) { - var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' + - '<div class="arrow"></div>' + - '<div class="popover-title">' + - '<div class="popover-title-label">' + - options.title + - '</div>'; - - // add close icon - if (options.with_close) { - tmpl += '<div id="close" class="popover-close fa fa-times-circle"></div>'; - } - - // finalize - tmpl += '</div>' + - '<div class="popover-content"></div>' + - '</div>'; - - // return - return tmpl; - } -}); - -return { - View: View -} - -}); \ No newline at end of file diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/ui/select.js --- a/static/scripts/mvc/ui/select.js +++ /dev/null @@ -1,193 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// plugin -var View = Backbone.View.extend( -{ - // options - optionsDefault: { - css : '', - placeholder : 'No data available', - data : [] - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // add to dom - this.options.container.append(this.$el); - - // link selection dictionary - this.select_data = this.options.data; - - // refresh - this._refresh(); - - // initial value - if (this.options.value) { - this._setValue(this.options.value); - } - - // add change event - var self = this; - if (this.options.onchange) { - this.$el.on('change', function() { - self.options.onchange(self.value()); - }); - } - }, - - // value - value : function (new_value) { - // get current id/value - var before = this._getValue(); - - // check if new_value is defined - if (new_value !== undefined) { - this._setValue(new_value); - } - - // get current id/value - var after = this._getValue(); - if(after === undefined) { - return null; - } else { - // fire onchange - if ((after != before && this.options.onchange)) { - this.options.onchange(after); - } - - // return current value - return after; - } - }, - - // label - text : function () { - return this.$el.select2('data').text; - }, - - // disabled - disabled: function() { - return !this.$el.select2('enable'); - }, - - // enable - enable: function() { - this.$el.select2('enable', true); - }, - - // disable - disable: function() { - this.$el.select2('enable', false); - }, - - // add - add: function(options) { - // add options - this.select_data.push({ - id : options.id, - text : options.text - }); - - // refresh - this._refresh(); - }, - - // remove - del: function(id) { - // search option - var index = this._getIndex(id); - - // check if found - if (index != -1) { - // remove options - this.select_data.splice(index, 1); - - // refresh - this._refresh(); - } - }, - - // remove - remove: function() { - this.$el.select2('destroy'); - }, - - // update - update: function(options) { - // copy options - this.select_data = []; - for (var key in options.data) { - this.select_data.push(options.data[key]); - } - - // refresh - this._refresh(); - }, - - // refresh - _refresh: function() { - - // link select data - var select_data = this.select_data; - if (!select_data || select_data.length == 0) { - select_data = []; - } - - // selected - var selected = this._getValue(); - - // add select2 data - this.$el.select2({ - data : select_data, - containerCssClass : this.options.css, - placeholder : this.options.placeholder - }); - - // select - var index = this._getIndex(selected); - if (index != -1) { - this._setValue(selected); - } - }, - - // get index - _getIndex: function(value) { - // search index - for (var key in this.select_data) { - if (this.select_data[key].id == value) { - return key; - } - } - - // not found - return -1; - }, - - // get value - _getValue: function() { - return this.$el.select2('val'); - }, - - // set value - _setValue: function(new_value) { - this.$el.select2('val', new_value); - }, - - // element - _template: function(options) { - return '<input type="hidden"/>'; - } -}); - -return { - View : View -} - -}); diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/ui/ui-popover.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-popover.js @@ -0,0 +1,169 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +var View = Backbone.View.extend({ + + // default options + optionsDefault: { + with_close : true, + container : 'body', + title : null, + placement : 'top' + }, + + // visibility flag + visible: false, + + // initialize + initialize: function (options) { + + // link this + var self = this; + + // update options + this.options = _.defaults(options, this.optionsDefault); + + // set element + this.setElement(this._template(this.options)); + + // attach popover to parent + this.options.container.parent().append(this.$el); + + // attach close + if (this.options.with_close) { + this.$el.find('#close').on('click', function() { self.hide(); }); + } + + // generate unique id + this.uuid = Utils.uuid(); + + // add event to hide if click is outside of popup + var self = this; + $('body').on('mousedown.' + this.uuid, function(e) { self._hide(e) }); + }, + + // title + title: function(val) { + if (val !== undefined) { + this.$el.find('.popover-title-label').html(val); + } + }, + + // show + show: function () { + // show popover + this.$el.show(); + this.visible = true; + + // calculate position + var position = this._get_placement(this.options.placement); + + // set position + this.$el.css(position); + }, + + // calculate position and error + _get_placement: function(placement) { + // get popover dimensions + var width = this._get_width(this.$el); + var height = this.$el.height(); + + // get container details + var $container = this.options.container; + var container_width = this._get_width($container); + var container_height = this._get_height($container); + var container_position = $container.position(); + + // initialize position + var top = 0; + var left = 0; + + // calculate position + if (placement == 'top' || placement == 'bottom') { + left = container_position.left - width + (container_width + width) / 2; + if (placement == 'top') { + top = container_position.top - height - 5; + } else { + top = container_position.top + container_height + 5; + } + } + + // return + return {top: top, left: left}; + }, + + // width + _get_width: function($el) { + return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('padding-right')) + }, + + // heigth + _get_height: function($el) { + return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom')) + }, + + // hide + hide: function () { + this.$el.hide(); + this.visible = false; + }, + + // append + append: function($el) { + this.$el.find('.popover-content').append($el); + }, + + // empty + empty: function($el) { + this.$el.find('.popover-content').empty(); + }, + + // remove + remove: function() { + // remove event handler + $('body').off('mousedown.' + this.uuid); + + // remove element from dom + this.$el.remove(); + }, + + // remove + _hide : function(e) { + //the 'is' for buttons that trigger popups + //the 'has' for icons within a button that triggers a popup + if (!$(this.options.container).is(e.target) && + !$(this.el).is(e.target) && + $(this.el).has(e.target).length === 0) { + this.hide(); + } + }, + + // template + _template: function(options) { + var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' + + '<div class="arrow"></div>' + + '<div class="popover-title">' + + '<div class="popover-title-label">' + + options.title + + '</div>'; + + // add close icon + if (options.with_close) { + tmpl += '<div id="close" class="popover-close fa fa-times-circle"></div>'; + } + + // finalize + tmpl += '</div>' + + '<div class="popover-content"></div>' + + '</div>'; + + // return + return tmpl; + } +}); + +return { + View: View +} + +}); \ No newline at end of file diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/ui/ui-select.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-select.js @@ -0,0 +1,193 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +var View = Backbone.View.extend( +{ + // options + optionsDefault: { + css : '', + placeholder : 'No data available', + data : [] + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // add to dom + this.options.container.append(this.$el); + + // link selection dictionary + this.select_data = this.options.data; + + // refresh + this._refresh(); + + // initial value + if (this.options.value) { + this._setValue(this.options.value); + } + + // add change event + var self = this; + if (this.options.onchange) { + this.$el.on('change', function() { + self.options.onchange(self.value()); + }); + } + }, + + // value + value : function (new_value) { + // get current id/value + var before = this._getValue(); + + // check if new_value is defined + if (new_value !== undefined) { + this._setValue(new_value); + } + + // get current id/value + var after = this._getValue(); + if(after === undefined) { + return null; + } else { + // fire onchange + if ((after != before && this.options.onchange)) { + this.options.onchange(after); + } + + // return current value + return after; + } + }, + + // label + text : function () { + return this.$el.select2('data').text; + }, + + // disabled + disabled: function() { + return !this.$el.select2('enable'); + }, + + // enable + enable: function() { + this.$el.select2('enable', true); + }, + + // disable + disable: function() { + this.$el.select2('enable', false); + }, + + // add + add: function(options) { + // add options + this.select_data.push({ + id : options.id, + text : options.text + }); + + // refresh + this._refresh(); + }, + + // remove + del: function(id) { + // search option + var index = this._getIndex(id); + + // check if found + if (index != -1) { + // remove options + this.select_data.splice(index, 1); + + // refresh + this._refresh(); + } + }, + + // remove + remove: function() { + this.