June 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c68aa8a8e769/ Changeset: c68aa8a8e769 Branch: stable User: dan Date: 2014-06-03 23:03:17 Summary: Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm Affected #: 1 file diff -r f9c050410d6a56d7f6fe503b4f22f286bd5a40e2 -r c68aa8a8e769437473bd23586d1b55fc66cc8c47 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -738,6 +738,8 @@ return rval elif app_action == None: #redirect user to url generated by display link + #Fix for Safari caching display links, which can change if the underlying dataset has an attribute change, e.g. name, metadata, etc + trans.response.headers[ 'Cache-Control' ] = [ 'no-cache', 'max-age=0', 'no-store', 'must-revalidate' ] return trans.response.send_redirect( display_link.display_url() ) else: msg.append( ( 'Invalid action provided: %s' % app_action, 'error' ) ) 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: Charts: Improve notifications and error handling
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0cb88fa06c32/ Changeset: 0cb88fa06c32 User: guerler Date: 2014-06-04 09:54:54 Summary: Charts: Improve notifications and error handling Affected #: 4 files diff -r 9c1a51c9f85f52d4570dede166155700130d8234 -r 0cb88fa06c32e13c8881ed90af02b239aa574313 config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js @@ -30,22 +30,28 @@ this.app.datasets.request(request_dictionary, function() { if (self.options.canvas.length == 1) { // groups - self._drawGroups(hc_type, chart, request_dictionary.groups, self.options.canvas[0]); - - // set chart state - chart.state('ok', 'Chart drawn.'); + if (self._drawGroups(hc_type, chart, request_dictionary.groups, self.options.canvas[0])) { + // set chart state + chart.state('ok', 'Chart drawn.'); + } } else { // loop through data groups + var valid = true; for (var group_index in request_dictionary.groups) { // get group var group = request_dictionary.groups[group_index]; // draw group - self._drawGroups(hc_type, chart, [group], self.options.canvas[group_index]); + if (!self._drawGroups(hc_type, chart, [group], self.options.canvas[group_index])) { + valid = false; + break; + } } // set chart state - chart.state('ok', 'Multi-panel chart drawn.'); + if (valid) { + chart.state('ok', 'Multi-panel chart drawn.'); + } } // unregister process @@ -90,7 +96,19 @@ } // draw plot - canvas.highcharts(this.hc_config); + try { + canvas.highcharts(this.hc_config); + return true; + } catch (err) { + var regex = /\www\.highcharts\.com([^&]+)/; + var match = err.match(regex); + if (match.length > 0) { + chart.state('failed', 'Highcharts error: <a target="_blank" href="http://' + match[0] + '">' + match[0] + '</a>'); + } else { + chart.state('failed', err); + } + return false; + } } }); diff -r 9c1a51c9f85f52d4570dede166155700130d8234 -r 0cb88fa06c32e13c8881ed90af02b239aa574313 config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -28,6 +28,9 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); + // message element + this.message = new Ui.Message(); + // create portlet this.portlet = new Portlet.View({ icon : 'fa-bar-chart-o', @@ -38,10 +41,6 @@ tooltip : 'Draw Chart', title : 'Draw', onclick : function() { - // show viewport - self.app.go('viewer'); - - // save chart self._saveChart(); } }), @@ -75,10 +74,6 @@ self.chart.set('modified', true); }, ondblclick : function(chart_id) { - // show viewport - self.app.go('viewer'); - - // save chart self._saveChart(); } }); @@ -135,6 +130,7 @@ }); // append tabs + this.portlet.append(this.message.$el); this.portlet.append(this.tabs.$el); // elements @@ -266,6 +262,35 @@ // create chart _saveChart: function() { + // ensure that data group is available + if (this.chart.groups.length == 0) { + var group = this._addGroupModel(); + this.tabs.show(group.id); + return; + } + + // very selected group columns + var self = this; + var valid = true; + this.chart.groups.each(function(group) { + for (var key in group.attributes) { + if (group.attributes[key] == 'null') { + self.message.update({status: 'danger', message: 'This chart type requires column types not found in your tabular file.'}); + self.tabs.show(group.id); + valid = false; + return; + } + } + }); + + // validate if columns have been selected + if (!valid) { + return; + } + + // show viewport + this.app.go('viewer'); + // update chart data this.chart.set({ type : this.types.value(), @@ -273,11 +298,6 @@ date : Utils.time() }); - // ensure that data group is available - if (this.chart.groups.length == 0) { - this._addGroupModel(); - } - // wait until chart is ready var self = this; this.chart.deferred.execute(function() { diff -r 9c1a51c9f85f52d4570dede166155700130d8234 -r 0cb88fa06c32e13c8881ed90af02b239aa574313 config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -21,6 +21,9 @@ // link this var self = this; + // message element + this.message = new Ui.Message(); + // create portlet this.portlet = new Portlet.View({ icon : 'fa-bar-chart-o', @@ -53,6 +56,7 @@ }); // append portlet + this.portlet.append(this.message.$el); this.portlet.append(this.viewport_view.