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May 2014
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commit/galaxy-central: davebgx: Fix functional test dataset error reporting.
by commits-noreply＠bitbucket.org 09 May '14
by commits-noreply＠bitbucket.org 09 May '14
09 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3210eaa1db6c/
Changeset: 3210eaa1db6c
User: davebgx
Date: 2014-05-09 18:35:23
Summary: Fix functional test dataset error reporting.
Affected #: 1 file
diff -r c0af07ce3b0beb686cee26428dfcc229ebe34334 -r 3210eaa1db6cb6af4e5c4846c1fec39585405cd9 test/base/twilltestcase.py
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -2244,7 +2244,6 @@
if wait:
self.wait( maxseconds=maxseconds ) # wait for job to finish
data_list = self.get_history_from_api( encoded_history_id=None, show_deleted=False, show_details=False )
- log.debug( data_list )
self.assertTrue( data_list )
if hid is None: # take last hid
dataset = data_list[-1]
@@ -2254,6 +2253,7 @@
self.assertTrue( len( datasets ) == 1 )
dataset = datasets[0]
self.assertTrue( hid )
+ dataset = self.json_from_url( dataset[ 'url' ] )
self._assert_dataset_state( dataset, 'ok' )
if filename is not None and self.is_zipped( filename ):
errmsg = 'History item %s is a zip archive which includes invalid files:\n' % hid
@@ -2466,10 +2466,11 @@
f.close()
return fname
- def _assert_dataset_state( self, elem, state ):
- if elem.get( 'state' ) != state:
- errmsg = "Expecting dataset state '%s', but state is '%s'. Dataset blurb: %s\n\n" % ( state, elem.get('state'), elem.text.strip() )
- errmsg += self.get_job_stderr( elem.get( 'id' ), format=True )
+ def _assert_dataset_state( self, dataset, state ):
+ if dataset.get( 'state' ) != state:
+ blurb = dataset.get( 'misc_blurb' )
+ errmsg = "Expecting dataset state '%s', but state is '%s'. Dataset blurb: %s\n\n" % ( state, dataset.get('state'), blurb.strip() )
+ errmsg += self.get_job_stderr( dataset.get( 'id' ), format=True )
raise AssertionError( errmsg )
def _bam_to_sam( self, local_name, temp_name ):
@@ -2504,7 +2505,6 @@
page_url = "/display?encoded_id=%s" % hda_id
else:
page_url = "/datasets/%s/display/%s" % ( hda_id, filename )
- log.debug( page_url )
self.visit_url( page_url )
data = self.last_page()
return data
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: davebgx: Clean up twilltestcase.py, fix functional tests for tools with spaces in the tool ID.
by commits-noreply＠bitbucket.org 09 May '14
by commits-noreply＠bitbucket.org 09 May '14
09 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c0af07ce3b0b/
Changeset: c0af07ce3b0b
User: davebgx
Date: 2014-05-09 15:57:26
Summary: Clean up twilltestcase.py, fix functional tests for tools with spaces in the tool ID.