$el.select2('destroy'); + }, + + // update + update: function(options) { + // copy options + this.select_data = []; + for (var key in options.data) { + this.select_data.push(options.data[key]); + } + + // refresh + this._refresh(); + }, + + // refresh + _refresh: function() { + + // link select data + var select_data = this.select_data; + if (!select_data || select_data.length == 0) { + select_data = []; + } + + // selected + var selected = this._getValue(); + + // add select2 data + this.$el.select2({ + data : select_data, + containerCssClass : this.options.css, + placeholder : this.options.placeholder + }); + + // select + var index = this._getIndex(selected); + if (index != -1) { + this._setValue(selected); + } + }, + + // get index + _getIndex: function(value) { + // search index + for (var key in this.select_data) { + if (this.select_data[key].id == value) { + return key; + } + } + + // not found + return -1; + }, + + // get value + _getValue: function() { + return this.$el.select2('val'); + }, + + // set value + _setValue: function(new_value) { + this.$el.select2('val', new_value); + }, + + // element + _template: function(options) { + return '<input type="hidden"/>'; + } +}); + +return { + View : View +} + +}); diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -3,8 +3,8 @@ 'mvc/upload/upload-model', 'mvc/upload/upload-extensions', 'mvc/upload/upload-settings', - 'mvc/ui/popover', - 'mvc/ui/select'], + 'mvc/ui/ui-popover', + 'mvc/ui/ui-select'], function( Utils, UploadModel, diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -5,7 +5,7 @@ "mvc/upload/upload-model", "mvc/upload/upload-row", "mvc/upload/upload-ftp", - "mvc/ui/popover", + "mvc/ui/ui-popover", "mvc/ui", "utils/uploadbox"], diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/ui/popover.js --- a/static/scripts/packed/mvc/ui/popover.js +++ /dev/null @@ -1,1 +0,0 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}}); \ No newline at end of file diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/ui/select.js --- a/static/scripts/packed/mvc/ui/select.js +++ /dev/null @@ -1,1 +0,0 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$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(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/ui/ui-popover.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-popover.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}}); \ No newline at end of file diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/ui/ui-select.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-select.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$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(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui/popover","mvc/ui/select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file diff -r b6acb69067f808147e4e69a1cde74cbb8868c600 -r 75a8d88ba72893daaf27e57d496ca799c20df0b9 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Ui: Move ui classes into a separate directory
by commits-noreply＠bitbucket.org 13 Feb '14

13 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b6acb69067f8/ Changeset: b6acb69067f8 User: guerler Date: 2014-02-13 10:12:41 Summary: Ui: Move ui classes into a separate directory Affected #: 12 files diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/ui.popover.js --- a/static/scripts/mvc/ui.popover.js +++ /dev/null @@ -1,169 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -var View = Backbone.View.extend({ - - // default options - optionsDefault: { - with_close : true, - container : 'body', - title : null, - placement : 'top' - }, - - // visibility flag - visible: false, - - // initialize - initialize: function (options) { - - // link this - var self = this; - - // update options - this.options = _.defaults(options, this.optionsDefault); - - // set element - this.setElement(this._template(this.options)); - - // attach popover to parent - this.options.container.parent().append(this.$el); - - // attach close - if (this.options.with_close) { - this.$el.find('#close').on('click', function() { self.hide(); }); - } - - // generate unique id - this.uuid = Utils.uuid(); - - // add event to hide if click is outside of popup - var self = this; - $('body').on('mousedown.' + this.uuid, function(e) { self._hide(e) }); - }, - - // title - title: function(val) { - if (val !== undefined) { - this.$el.find('.popover-title-label').html(val); - } - }, - - // show - show: function () { - // show popover - this.$el.show(); - this.visible = true; - - // calculate position - var position = this._get_placement(this.options.placement); - - // set position - this.$el.css(position); - }, - - // calculate position and error - _get_placement: function(placement) { - // get popover dimensions - var width = this._get_width(this.$el); - var height = this.$el.height(); - - // get container details - var $container = this.options.container; - var container_width = this._get_width($container); - var container_height = this._get_height($container); - var container_position = $container.position(); - - // initialize position - var top = 0; - var left = 0; - - // calculate position - if (placement == 'top' || placement == 'bottom') { - left = container_position.left - width + (container_width + width) / 2; - if (placement == 'top') { - top = container_position.top - height - 5; - } else { - top = container_position.top + container_height + 5; - } - } - - // return - return {top: top, left: left}; - }, - - // width - _get_width: function($el) { - return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('padding-right')) - }, - - // heigth - _get_height: function($el) { - return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom')) - }, - - // hide - hide: function () { - this.$el.hide(); - this.visible = false; - }, - - // append - append: function($el) { - this.$el.find('.popover-content').append($el); - }, - - // empty - empty: function($el) { - this.$el.find('.popover-content').empty(); - }, - - // remove - remove: function() { - // remove event handler - $('body').off('mousedown.' + this.uuid); - - // remove element from dom - this.$el.remove(); - }, - - // remove - _hide : function(e) { - //the 'is' for buttons that trigger popups - //the 'has' for icons within a button that triggers a popup - if (!$(this.options.container).is(e.target) && - !$(this.el).is(e.target) && - $(this.el).has(e.target).length === 0) { - this.hide(); - } - }, - - // template - _template: function(options) { - var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' + - '<div class="arrow"></div>' + - '<div class="popover-title">' + - '<div class="popover-title-label">' + - options.title + - '</div>'; - - // add close icon - if (options.with_close) { - tmpl += '<div id="close" class="popover-close fa fa-times-circle"></div>'; - } - - // finalize - tmpl += '</div>' + - '<div class="popover-content"></div>' + - '</div>'; - - // return - return tmpl; - } -}); - -return { - View: View -} - -}); \ No newline at end of file diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/ui.select.js --- a/static/scripts/mvc/ui.select.js +++ /dev/null @@ -1,193 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// plugin -var View = Backbone.View.extend( -{ - // options - optionsDefault: { - css : '', - placeholder : 'No data available', - data : [] - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // add to dom - this.options.container.append(this.$el); - - // link selection dictionary - this.select_data = this.options.data; - - // refresh - this._refresh(); - - // initial value - if (this.options.value) { - this._setValue(this.options.value); - } - - // add change event - var self = this; - if (this.options.onchange) { - this.$el.on('change', function() { - self.options.onchange(self.value()); - }); - } - }, - - // value - value : function (new_value) { - // get current id/value - var before = this._getValue(); - - // check if new_value is defined - if (new_value !== undefined) { - this._setValue(new_value); - } - - // get current id/value - var after = this._getValue(); - if(after === undefined) { - return null; - } else { - // fire onchange - if ((after != before && this.options.onchange)) { - this.options.onchange(after); - } - - // return current value - return after; - } - }, - - // label - text : function () { - return this.$el.select2('data').text; - }, - - // disabled - disabled: function() { - return !this.$el.select2('enable'); - }, - - // enable - enable: function() { - this.$el.select2('enable', true); - }, - - // disable - disable: function() { - this.$el.select2('enable', false); - }, - - // add - add: function(options) { - // add options - this.select_data.push({ - id : options.id, - text : options.text - }); - - // refresh - this._refresh(); - }, - - // remove - del: function(id) { - // search option - var index = this._getIndex(id); - - // check if found - if (index != -1) { - // remove options - this.select_data.splice(index, 1); - - // refresh - this._refresh(); - } - }, - - // remove - remove: function() { - this.$el.select2('destroy'); - }, - - // update - update: function(options) { - // copy options - this.select_data = []; - for (var key in options.data) { - this.select_data.push(options.data[key]); - } - - // refresh - this._refresh(); - }, - - // refresh - _refresh: function() { - - // link select data - var select_data = this.select_data; - if (!select_data || select_data.length == 0) { - select_data = []; - } - - // selected - var selected = this._getValue(); - - // add select2 data - this.