$el); // set element @@ -91,22 +95,7 @@ if (chart.deferred.ready()) { callback(); } else { - // show modal - var self = this; - this.app.modal.show({ - title : 'Please wait!', - body : 'Your chart is currently being processed. Please wait and try again.', - buttons : { - 'Close' : function() {self.app.modal.hide();}, - 'Retry' : function() { - // hide modal - self.app.modal.hide(); - - // retry - setTimeout(function() { self._wait(chart, callback); }, self.app.config.get('query_timeout')); - } - } - }); + this.message.update({message: 'Your chart is currently being processed. Please wait and try again.'}); } } }); diff -r 9c1a51c9f85f52d4570dede166155700130d8234 -r 0cb88fa06c32e13c8881ed90af02b239aa574313 config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -39,7 +39,7 @@ this.chart.on('set:state', function() { // get info element var $info = self.$el.find('#info'); - var $container = self.$el.find('container'); + var $container = self.$el.find('.charts-viewport-container'); // get icon var $icon = $info.find('#icon'); @@ -51,21 +51,20 @@ $info.show(); $info.find('#text').html(self.chart.get('state_info')); - // hide containers - $container.hide(); - // check status var state = self.chart.get('state'); switch (state) { case 'ok': $info.hide(); - $container.show() + $container.show(); break; case 'failed': $icon.addClass('icon fa fa-warning'); + $container.hide(); break; default: $icon.addClass('icon fa fa-spinner fa-spin'); + $container.show(); } }); }, @@ -182,7 +181,6 @@ } ); } else { - // load data into view view.draw(process_id, chart, self._defaultRequestDictionary(chart)); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Charts: Extend boxplot options
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9c1a51c9f85f/ Changeset: 9c1a51c9f85f User: guerler Date: 2014-06-04 08:10:32 Summary: Charts: Extend boxplot options Affected #: 3 files diff -r c93e85d8ac0d28ea07a985ddd15f014216dd6ddb -r 9c1a51c9f85f52d4570dede166155700130d8234 config/plugins/visualizations/charts/static/charts/highcharts/boxplot/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/config.js @@ -1,6 +1,6 @@ -define([], function() { +define(['plugin/charts/highcharts/common/config'], function(config) { -return $.extend(true, {}, { +return $.extend(true, {}, config, { title : 'Box plot', category : 'Data processing (requires \'charts\' tool from Toolshed)', library : 'Highcharts', diff -r c93e85d8ac0d28ea07a985ddd15f014216dd6ddb -r 9c1a51c9f85f52d4570dede166155700130d8234 config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js @@ -29,7 +29,7 @@ chart.settings.set('legend_enabled', 'false') // create configuration - this.hc_config = configmaker(chart.settings); + this.hc_config = configmaker(chart, chart.settings); // request data var self = this; diff -r c93e85d8ac0d28ea07a985ddd15f014216dd6ddb -r 9c1a51c9f85f52d4570dede166155700130d8234 config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js @@ -36,6 +36,8 @@ }, labels: { formatter : function() { + if (settings.get('x_axis_type') == 'auto') + return this.value; var format = d3.format(settings.get('x_axis_tick') + settings.get('x_axis_type')); return format(this.value); }, @@ -50,6 +52,8 @@ }, labels: { formatter : function() { + if (settings.get('y_axis_type') == 'auto') + return this.value; var format = d3.format(settings.get('y_axis_tick') + settings.get('y_axis_type')); return format(this.value); }, 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: Charts: Remove helper function
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c93e85d8ac0d/ Changeset: c93e85d8ac0d User: guerler Date: 2014-06-04 07:52:58 Summary: Charts: Remove helper function Affected #: 1 file diff -r 2df424fc0536831e49b09d4d2ffa3a111fba1282 -r c93e85d8ac0d28ea07a985ddd15f014216dd6ddb config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js @@ -3,15 +3,6 @@ // widget return function(chart, settings) { - // helper label enabled - var labelEnabled = function(axis) { - if (settings.get(axis + '_type') == 'hide') { - return false; - } else { - return true; - } - }; - // highcharts configuration return { chart: { @@ -48,7 +39,7 @@ var format = d3.format(settings.get('x_axis_tick') + settings.get('x_axis_type')); return format(this.value); }, - enabled : labelEnabled('x_axis') + enabled : !(settings.get('x_axis_type') == 'hide') }, tickPixelInterval : 100 }, @@ -62,7 +53,7 @@ var format = d3.format(settings.get('y_axis_tick') + settings.get('y_axis_type')); return format(this.value); }, - enabled : labelEnabled('y_axis') + enabled : !(settings.get('y_axis_type') == 'hide') } }, 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: Charts: Adding chart subset selection filter, setting zoomable charts as default
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