Affected #: 3 files
diff -r f6bf49aca8da9707937ebaebbfa869d10735dc81 -r c0af07ce3b0beb686cee26428dfcc229ebe34334 test/base/interactor.py
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -474,8 +474,8 @@
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
.first()
assert latest_history is not None, "Problem retrieving latest_history from database"
- if len( self.twill_test_case.get_history_as_data_list() ) > 0:
- raise AssertionError("ToolTestCase.do_it failed")
+ if len( self.twill_test_case.get_hids_in_history( self.twill_test_case.get_latest_history()[ 'id' ] ) ) > 0:
+ raise AssertionError("ToolTestCase.do_it failed to create a new empty history")
return latest_history
def delete_history( self, latest_history ):
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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09 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f6bf49aca8da/
Changeset: f6bf49aca8da
User: guerler
Date: 2014-05-09 13:58:26
Summary: Charts: Pack scripts
Affected #: 3 files
diff -r 7c9b64b44298ceef9d5d9935ce5cd3736f9b36f6 -r f6bf49aca8da9707937ebaebbfa869d10735dc81 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
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Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({canvas:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._create_canvas("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_create_canvas:function(e,t){t=t||1;for(var n in this.canvas)this.canvas[n].remove(),this.canvas.slice(n,0);for(var n=0;n<t;n++){var r=$(this._template_canvas(e,parseInt(100/t)));this.$el.append(r),e=="svg"?this.canvas[n]=d3.select(r[0]):this.canvas[n]=r}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._create_canvas(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var i=new r(t.app,{canvas:t.canvas});t.chart_settings.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e)):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div style="height: inherit; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_canvas:function(e,t){return"<"+e+' class="canvas" style="float: left; display: block; width:'+t+'%; height: 100%;"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var 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'+e.title+"</div>"}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),a=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),f=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:i,Icon:s,ButtonIcon:o,Input:h,Anchor:u,Message:a,Searchbox:f,Title:l,Text:r,Select:t,ButtonMenu:c}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div style="height: inherit; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_templateContainer:function(e,t){return'<div class="container" style="float: left; display: block; width:'+t+'%; height: 100%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas" style="display: block; width:100%; height: inherit;">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onchange:function(e){u.chart.settings.clear(),u.chart.set({type:e}),u.chart.set("modified",!0)},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"}),this.table.addHeader("No."),this.table.addHeader("Type"),this.table.addHeader("Processing*"),this.table.appendHeader();var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),this.table.add(h.title),h.execute?this.table.add((new n.Icon({icon:"fa-check"})).$el,"10%","center"):this.table.add(""),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),p.append((new n.Text({title:"*Certain chart types pre-process data before rendering the visualization. The pre-processing is done using the charts tool available in the Toolshed.",cls:"toolParamHelp"})).$el),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","nvd3_bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bardiagram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/nvd3_linewithfocus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/nvd3_piechart/config",[],function(){return{title:"Pie chart",library:"nvd3.js",tag:"svg",use_panels:!0,columns:{label:{title:"Labels",is_label:!0},y:{title:"Values"}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatterplot/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bardiagram/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_horizontal/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_linewithfocus/config","plugin/charts/nvd3_piechart/config","plugin/charts/nvd3_scatterplot/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f){return Backbone.Model.extend({defaults:{nvd3_bardiagram:e,nvd3_horizontal:n,nvd3_histogram:t,nvd3_line:r,nvd3_linewithfocus:i,nvd3_piechart:s,nvd3_scatterplot:o,nvd3_stackedarea:u,highcharts_boxplot:a}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r 7c9b64b44298ceef9d5d9935ce5cd3736f9b36f6 -r f6bf49aca8da9707937ebaebbfa869d10735dc81 config/plugins/visualizations/charts/static/charts/types.js