$el.select2({ - data : select_data, - containerCssClass : this.options.css, - placeholder : this.options.placeholder - }); - - // select - var index = this._getIndex(selected); - if (index != -1) { - this._setValue(selected); - } - }, - - // get index - _getIndex: function(value) { - // search index - for (var key in this.select_data) { - if (this.select_data[key].id == value) { - return key; - } - } - - // not found - return -1; - }, - - // get value - _getValue: function() { - return this.$el.select2('val'); - }, - - // set value - _setValue: function(new_value) { - this.$el.select2('val', new_value); - }, - - // element - _template: function(options) { - return '<input type="hidden"/>'; - } -}); - -return { - View : View -} - -}); diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/ui/popover.js --- /dev/null +++ b/static/scripts/mvc/ui/popover.js @@ -0,0 +1,169 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +var View = Backbone.View.extend({ + + // default options + optionsDefault: { + with_close : true, + container : 'body', + title : null, + placement : 'top' + }, + + // visibility flag + visible: false, + + // initialize + initialize: function (options) { + + // link this + var self = this; + + // update options + this.options = _.defaults(options, this.optionsDefault); + + // set element + this.setElement(this._template(this.options)); + + // attach popover to parent + this.options.container.parent().append(this.$el); + + // attach close + if (this.options.with_close) { + this.$el.find('#close').on('click', function() { self.hide(); }); + } + + // generate unique id + this.uuid = Utils.uuid(); + + // add event to hide if click is outside of popup + var self = this; + $('body').on('mousedown.' + this.uuid, function(e) { self._hide(e) }); + }, + + // title + title: function(val) { + if (val !== undefined) { + this.$el.find('.popover-title-label').html(val); + } + }, + + // show + show: function () { + // show popover + this.$el.show(); + this.visible = true; + + // calculate position + var position = this._get_placement(this.options.placement); + + // set position + this.$el.css(position); + }, + + // calculate position and error + _get_placement: function(placement) { + // get popover dimensions + var width = this._get_width(this.$el); + var height = this.$el.height(); + + // get container details + var $container = this.options.container; + var container_width = this._get_width($container); + var container_height = this._get_height($container); + var container_position = $container.position(); + + // initialize position + var top = 0; + var left = 0; + + // calculate position + if (placement == 'top' || placement == 'bottom') { + left = container_position.left - width + (container_width + width) / 2; + if (placement == 'top') { + top = container_position.top - height - 5; + } else { + top = container_position.top + container_height + 5; + } + } + + // return + return {top: top, left: left}; + }, + + // width + _get_width: function($el) { + return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('padding-right')) + }, + + // heigth + _get_height: function($el) { + return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom')) + }, + + // hide + hide: function () { + this.$el.hide(); + this.visible = false; + }, + + // append + append: function($el) { + this.$el.find('.popover-content').append($el); + }, + + // empty + empty: function($el) { + this.$el.find('.popover-content').empty(); + }, + + // remove + remove: function() { + // remove event handler + $('body').off('mousedown.' + this.uuid); + + // remove element from dom + this.$el.remove(); + }, + + // remove + _hide : function(e) { + //the 'is' for buttons that trigger popups + //the 'has' for icons within a button that triggers a popup + if (!$(this.options.container).is(e.target) && + !$(this.el).is(e.target) && + $(this.el).has(e.target).length === 0) { + this.hide(); + } + }, + + // template + _template: function(options) { + var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' + + '<div class="arrow"></div>' + + '<div class="popover-title">' + + '<div class="popover-title-label">' + + options.title + + '</div>'; + + // add close icon + if (options.with_close) { + tmpl += '<div id="close" class="popover-close fa fa-times-circle"></div>'; + } + + // finalize + tmpl += '</div>' + + '<div class="popover-content"></div>' + + '</div>'; + + // return + return tmpl; + } +}); + +return { + View: View +} + +}); \ No newline at end of file diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/ui/select.js --- /dev/null +++ b/static/scripts/mvc/ui/select.js @@ -0,0 +1,193 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +var View = Backbone.View.extend( +{ + // options + optionsDefault: { + css : '', + placeholder : 'No data available', + data : [] + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // add to dom + this.options.container.append(this.$el); + + // link selection dictionary + this.select_data = this.options.data; + + // refresh + this._refresh(); + + // initial value + if (this.options.value) { + this._setValue(this.options.value); + } + + // add change event + var self = this; + if (this.options.onchange) { + this.$el.on('change', function() { + self.options.onchange(self.value()); + }); + } + }, + + // value + value : function (new_value) { + // get current id/value + var before = this._getValue(); + + // check if new_value is defined + if (new_value !== undefined) { + this._setValue(new_value); + } + + // get current id/value + var after = this._getValue(); + if(after === undefined) { + return null; + } else { + // fire onchange + if ((after != before && this.options.onchange)) { + this.options.onchange(after); + } + + // return current value + return after; + } + }, + + // label + text : function () { + return this.$el.select2('data').text; + }, + + // disabled + disabled: function() { + return !this.$el.select2('enable'); + }, + + // enable + enable: function() { + this.$el.select2('enable', true); + }, + + // disable + disable: function() { + this.$el.select2('enable', false); + }, + + // add + add: function(options) { + // add options + this.select_data.push({ + id : options.id, + text : options.text + }); + + // refresh + this._refresh(); + }, + + // remove + del: function(id) { + // search option + var index = this._getIndex(id); + + // check if found + if (index != -1) { + // remove options + this.select_data.splice(index, 1); + + // refresh + this._refresh(); + } + }, + + // remove + remove: function() { + this.$el.select2('destroy'); + }, + + // update + update: function(options) { + // copy options + this.select_data = []; + for (var key in options.data) { + this.select_data.push(options.data[key]); + } + + // refresh + this._refresh(); + }, + + // refresh + _refresh: function() { + + // link select data + var select_data = this.select_data; + if (!select_data || select_data.length == 0) { + select_data = []; + } + + // selected + var selected = this._getValue(); + + // add select2 data + this.$el.select2({ + data : select_data, + containerCssClass : this.options.css, + placeholder : this.options.placeholder + }); + + // select + var index = this._getIndex(selected); + if (index != -1) { + this._setValue(selected); + } + }, + + // get index + _getIndex: function(value) { + // search index + for (var key in this.select_data) { + if (this.select_data[key].id == value) { + return key; + } + } + + // not found + return -1; + }, + + // get value + _getValue: function() { + return this.$el.select2('val'); + }, + + // set value + _setValue: function(new_value) { + this.$el.select2('val', new_value); + }, + + // element + _template: function(options) { + return '<input type="hidden"/>'; + } +}); + +return { + View : View +} + +}); diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -3,8 +3,8 @@ 'mvc/upload/upload-model', 'mvc/upload/upload-extensions', 'mvc/upload/upload-settings', - 'mvc/ui.popover', - 'mvc/ui.select'], + 'mvc/ui/popover', + 'mvc/ui/select'], function( Utils, UploadModel, diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -5,7 +5,7 @@ "mvc/upload/upload-model", "mvc/upload/upload-row", "mvc/upload/upload-ftp", - "mvc/ui.popover", + "mvc/ui/popover", "mvc/ui", "utils/uploadbox"], diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/ui.popover.js --- a/static/scripts/packed/mvc/ui.popover.js +++ /dev/null @@ -1,1 +0,0 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}}); \ No newline at end of file diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/ui.select.js --- a/static/scripts/packed/mvc/ui.select.js +++ /dev/null @@ -1,1 +0,0 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$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(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/ui/popover.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/popover.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}}); \ No newline at end of file diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/ui/select.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/select.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$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(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover","mvc/ui.select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui/popover","mvc/ui/select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file diff -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 -r b6acb69067f808147e4e69a1cde74cbb8868c600 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Upload: Improve select style