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commit/galaxy-central: dannon: Pack scripts.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1be07de86c2a/ Changeset: 1be07de86c2a User: dannon Date: 2014-06-03 23:42:17 Summary: Pack scripts. Affected #: 1 file diff -r e33a715ee045acac64b9e8e4ac14bcdc31ef6ca7 -r 1be07de86c2a606518a7cfc2913230c29a7210f8 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var s=$("<div/>").attr("id","loading_indicator");this.$el.append(s);var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(t){o._renderChunk(t)})}var p=false;this.scroll_elt.scroll(function(){if(!p&&o.scrolled_to_bottom()){p=true;s.show();$.when(o.model.get_next_chunk()).then(function(t){if(t){o._renderChunk(t);p=false;s.hide()}})}})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file +define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var s=$("<div/>").attr("id","loading_indicator");this.$el.append(s);var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(t){o._renderChunk(t)})}var p=false;this.scroll_elt.scroll(function(){if(!p&&o.scrolled_to_bottom()){p=true;s.show();$.when(o.model.get_next_chunk()).then(function(t){if(t){o._renderChunk(t);p=false}s.hide()})}})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ 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: dannon: Stop loading indicator at the end of get_next_chunk regardless of result.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e33a715ee045/ Changeset: e33a715ee045 User: dannon Date: 2014-06-03 23:40:00 Summary: Stop loading indicator at the end of get_next_chunk regardless of result. Affected #: 1 file diff -r 58a057a02b896ae6d32571f7141f46ccb9006e54 -r e33a715ee045acac64b9e8e4ac14bcdc31ef6ca7 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -180,8 +180,8 @@ if (result) { self._renderChunk(result); loading_chunk = false; - loading_indicator.hide(); } + loading_indicator.hide(); }); } }); 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: davebgx: Merge fix from stable.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/58a057a02b89/ Changeset: 58a057a02b89 User: davebgx Date: 2014-06-03 23:04:13 Summary: Merge fix from stable. Affected #: 1 file diff -r d1d3a8f09b2bcaf23962310f5d535758823e13d7 -r 58a057a02b896ae6d32571f7141f46ccb9006e54 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -623,11 +623,11 @@ # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = hg_util.get_config_from_disk( 'tool_dependencies.xml', install_dir ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_shed_repository.tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies, + from_tool_migration_manager=False ) basic_util.remove_dir( work_dir ) suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, @@ -881,11 +881,11 @@ # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = hg_util.get_config_from_disk( 'tool_dependencies.xml', repository.repo_path( trans.app ) ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=repository.tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=repository.tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR ]: repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message ) 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: dan: Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1d3a8f09b2b/ Changeset: d1d3a8f09b2b User: dan Date: 2014-06-03 23:03:17 Summary: Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm Affected #: 1 file diff -r 72dea09e14ab6e87e7537b23f8c9af2cd6f50c6b -r d1d3a8f09b2bcaf23962310f5d535758823e13d7 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -738,6 +738,8 @@ return rval elif app_action == None: #redirect user to url generated by display link + #Fix for Safari caching display links, which can change if the underlying dataset has an attribute change, e.g. name, metadata, etc + trans.response.headers[ 'Cache-Control' ] = [ 'no-cache', 'max-age=0', 'no-store', 'must-revalidate' ] return trans.response.send_redirect( display_link.display_url() ) else: msg.append( ( 'Invalid action provided: %s' % app_action, 'error' ) ) 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: davebgx: Add change that was lost when resolving a merge conflict.
by commits-noreply＠bitbucket.org 03 Jun '14

03 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f9c050410d6a/ Changeset: f9c050410d6a Branch: stable User: davebgx Date: 2014-06-03 22:52:18 Summary: Add change that was lost when resolving a merge conflict. Affected #: 1 file diff -r 96fdb9168f28b2ffa463195d084c9278efb2465a -r f9c050410d6a56d7f6fe503b4f22f286bd5a40e2 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -622,11 +622,11 @@ # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_shed_repository.tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies, + from_tool_migration_manager=False ) suc.remove_dir( work_dir ) suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, @@ -880,11 +880,11 @@ # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repository.repo_path( trans.app ) ) installed_tool_dependencies = \ - common_install_util.install_specified_packages( app=trans.app, - tool_shed_repository=repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=repository.tool_dependencies, - from_tool_migration_manager=False ) + common_install_util.install_specified_tool_dependencies( app=trans.app, + tool_shed_repository=repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=repository.tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR ]: repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message ) 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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