--- a/config/plugins/visualizations/charts/static/charts/types.js
+++ b/config/plugins/visualizations/charts/static/charts/types.js
@@ -28,7 +28,7 @@
defaults: {
'nvd3_bardiagram' : nvd3_bardiagram,
'nvd3_horizontal' : nvd3_horizontal,
- 'heatmap' : heatmap,
+ //'heatmap' : heatmap,
'nvd3_histogram' : nvd3_histogram,
'nvd3_line' : nvd3_line,
'nvd3_linewithfocus' : nvd3_linewithfocus,
diff -r 7c9b64b44298ceef9d5d9935ce5cd3736f9b36f6 -r f6bf49aca8da9707937ebaebbfa869d10735dc81 config/plugins/visualizations/charts/static/library/jobs.js
--- a/config/plugins/visualizations/charts/static/library/jobs.js
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -170,7 +170,7 @@
_refreshHdas: function() {
// update galaxy history
if (Galaxy && Galaxy.currHistoryPanel) {
- Galaxy.currHistoryPanel.refreshHdas();
+ Galaxy.currHistoryPanel.refreshContents();
}
}
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Charts: Improve job handling and heatmaps
by commits-noreply＠bitbucket.org 09 May '14
by commits-noreply＠bitbucket.org 09 May '14
09 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7c9b64b44298/
Changeset: 7c9b64b44298
User: guerler
Date: 2014-05-09 07:09:54
Summary: Charts: Improve job handling and heatmaps
Affected #: 5 files
diff -r 96242495c567a287bdb4bc26e05b70403c732f24 -r 7c9b64b44298ceef9d5d9935ce5cd3736f9b36f6 config/plugins/visualizations/charts/static/charts/heatmap/config.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/config.js
@@ -5,15 +5,16 @@
library : '',
tag : 'div',
use_panels : true,
+ execute : 'heatmap',
// columns
columns : {
- col_label : {
- title : 'Columns',
+ row_label : {
+ title : 'Row labels',
is_label : true
},
- row_label : {
- title : 'Rows',
+ col_label : {
+ title : 'Column labels',
is_label : true
},
value : {
@@ -23,6 +24,50 @@
// settings
settings: {
+ /*limit : {
+ title : 'Limit',
+ info : 'Which to ranked clusters would you like to visualize',
+ type : 'select',
+ init : '20',
+ data : [
+ {
+ label : '20',
+ value : '20'
+ },
+ {
+ label : '30',
+ value : '30'
+ },
+ {
+ label : '40',
+ value : '40'
+ },
+ {
+ label : '50',
+ value : '50'
+ },
+ {
+ label : '60',
+ value : '60'
+ },
+ {
+ label : '70',
+ value : '70'
+ },
+ {
+ label : '80',
+ value : '80'
+ },
+ {
+ label : '90',
+ value : '90'
+ },
+ {
+ label : '100',
+ value : '100'
+ }
+ ]
+ },*/
color_set : {
title : 'Color scheme',
info : 'Select a color scheme for your heatmap',
diff -r 96242495c567a287bdb4bc26e05b70403c732f24 -r 7c9b64b44298ceef9d5d9935ce5cd3736f9b36f6 config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js
@@ -14,12 +14,35 @@
// render
draw : function(process_id, chart, request_dictionary)
{
- // request data
+ // link this
var self = this;
- this.app.datasets.request(request_dictionary, function() {
+
+ // loop through data groups
+ var index = 0;
+ for (var group_index in request_dictionary.groups) {
- // loop through data groups
- for (var group_index in request_dictionary.groups) {
+ // configure request
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = null;
+ group.columns = {
+ row_label: {
+ index : index++,
+ is_label : true
+ },
+ col_label: {
+ index : index++,
+ is_label : true
+ },
+ value: {
+ index : index++
+ }
+ }
+ }
+
+ // request data
+ this.app.datasets.request(request_dictionary, function() {
+
// get group
var group = request_dictionary.groups[group_index];
var div = self.options.canvas[group_index];
@@ -31,14 +54,17 @@
'data' : group.values,
'div' : div
});
- }
-
- // set chart state
- chart.state('ok', 'Heat map drawn.');
- // unregister process
- chart.deferred.done(process_id);
- });
+ // check if done