by commits-noreply＠bitbucket.org 13 Feb '14

13 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0ef8c71a3ed1/ Changeset: 0ef8c71a3ed1 User: guerler Date: 2014-02-13 09:33:39 Summary: Upload: Improve select style Affected #: 2 files diff -r e8810dcb7d7295fc61288c338c2ea9e36b083225 -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1264,6 +1264,7 @@ .upload-box .table td{margin:0px;paddign:0px} .upload-box .upload-item .select2-arrow b{background-position:0 -3px} .upload-box .upload-item .select2-choice{max-height:20px;line-height:18px;background:transparent} +.upload-box .upload-item .select2-container-disabled .select2-arrow{background:transparent} .upload-box .mode{float:left;font-size:1.2em;width:1.2em;color:#555} .upload-box .title{width:130px;word-wrap:break-word;font-size:11px;float:left} .upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none;background:inherit;color:#000} @@ -1684,15 +1685,15 @@ div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{line-height:16px;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-paused .state-icon:before{content:"\f04c"} div.historyItem-new .state-icon{line-height:16px;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-new .state-icon:before{content:"\f071"} div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important} -div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px} -div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px} -div.historyItemButtons .icon-button.display_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px} -div.historyItemButtons .icon-button.delete{background-image:url(sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px} -div.historyItemButtons .icon-button.delete:hover{background-image:url(sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px} -div.historyItemButtons .icon-button.delete_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px} -div.historyItemButtons .icon-button.edit{background-image:url(sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px} -div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px} -div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px} +div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px;height:16px} +div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px;height:16px} +div.historyItemButtons .icon-button.display_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px;height:16px} +div.historyItemButtons .icon-button.delete{background-image:url(sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px;height:16px} +div.historyItemButtons .icon-button.delete:hover{background-image:url(sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px;height:16px} +div.historyItemButtons .icon-button.delete_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px;height:16px} +div.historyItemButtons .icon-button.edit{background-image:url(sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px;height:16px} +div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px;height:16px} +div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px;height:16px} div.historyItemBody div{padding-top:2px} pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto}pre.peek th{color:white;background:#5f6990} pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} diff -r e8810dcb7d7295fc61288c338c2ea9e36b083225 -r 0ef8c71a3ed14f7f6f8d53a43969501b39f83496 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -95,6 +95,12 @@ line-height: 18px; background: transparent; } + + .select2-container-disabled { + .select2-arrow { + background: transparent; + } + } } .mode { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Upload: Fix select removal
by commits-noreply＠bitbucket.org 13 Feb '14

13 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e8810dcb7d72/ Changeset: e8810dcb7d72 User: guerler Date: 2014-02-13 09:14:26 Summary: Upload: Fix select removal Affected #: 4 files diff -r 086352011e076cc658ce75b9d8caa665e54b31c8 -r e8810dcb7d7295fc61288c338c2ea9e36b083225 static/scripts/mvc/ui.select.js --- a/static/scripts/mvc/ui.select.js +++ b/static/scripts/mvc/ui.select.js @@ -100,7 +100,7 @@ }, // remove - remove: function(id) { + del: function(id) { // search option var index = this._getIndex(id); @@ -114,6 +114,11 @@ } }, + // remove + remove: function() { + this.$el.select2('destroy'); + }, + // update update: function(options) { // copy options diff -r 086352011e076cc658ce75b9d8caa665e54b31c8 -r e8810dcb7d7295fc61288c338c2ea9e36b083225 static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -195,6 +195,16 @@ } }, + // remove + remove: function() { + // trigger remove event + this.select_genome.remove(); + this.select_extension.remove(); + + // call the base class remove method + Backbone.View.prototype.remove.apply(this); + }, + // // handle model events // diff -r 086352011e076cc658ce75b9d8caa665e54b31c8 -r e8810dcb7d7295fc61288c338c2ea9e36b083225 static/scripts/packed/mvc/ui.select.js --- a/static/scripts/packed/mvc/ui.select.js +++ b/static/scripts/packed/mvc/ui.select.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},remove:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_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.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});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:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$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===undefined){return null}else{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.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_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.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file diff -r 086352011e076cc658ce75b9d8caa665e54b31c8 -r e8810dcb7d7295fc61288c338c2ea9e36b083225 static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover","mvc/ui.select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover","mvc/ui.select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Upload: Add select2 selection fields, add select2 backbone wrapper
by commits-noreply＠bitbucket.org 13 Feb '14

13 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/086352011e07/ Changeset: 086352011e07 User: guerler Date: 2014-02-13 08:37:10 Summary: Upload: Add select2 selection fields, add select2 backbone wrapper Affected #: 8 files diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/mvc/ui.select.js --- /dev/null +++ b/static/scripts/mvc/ui.select.js @@ -0,0 +1,188 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +var View = Backbone.View.extend( +{ + // options + optionsDefault: { + css : '', + placeholder : 'No data available', + data : [] + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // add to dom + this.options.container.append(this.$el); + + // link selection dictionary + this.select_data = this.options.data; + + // refresh + this._refresh(); + + // initial value + if (this.options.value) { + this._setValue(this.options.value); + } + + // add change event + var self = this; + if (this.options.onchange) { + this.$el.on('change', function() { + self.options.onchange(self.value()); + }); + } + }, + + // value + value : function (new_value) { + // get current id/value + var before = this._getValue(); + + // check if new_value is defined + if (new_value !== undefined) { + this._setValue(new_value); + } + + // get current id/value + var after = this._getValue(); + if(after === undefined) { + return null; + } else { + // fire onchange + if ((after != before && this.options.onchange)) { + this.options.onchange(after); + } + + // return current value + return after; + } + }, + + // label + text : function () { + return this.$el.select2('data').text; + }, + + // disabled + disabled: function() { + return !this.$el.select2('enable'); + }, + + // enable + enable: function() { + this.$el.select2('enable', true); + }, + + // disable + disable: function() { + this.$el.select2('enable', false); + }, + + // add + add: function(options) { + // add options + this.select_data.push({ + id : options.id, + text : options.text + }); + + // refresh + this._refresh(); + }, + + // remove + remove: function(id) { + // search option + var index = this._getIndex(id); + + // check if found + if (index != -1) { + // remove options + this.select_data.splice(index, 1); + + // refresh + this._refresh(); + } + }, + + // update + update: function(options) { + // copy options + this.select_data = []; + for (var key in options.data) { + this.select_data.push(options.data[key]); + } + + // refresh + this._refresh(); + }, + + // refresh + _refresh: function() { + + // link select data + var select_data = this.select_data; + if (!select_data || select_data.length == 0) { + select_data = []; + } + + // selected + var selected = this._getValue(); + + // add select2 data + this.$el.select2({ + data : select_data, + containerCssClass : this.options.css, + placeholder : this.options.placeholder + }); + + // select + var index = this._getIndex(selected); + if (index != -1) { + this._setValue(selected); + } + }, + + // get index + _getIndex: function(value) { + // search index + for (var key in this.select_data) { + if (this.select_data[key].id == value) { + return key; + } + } + + // not found + return -1; + }, + + // get value + _getValue: function() { + return this.$el.select2('val'); + }, + + // set value + _setValue: function(new_value) { + this.$el.select2('val', new_value); + }, + + // element + _template: function(options) { + return '<input type="hidden"/>'; + } +}); + +return { + View : View +} + +}); diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -3,13 +3,15 @@ 'mvc/upload/upload-model', 'mvc/upload/upload-extensions', 'mvc/upload/upload-settings', - 'mvc/ui.popover'], + 'mvc/ui.popover', + 'mvc/ui.select'], function( Utils, UploadModel, UploadExtensions, UploadSettings, - Popover + Popover, + Select ) { // item view @@ -31,6 +33,12 @@ // handle for settings popover settings: null, + // genome selector + select_genome : null, + + // extension selector + select_extension : null, + // render initialize: function(app, options) { // link app @@ -55,6 +63,28 @@ placement : 'bottom' }); + // select genomes + this.select_genome = new Select.View({ + css: 'genome', + onchange : function() { + self.model.set('genome', self.select_genome.value()); + }, + data: self.app.list_genomes, + container: it.find('#genome'), + value: self.model.get('genome') + }); + + // select extension + this.select_extension = new Select.View({ + css: 'extension', + onchange : function() { + self.model.set('extension', self.select_extension.value()); + }, + data: self.app.list_extensions, + container: it.find('#extension'), + value: self.model.get('extension') + }); + // // ui events // @@ -76,16 +106,6 @@ self.model.set('file_size', $(e.target).val().length); }); - // handle genome selection - it.find('#genome').on('change', function(e) { - self.model.set('genome', $(e.target).val()); - }); - - // handle extension selection - it.find('#extension').on('change', function(e) { - self.model.set('extension', $(e.target).val()); - }); - // handle space to tabs button it.find('#space_to_tabs').on('change', function(e) { self.model.set('space_to_tabs', $(e.target).prop('checked')); @@ -100,9 +120,6 @@ this.model.on('change:status', function() { self._refreshStatus(); }); - this.model.on('change:extension', function() { - self._destroyExtensionInfo(); - }); this.model.on('change:info', function() { self._refreshInfo(); }); @@ -113,11 +130,9 @@ self._refreshFileSize(); }); this.model.on('remove', function() { - self._destroyExtensionInfo(); self.remove(); }); this.app.collection.on('reset', function() { - self._destroyExtensionInfo(); self.remove(); }); }, @@ -189,7 +204,7 @@ { // update genome info on screen var genome = this.model.get('genome'); - this.$el.find('#genome').val(genome); + this.select_genome.value(genome); }, // progress @@ -231,17 +246,23 @@ // set new status class sy.addClass(status_class); - + // enable form fields if (status == 'init') { + // select fields + this.select_genome.enable(); + this.select_extension.enable(); + + // default fields it.find('#text-content').attr('disabled', false); - it.find('#genome').attr('disabled', false); - it.find('#extension').attr('disabled', false); it.find('#space_to_tabs').attr('disabled', false); } else { + // select fields + this.select_genome.disable(); + this.select_extension.disable(); + + // default fields it.find('#text-content').attr('disabled', true); - it.find('#genome').attr('disabled', true); - it.find('#extension').attr('disabled', true); it.find('#space_to_tabs').attr('disabled', true); } @@ -275,7 +296,6 @@ // only remove from queue if not in processing line if (status == 'init' || status == 'success' || status == 'error') { - // remove from collection this.app.collection.remove(this.model); } }, @@ -286,7 +306,7 @@ // initialize var $el = $(this.el).find('#extension-info'); var extension = this.model.get('extension'); - var title = $(this.el).find('#extension').find('option:selected').text(); + var title = this.select_extension.text(); // create popup if (!this.extension_popup) { @@ -323,66 +343,43 @@ } }, - // attach file info popup - _destroyExtensionInfo : function() - { - this.$el.find('#extension-info').popover('destroy'); - }, - // template _template: function(options) { - // link this - var self = this; - - // construct template - var tmpl = '<tr id="upload-item-' + options.id + '" class="upload-item">' + - '<td>' + - '<div style="position: relative;">' + - '<div id="mode"></div>' + - '<div id="title" class="title"></div>' + - '<div id="text" class="text">' + - '<div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div>' + - '<textarea id="text-content" class="text-content form-control"></textarea>' + - '</div>' + + return '<tr id="upload-item-' + options.id + '" class="upload-item">' + + '<td>' + + '<div style="position: relative;">' + + '<div id="mode"></div>' + + '<div id="title" class="title"></div>' + + '<div id="text" class="text">' + + '<div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div>' + + '<textarea id="text-content" class="text-content form-control"></textarea>' + '</div>' + - '</td>' + - '<td>' + - '<div id="size" class="size"></div>' + - '</td>'; - - // add file type selectore - tmpl += '<td>' + - '<select id="extension" class="extension">'; - for (key in self.app.select_extension) - tmpl += '<option value="' + self.app.select_extension[key][1] + '">' + self.app.select_extension[key][0] + '</option>'; - tmpl += '</select>' + - '  <i id="extension-info" class="upload-icon-button fa fa-search"/>' + - '</td>'; - - // add genome selector - tmpl += '<td>' + - '<select id="genome" class="genome">'; - for (key in self.app.select_genome) - tmpl += '<option value="' + self.app.select_genome[key][1] + '">' + self.app.select_genome[key][0] + '</option>'; - tmpl += '</select>' + - '</td>'; - - // add next row - tmpl += '<td><div id="settings" class="upload-icon-button fa fa-gear"></div>' + - '<td>' + - '<div id="info" class="info">' + - '<div class="progress">' + - '<div class="progress-bar progress-bar-success"></div>' + - '<div id="percentage" class="percentage">0%</div>' + - '</div>' + + '</div>' + + '</td>' + + '<td>' + + '<div id="size" class="size"></div>' + + '</td>' + + '<td>' + + '<div id="extension" class="extension" style="float: left;"/> &nbsp' + + '<div id="extension-info" class="upload-icon-button fa fa-search"/>' + + '</td>' + + '<td>' + + '<div id="genome" class="genome" />' + + '</td>' + + '<td><div id="settings" class="upload-icon-button fa fa-gear"></div>' + + '<td>' + + '<div id="info" class="info">' + + '<div class="progress">' + + '<div class="progress-bar progress-bar-success"></div>' + + '<div id="percentage" class="percentage">0%</div>' + '</div>' + - '</td>' + - '<td><div id="symbol" class="' + this.status_classes.init + '"></div></td>' + - '</tr>'; - - // return html string - return tmpl; + '</div>' + + '</td>' + + '<td>' + + '<div id="symbol" class="' + this.status_classes.init + '"></div>' + + '</td>' + + '</tr>'; } }); diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -42,10 +42,10 @@ upload_size: 0, // extension types - select_extension :[['Auto-detect', 'auto']], + list_extensions :[{id: 'auto', text: 'Auto-detect'}], // genomes - select_genome : [['Unspecified (?)', '?']], + list_genomes : [], // collection collection : new UploadModel.Collection(), @@ -107,32 +107,30 @@ var self = this; Utils.jsonFromUrl(galaxy_config.root + "api/datatypes?upload_only=True", function(datatypes) { - for (key in datatypes) - self.select_extension.push([datatypes[key], datatypes[key]]); + for (key in datatypes) { + self.list_extensions.push({ + id : datatypes[key], + text : datatypes[key] + }); + } }); // load genomes Utils.jsonFromUrl(galaxy_config.root + "api/genomes", function(genomes) { - // backup default - var def = self.select_genome[0]; - - // fill array - self.select_genome = []; - for (key in genomes) - if (genomes[key].length > 1) - if (genomes[key][1] !== def[1]) - self.select_genome.push(genomes[key]); - + for (key in genomes) { + self.list_genomes.push({ + id : genomes[key][1], + text : genomes[key][0] + }); + } + // sort - self.select_genome.sort(function(a, b) { - return a[0] > b[0] ? 1 : a[0] < b[0] ? -1 : 0; + self.list_genomes.sort(function(a, b) { + return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; }); - - // insert default back to array - self.select_genome.unshift(def); }); - + // read in options if (options) { this.options = _.defaults(options, this.options); @@ -296,9 +294,6 @@ // configure uploadbox this.uploadbox.configure({url : this.options.nginx_upload_path}); - // configure tool - tool_input = {}; - // local files if (file_mode == 'local') { this.uploadbox.configure({paramname : 'files_0|file_data'}); @@ -306,6 +301,9 @@ this.uploadbox.configure({paramname : null}); } + // configure tool + tool_input = {}; + // new files if (file_mode == 'new') { tool_input['files_0|url_paste'] = url_paste; @@ -313,7 +311,6 @@ // files from ftp if (file_mode == 'ftp') { - // add to tool configuration tool_input['files_0|ftp_files'] = file_path; } diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/packed/mvc/ui.select.js --- /dev/null +++ b/static/scripts/packed/mvc/ui.select.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$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===undefined){return null}else{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()},remove:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover"],function(d,b,e,a,c){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#genome").on("change",function(j){f.model.set("genome",$(j.target).val())});h.find("#extension").on("change",function(j){f.model.set("extension",$(j.target).val())});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:extension",function(){f._destroyExtensionInfo()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f._destroyExtensionInfo();f.remove()});this.app.collection.on("reset",function(){f._destroyExtensionInfo();f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},_refreshGenome:function(){var f=this.model.get("genome");this.$el.find("#genome").val(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){g.find("#text-content").attr("disabled",false);g.find("#genome").attr("disabled",false);g.find("#extension").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{g.find("#text-content").attr("disabled",true);g.find("#genome").attr("disabled",true);g.find("#extension").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var h=this.model.get("extension");var g=$(this.el).find("#extension").find("option:selected").text();if(!this.extension_popup){this.extension_popup=new c.View({content:e(h),placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(g);this.extension_popup.empty();this.extension_popup.append(e(h));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_destroyExtensionInfo:function(){this.$el.find("#extension-info").popover("destroy")},_template:function(h){var g=this;var f='<tr id="upload-item-'+h.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';f+='<td><select id="extension" class="extension">';for(key in g.app.select_extension){f+='<option value="'+g.app.select_extension[key][1]+'">'+g.app.select_extension[key][0]+"</option>"}f+='</select>  <i id="extension-info" class="upload-icon-button fa fa-search"/></td>';f+='<td><select id="genome" class="genome">';for(key in g.app.select_genome){f+='<option value="'+g.app.select_genome[key][1]+'">'+g.app.select_genome[key][0]+"</option>"}f+="</select></td>";f+='<td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>';return f}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover","mvc/ui.select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]<l[0]?-1:0});h.select_genome.unshift(k)});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});tool_input={};if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1259,16 +1259,17 @@ .upload-icon{font-size:1.2em;width:1.2em} .upload-icon-button{font-size:1.2em;width:1.2em;cursor:pointer} .upload-info{font-weight:normal;text-align:center} -.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .popover{max-width:500px;width:auto} -.upload-box .table{width:100%} +.upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%} .upload-box .table th{text-align:center;white-space:nowrap} .upload-box .table td{margin:0px;paddign:0px} +.upload-box .upload-item .select2-arrow b{background-position:0 -3px} +.upload-box .upload-item .select2-choice{max-height:20px;line-height:18px;background:transparent} .upload-box .mode{float:left;font-size:1.2em;width:1.2em;color:#555} .upload-box .title{width:130px;word-wrap:break-word;font-size:11px;float:left} .upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none;background:inherit;color:#000} .upload-box .text .text-info{font-size:11px} -.upload-box .extension{width:100px;font-size:11px} -.upload-box .genome{width:150px;font-size:11px} +.upload-box .extension{width:100px;min-width:100px;font-size:11px} +.upload-box .genome{width:150px;min-width:150px;font-size:11px} .upload-box .size{width:60px;white-space:nowrap} .upload-box .info{width:130px;font-size:11px;line-height:1.2em}.upload-box .info .progress{top:1px;position:relative;width:100%;padding:0px;margin:0px;line-height:1.55em}.upload-box .info .progress .progress-bar{border-radius:inherit;-moz-border-radius:inherit} .upload-box .info .progress .percentage{position:absolute;text-align:center;width:100%;color:#fff} @@ -1683,15 +1684,15 @@ div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{line-height:16px;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-paused .state-icon:before{content:"\f04c"} div.historyItem-new .state-icon{line-height:16px;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}div.historyItem-new .state-icon:before{content:"\f071"} div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important} -div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px;height:16px} -div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px;height:16px} -div.historyItemButtons .icon-button.display_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px;height:16px} -div.historyItemButtons .icon-button.delete{background-image:url(sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px;height:16px} -div.historyItemButtons .icon-button.delete:hover{background-image:url(sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px;height:16px} -div.historyItemButtons .icon-button.delete_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px;height:16px} -div.historyItemButtons .icon-button.edit{background-image:url(sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px;height:16px} -div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px;height:16px} -div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px;height:16px} +div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px} +div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px} +div.historyItemButtons .icon-button.display_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -80px;width:16px;height:16px} +div.historyItemButtons .icon-button.delete{background-image:url(sprite-history-buttons.png);background-position:0px 0px;width:16px;height:16px} +div.historyItemButtons .icon-button.delete:hover{background-image:url(sprite-history-buttons.png);background-position:0px -16px;width:16px;height:16px} +div.historyItemButtons .icon-button.delete_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -32px;width:16px;height:16px} +div.historyItemButtons .icon-button.edit{background-image:url(sprite-history-buttons.png);background-position:0px -96px;width:16px;height:16px} +div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px} +div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px} div.historyItemBody div{padding-top:2px} pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto}pre.peek th{color:white;background:#5f6990} pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} diff -r 64e6873c8825164718ca14f17379b114e3539b09 -r 086352011e076cc658ce75b9d8caa665e54b31c8 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -71,11 +71,6 @@ overflow-x : hidden; -ms-overflow-style: none; - .popover { - max-width: 500px; - width: auto; - } - .table { width : 100%; } @@ -89,7 +84,19 @@ margin: 0px; paddign: 0px; } - + + .upload-item { + .select2-arrow b { + background-position: 0 -3px; + } + + .select2-choice { + max-height: 20px; + line-height: 18px; + background: transparent; + } + } + .mode { float: left; font-size: 1.2em; @@ -119,20 +126,21 @@ .text-info { font-size : @font-size-small; - // color : @gray-light; } } .extension { width: 100px; + min-width: 100px; font-size : @font-size-small; } .genome { width: 150px; + min-width: 150px; font-size : @font-size-small; } - + .size { width: 60px; white-space: nowrap; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 12 Feb '14

12 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b463c73f3348/ Changeset: b463c73f3348 Branch: stable User: greg Date: 2014-02-12 16:17:38 Summary: Fixes for repositories in the tool shed whose repository tip changeset has no files (because they were all deleted) but have valid tools and other utilities in previous changeset revisions. Affected #: 2 files diff -r e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211 -r b463c73f334811d4c48298c40de9ac489261c32d 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 @@ -2312,6 +2312,7 @@ revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision, include_date=False ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious + changeset_revision = previous_changeset_revision if repository_metadata: skip_tool_test = repository_metadata.skip_tool_tests if skip_tool_test: @@ -2719,10 +2720,15 @@ status = "error" repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) changeset_revision = repository.tip( trans.app ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + id, + changeset_revision, + metadata_only=True ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repo=repo, repository=repository, changeset_revision=changeset_revision, + metadata=metadata, commit_message=commit_message, repository_type_select_field=repository_type_select_field, message=message, diff -r e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211 -r b463c73f334811d4c48298c40de9ac489261c32d templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -74,7 +74,7 @@ else: can_rate = False - if changeset_revision is not None: + if metadata is not None and changeset_revision is not None: if has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ): can_review_repository = True else: @@ -177,7 +177,7 @@ <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='manage_repository_admins', id=trans.security.encode_id( repository.id ) )}">Manage repository administrators</a> %endif %if can_download: - %if changeset_revision is not None: + %if metadata is not None and changeset_revision is not None: <a class="action-button" href="${h.url_for( controller='repository', action='export', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Export this revision</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> https://bitbucket.org/galaxy/galaxy-central/commits/64e6873c8825/ Changeset: 64e6873c8825 User: inithello Date: 2014-02-12 16:19:19 Summary: Merge stable. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for repositories in the tool shed whose repository tip changeset has no files (because they were all deleted) but have valid tools and other utilities in previous changeset revisions.
by commits-noreply＠bitbucket.org 12 Feb '14

12 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f50a5a4391ee/ Changeset: f50a5a4391ee User: greg Date: 2014-02-12 16:17:38 Summary: Fixes for repositories in the tool shed whose repository tip changeset has no files (because they were all deleted) but have valid tools and other utilities in previous changeset revisions. Affected #: 2 files diff -r b8d2ef92592257a76abeba73630e71b44a708fa8 -r f50a5a4391ee589b55516c6d0fc94a9805840900 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 @@ -2312,6 +2312,7 @@ revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision, include_date=False ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious + changeset_revision = previous_changeset_revision if repository_metadata: skip_tool_test = repository_metadata.skip_tool_tests if skip_tool_test: @@ -2719,10 +2720,15 @@ status = "error" repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) changeset_revision = repository.tip( trans.app ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + id, + changeset_revision, + metadata_only=True ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repo=repo, repository=repository, changeset_revision=changeset_revision, + metadata=metadata, commit_message=commit_message, repository_type_select_field=repository_type_select_field, message=message, diff -r b8d2ef92592257a76abeba73630e71b44a708fa8 -r f50a5a4391ee589b55516c6d0fc94a9805840900 templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -74,7 +74,7 @@ else: can_rate = False - if changeset_revision is not None: + if metadata is not None and changeset_revision is not None: if has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ): can_review_repository = True else: @@ -177,7 +177,7 @@ <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='manage_repository_admins', id=trans.security.encode_id( repository.id ) )}">Manage repository administrators</a> %endif %if can_download: - %if changeset_revision is not None: + %if metadata is not None and changeset_revision is not None: <a class="action-button" href="${h.url_for( controller='repository', action='export', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Export this revision</a> %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 12 Feb '14

12 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e3a4d4d813fd/ Changeset: e3a4d4d813fd Branch: stable User: greg Date: 2014-02-11 22:41:03 Summary: Fixes for the tool shed's install and test framework. Affected #: 5 files diff -r bb744d8d3d6a74872a7b42b511d087c16b1ee8b3 -r e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -56,6 +56,10 @@ mkdir -p $GALAXY_INSTALL_TEST_SHED_TOOL_PATH fi +if [ ! -d $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR ] ; then + mkdir -p $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR +fi + test_tool_dependency_definitions () { # Test installation of repositories of type tool_dependency_definition. if [ -f $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR/stage_1_complete ] ; then @@ -102,6 +106,7 @@ ;; # Use "-w repositories_with_tools" parameter when you want to test repositories that contain tools. repositories_with_tools) + touch $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR/stage_1_complete test_repositories_with_tools ;; # No received parameters or any received parameter not in [ tool_dependency_definitions, repositories_with_tools ] diff -r bb744d8d3d6a74872a7b42b511d087c16b1ee8b3 -r e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211 test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -156,3 +156,22 @@ ( timeout_counter, repository.status ) ) break time.sleep( 1 ) + # Set all metadata on each installed repository. + for repository_id in repository_ids: + galaxy_repository = test_db_util.get_repository( self.security.decode_id( repository_id ) ) + if not galaxy_repository.metadata: + log.debug( 'Setting metadata on repository %s' % str( galaxy_repository.name ) ) + timeout_counter = 0 + url = '/admin_toolshed/reset_repository_metadata?id=%s' % repository_id + self.visit_url( url ) + while not galaxy_repository.metadata: + test_db_util.refresh( galaxy_repository ) + timeout_counter = timeout_counter + 1 + if timeout_counter % 10 == 0: + log.debug( 'Waited %d seconds for repository %s.' % ( timeout_counter, str( galaxy_repository.name ) ) ) + # This timeout currently defaults to 10 minutes. + if timeout_counter > repository_installation_timeout: + raise AssertionError( 'Repository installation timed out after %d seconds, repository state is %s.' % \ + ( timeout_counter, repository.status ) ) + break + time.sleep( 1 ) diff -r bb744d8d3d6a74872a7b42b511d087c16b1ee8b3 -r e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -18,6 +18,7 @@ import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories import nose import platform +import string import time import tool_shed.repository_types.util as rt_util import tool_shed.util.shed_util_common as suc @@ -35,7 +36,7 @@ from galaxy.util import asbool from galaxy.util import listify from galaxy.util import unicodify -from galaxy.util.json import from_json_string +from galaxy.util.json import to_json_string import galaxy.webapps.tool_shed.model.mapping from nose.plugins import Plugin @@ -614,7 +615,7 @@ repository = get_repository( name, owner, changeset_revision ) if repository is None: error_message = 'Error getting revision %s of repository %s owned by %s: %s' % ( changeset_revision, name, owner, str( e ) ) - log.exception( error_message ) + log.exception( error_message ) return repository, error_message def is_excluded( exclude_list_dicts, name, owner, changeset_revision, encoded_repository_metadata_id ): @@ -981,6 +982,22 @@ print 'tool_shed: %s name: %s owner: %s changeset_revision: %s' % \ ( cleaned_tool_shed_url, name, owner, changeset_revision ) +def populate_shed_conf_file( shed_conf_file, tool_path, xml_elems=None ): + """Populate the file defined by shed_conf_file with xml_elems or initialize it with a template string.""" + if xml_elems is None: + tool_conf_template_parser = string.Template( shed_tool_conf_xml_template ) + xml_elems = tool_conf_template_parser.safe_substitute( shed_tool_path=tool_path ) + file( shed_conf_file, 'w' ).write( xml_elems ) + +def populate_galaxy_shed_tools_dict_file( galaxy_shed_tools_dict_file, shed_tools_dict=None ): + """ + Populate the file defined by galaxy_shed_tools_dict_file with the contents of the shed_tools_dict + dictionary. + """ + if shed_tools_dict is None: + shed_tools_dict = {} + file( galaxy_shed_tools_dict_file, 'w' ).write( to_json_string( shed_tools_dict ) ) + def print_install_and_test_results( install_stage_type, install_and_test_statistics_dict, error_message ): "Print statistics for the current test run." if error_message: diff -r bb744d8d3d6a74872a7b42b511d087c16b1ee8b3 -r e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -33,7 +33,6 @@ import re import shutil import socket -import string import tempfile import time import threading @@ -44,7 +43,6 @@ from galaxy.app import UniverseApplication from galaxy.util.json import from_json_string -from galaxy.util.json import to_json_string from galaxy.util import unicodify from galaxy.web import buildapp from functional_tests import generate_config_file @@ -134,7 +132,7 @@ tool_id = parts[ -2 ] return tool_id, tool_version -def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): +def install_and_test_repositories( app, galaxy_shed_tools_dict_file, galaxy_shed_tool_conf_file, galaxy_shed_tool_path ): # We must make sure that functional.test_toolbox is always imported after database_contexts.galaxy_content # is set (which occurs in the main method before this method is called). If functional.test_toolbox is # imported before database_contexts.galaxy_content is set, sa_session will be None in all methods that use it. @@ -166,6 +164,8 @@ # The traceback and captured output of the tool that was run will be recored for test failures. After all tests have # completed, the repository is uninstalled, so test cases don't interfere with the next repository's functional tests. for repository_dict in repositories_to_install: + # Re-initialize the received galaxy_shed_tool_conf_file to be an empty shed_tool_conf.xml. + install_and_test_base_util.populate_shed_conf_file( galaxy_shed_tool_conf_file, galaxy_shed_tool_path, xml_elems=None ) encoded_repository_metadata_id = repository_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_dict[ 'tool_shed_url' ] = install_and_test_base_util.galaxy_tool_shed_url @@ -210,6 +210,7 @@ repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1 if error_message: + remove_tests( app, repository ) # The repository installation failed. print 'Installation failed for revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) processed_repositories_with_installation_error = \ @@ -247,6 +248,12 @@ install_and_test_statistics_dict, tool_test_results_dict ) if params.get( 'test_install_error', False ): + # We cannot run functional tests for contained tools due to dependency installation errors. + remove_tests( app, repository ) + can_run_functional_tests = False + print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ + ( changeset_revision, name, owner ) + print 'because one or more dependencies has installation errors.' # The repository was successfully installed, but one or more dependencies had installation errors, # so we'll populate the test result containers since we cannot execute any tests. install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, @@ -255,12 +262,6 @@ repository_dict, params, can_update_tool_shed ) - # We cannot run functional tests for contained tools due to dependency installation errors. - print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ - ( changeset_revision, name, owner ) - print 'because one or more dependencies has installation errors.' - can_run_functional_tests = False - remove_tests( app ) # Populate the installation containers (success or error) for the repository's immediate repository # dependencies whose containers are not yet populated. install_and_test_base_util.populate_install_containers_for_repository_dependencies( app, @@ -280,32 +281,30 @@ install_and_test_base_util.get_missing_tool_dependencies( repository, all_missing_tool_dependencies=None ) print 'Missing tool dependencies:\n%s' % str( missing_tool_dependencies ) - if missing_repository_dependencies or missing_tool_dependencies: + if missing_repository_dependencies or missing_tool_dependencies: + # The repository was installed successfully, but one or more dependencies had installation errors. Since + # we cannot test the tools due to these errors, we'll remove tests and tools were created during the repository + # installation process so nose will not discover them and attempt to execute them. + remove_tests( app, repository ) print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ ( changeset_revision, name, owner ) print 'because one or more dependencies has installation errors.' - # The repository was installed successfully, but one or more dependencies had installation errors. Since - # we cannot test the tools due to these errors, we'll remove tests and tools were created during the repository - # installation process so nose will not discover them and attempt to execute them. - remove_tests( app ) else: print 'Revision %s of repository %s owned by %s installed successfully, so running tool tests.' % \ ( changeset_revision, name, owner ) # Generate the shed_tools_dict that specifies the location of test data contained within this repository. # and configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + install_and_test_base_util.populate_galaxy_shed_tools_dict_file( galaxy_shed_tools_dict_file, + shed_tools_dict=None ) # Find the path to the test-data directory within the installed repository. has_test_data, shed_tools_dict = \ parse_tool_panel_config( galaxy_shed_tool_conf_file, - from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + from_json_string( file( galaxy_shed_tools_dict_file, 'r' ).read() ) ) # If the repository has a test-data directory we write the generated shed_tools_dict to a temporary # file so the functional test framework can find it. - # TODO: Eliminate the need for this shed_tools_dict since it grows large over the course of each test run. - # If it cannot be eliminated altogether, reinitialize it with each new repository install so at this point - # it contains only entries for the current repository dependency hierarchy being tested. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) - print 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, shed_tools_dict ) + install_and_test_base_util.populate_galaxy_shed_tools_dict_file( galaxy_shed_tools_dict_file, + shed_tools_dict=shed_tools_dict ) try: install_and_test_statistics_dict = test_repository_tools( app, repository, @@ -314,6 +313,7 @@ tool_test_results_dict, install_and_test_statistics_dict ) except Exception, e: + remove_tests( app, repository ) exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) log.exception( exception_message ) tool_test_results_dict[ 'failed_tests' ].append( exception_message ) @@ -330,6 +330,7 @@ params, can_update_tool_shed ) else: + remove_tests( app, repository ) print 'Skipped attempt to install revision %s of repository %s owned by %s because ' % \ ( changeset_revision, name, owner ) print 'it was previously installed and currently has status %s' % str( repository.status ) @@ -379,12 +380,12 @@ os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) - galaxy_shed_tools_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', - os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + galaxy_shed_tools_dict_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', + os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) + install_and_test_base_util.populate_galaxy_shed_tools_dict_file( galaxy_shed_tools_dict_file, shed_tools_dict=None ) # Set the GALAXY_TOOL_SHED_TEST_FILE environment variable to the path of the shed_tools_dict file so that # test.base.twilltestcase.setUp will find and parse it properly. - os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict + os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict_file if 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' in os.environ: tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ) else: @@ -430,13 +431,10 @@ if 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF' not in os.environ: file( galaxy_tool_sheds_conf_file, 'w' ).write( install_and_test_base_util.tool_sheds_conf_xml ) # Generate the shed_tool_conf.xml file. - tool_conf_template_parser = string.Template( install_and_test_base_util.shed_tool_conf_xml_template ) - shed_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) - file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) + install_and_test_base_util.populate_shed_conf_file( galaxy_shed_tool_conf_file, galaxy_shed_tool_path, xml_elems=None ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file # Generate the migrated_tool_conf.xml file. - migrated_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path ) - file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml ) + install_and_test_base_util.populate_shed_conf_file( galaxy_migrated_tool_conf_file, galaxy_migrated_tool_path, xml_elems=None ) # Write the embedded web application's specific configuration to a temporary file. This is necessary in order for # the external metadata script to find the right datasets. kwargs = dict( admin_users = 'test(a)bx.psu.edu', @@ -548,8 +546,9 @@ print "# This run will not update the Tool Shed database." print "####################################################################################" install_and_test_statistics_dict, error_message = install_and_test_repositories( app, - galaxy_shed_tools_dict, - galaxy_shed_tool_conf_file ) + galaxy_shed_tools_dict_file, + galaxy_shed_tool_conf_file, + galaxy_shed_tool_path ) try: install_and_test_base_util.print_install_and_test_results( 'repositories with tools', install_and_test_statistics_dict, @@ -583,12 +582,17 @@ # Return a "successful" response to buildbot. return 0 -def remove_tests( app ): +def remove_tests( app, repository ): """ - Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them - and try to re-run the tests after uninstalling the repository, which will cause false failure reports, - since the test data has been deleted from disk by now. + Delete any configured tool functional tests from the test_toolbox.__dict__. """ + print '\n-------------------------------------------------------------\n' + if repository: + print 'Removing tests and tool ids for revision %s of repository %s owned by %s' % \ + ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) + else: + print 'Removing tests and tool ids when received repository is None...' + print 'app.toolbox.tools_by_id.keys():\n%s\n' % str( app.toolbox.tools_by_id.keys() ) tests_to_delete = [] tools_to_delete_by_id = [] for key in test_toolbox.__dict__: @@ -608,15 +612,31 @@ reset_spaces_tool_id = tool_id.replace( '_', ' ' ) if reset_spaces_app_tool_id == reset_spaces_tool_id: print 'Setting tool id %s for deletion from app.toolbox[ tools_by_id ].' % str( app_tool_id ) - tools_to_delete_by_id.append( app_tool_id ) + tools_to_delete_by_id.append( app_tool_id ) + if repository: + metadata = repository.metadata + print 'metadata:\n%s\n' % str( metadata ) + if metadata: + tools = metadata.get( 'tools', [] ) + print 'tools:\n%s\n' % str( tools ) + for tool_dict in tools: + print 'tool_dict:\n%s\n' % str( tool_dict ) + guid = tool_dict.get( 'guid', None ) + print 'guid:\n%s\n' % str( guid ) + if guid: + if guid in app.toolbox.tools_by_id: + print 'Setting tool id %s for deletion from app.toolbox[ tools_by_id ].' % str( guid ) + tools_to_delete_by_id.append( guid ) # Delete the discovered twill-generated tests. for key in tests_to_delete: if key in test_toolbox.__dict__: print 'Deleting test %s from test_toolbox.' % str( key ) del test_toolbox.__dict__[ key ] for tool_id in tools_to_delete_by_id: - print 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) - del app.toolbox.tools_by_id[ tool_id ] + if tool_id in app.toolbox.tools_by_id: + print 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) + del app.toolbox.tools_by_id[ tool_id ] + print '\n-------------------------------------------------------------\n' def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, install_and_test_statistics_dict ): @@ -700,7 +720,7 @@ can_update_tool_shed ) # Remove the just-executed tests so twill will not find and re-test them along with the tools # contained in the next repository. - remove_tests( app ) + remove_tests( app, repository ) return install_and_test_statistics_dict if __name__ == "__main__": diff -r bb744d8d3d6a74872a7b42b511d087c16b1ee8b3 -r e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -33,7 +33,6 @@ import re import shutil import socket -import string import tempfile import time import threading @@ -43,8 +42,6 @@ from base.tool_shed_util import parse_tool_panel_config from galaxy.app import UniverseApplication -from galaxy.util.json import from_json_string -from galaxy.util.json import to_json_string from galaxy.util import unicodify from galaxy.web import buildapp from functional_tests import generate_config_file @@ -75,7 +72,7 @@ test_framework = install_and_test_base_util.TOOL_DEPENDENCY_DEFINITIONS -def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): +def install_and_test_repositories( app, galaxy_shed_tools_dict_file, galaxy_shed_tool_conf_file, galaxy_shed_tool_path ): # Initialize a dictionary for the summary that will be printed to stdout. install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict() error_message = '' @@ -234,12 +231,13 @@ os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) - galaxy_shed_tools_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', - os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + galaxy_shed_tools_dict_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', + os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) + install_and_test_base_util.populate_galaxy_shed_tools_dict_file( galaxy_shed_tools_dict_file, + shed_tools_dict=None ) # Set the GALAXY_TOOL_SHED_TEST_FILE environment variable to the path of the shed_tools_dict file so that # test.base.twilltestcase.setUp will find and parse it properly. - os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict + os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict_file if 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' in os.environ: tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ) else: @@ -285,13 +283,10 @@ if 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF' not in os.environ: file( galaxy_tool_sheds_conf_file, 'w' ).write( install_and_test_base_util.tool_sheds_conf_xml ) # Generate the shed_tool_conf.xml file. - tool_conf_template_parser = string.Template( install_and_test_base_util.shed_tool_conf_xml_template ) - shed_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) - file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) + install_and_test_base_util.populate_shed_conf_file( galaxy_shed_tool_conf_file, galaxy_shed_tool_path, xml_elems=None ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file # Generate the migrated_tool_conf.xml file. - migrated_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path ) - file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml ) + install_and_test_base_util.populate_shed_conf_file( galaxy_migrated_tool_conf_file, galaxy_migrated_tool_path, xml_elems=None ) # Write the embedded web application's specific configuration to a temporary file. This is necessary in order for # the external metadata script to find the right datasets. kwargs = dict( admin_users = 'test(a)bx.psu.edu', @@ -402,8 +397,9 @@ print "# This run will not update the Tool Shed database." print "####################################################################################" install_and_test_statistics_dict, error_message = install_and_test_repositories( app, - galaxy_shed_tools_dict, - galaxy_shed_tool_conf_file ) + galaxy_shed_tools_dict_file, + galaxy_shed_tool_conf_file, + galaxy_shed_tool_path ) try: install_and_test_base_util.print_install_and_test_results( 'tool dependency definitions', install_and_test_statistics_dict, https://bitbucket.org/galaxy/galaxy-central/commits/b8d2ef925922/ Changeset: b8d2ef925922 User: inithello Date: 2014-02-11 22:42:24 Summary: Merge with stable. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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