+ if (group_index == request_dictionary.groups.length - 1) {
+ // set chart state
+ chart.state('ok', 'Heat map drawn.');
+
+ // unregister process
+ chart.deferred.done(process_id);
+ }
+ });
+ }
}
});
diff -r 96242495c567a287bdb4bc26e05b70403c732f24 -r 7c9b64b44298ceef9d5d9935ce5cd3736f9b36f6 config/plugins/visualizations/charts/static/charts/types.js
--- a/config/plugins/visualizations/charts/static/charts/types.js
+++ b/config/plugins/visualizations/charts/static/charts/types.js
@@ -27,8 +27,8 @@
// types
defaults: {
'nvd3_bardiagram' : nvd3_bardiagram,
+ 'nvd3_horizontal' : nvd3_horizontal,
'heatmap' : heatmap,
- 'nvd3_horizontal' : nvd3_horizontal,
'nvd3_histogram' : nvd3_histogram,
'nvd3_line' : nvd3_line,
'nvd3_linewithfocus' : nvd3_linewithfocus,
diff -r 96242495c567a287bdb4bc26e05b70403c732f24 -r 7c9b64b44298ceef9d5d9935ce5cd3736f9b36f6 config/plugins/visualizations/charts/static/library/jobs.js
--- a/config/plugins/visualizations/charts/static/library/jobs.js
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -13,12 +13,33 @@
this.options = Utils.merge(options, this.optionsDefault);
},
+ // request job results
+ request: function(chart, settings_string, columns_string, success, error) {
+ // link this
+ var self = this;
+
+ // set chart state
+ chart.state('wait', 'Requesting job results...');
+
+ // get dataset job id if already set
+ var dataset_id_job = chart.get('dataset_id_job');
+ if (dataset_id_job != '') {
+ // wait for job completion
+ self._wait(chart, success, error);
+ } else {
+ // post job
+ self._submit(chart, settings_string, columns_string, success, error);
+ }
+ },
+
// clean
cleanup: function(chart) {
+ // link this
+ var self = this;
+
// cleanup previous dataset file
var previous = chart.get('dataset_id_job');
if (previous != '') {
- var self = this;
Utils.request('PUT', config.root + 'api/histories/none/contents/' + previous, { deleted: true }, function() {
// update galaxy history
self._refreshHdas();
@@ -30,13 +51,13 @@
},
// create job
- submit: function(chart, settings_string, columns_string, success, error) {
+ _submit: function(chart, settings_string, columns_string, success, error) {
// link this
var self = this;
// backup chart details
- var chart_id = chart.id;
- var chart_type = chart.get('type');
+ var chart_id = chart.id;
+ var chart_type = chart.get('type');
// get chart settings
var chart_settings = this.app.types.get(chart_type);
@@ -75,7 +96,7 @@
var job = response.outputs[0];
// check dataset
- chart.state('wait', 'Job has been queued...');
+ chart.state('wait', 'Your job has been queued. You may close the browser window. The job will run in the background.');
// backup resulting dataset id
chart.set('dataset_id_job', job.id);
@@ -84,34 +105,7 @@
this.app.storage.save();
// wait for job completion
- self._loop(job.id, function(job) {
- switch (job.state) {
- case 'ok':
- // update state
- chart.state('wait', 'Job completed successfully...');
-
- // execute success
- success(job);
-
- // stop loop
- return true;
- case 'error':
- // update state
- chart.state('failed', 'Job has failed. Please check the history for details.');
-
- // call error
- error && error();
-
- // stop loop
- return true;
- case 'running':
- // wait
- chart.state('wait', 'Job is running...');
-
- // continue loop
- return false;
- }
- });
+ self._wait(chart, success, error);
}
},
// error handler
@@ -132,11 +126,42 @@
},
// request job details
- _loop: function(id, callback) {
+ _wait: function(chart, success, error) {
var self = this;
- Utils.request('GET', config.root + 'api/datasets/' + id, {}, function(job) {
- if (!callback(job)) {
- setTimeout(function() { self._loop(id, callback); }, self.app.config.get('query_timeout'));
+ Utils.request('GET', config.root + 'api/datasets/' + chart.get('dataset_id_job'), {}, function(dataset) {
+ // check dataset state
+ var ready = false;
+ switch (dataset.state) {
+ case 'ok':
+ // update state
+ chart.state('wait', 'Job completed successfully...');
+
+ // execute success
+ success && success(dataset);
+
+ // stop loop
+ ready = true;
+ break;
+ case 'error':
+ // update state
+ chart.state('failed', 'Job has failed. Please check the history for details.');
+
+ // call error
+ error && error(dataset);
+
+ // stop loop
+ ready = true;
+ break;
+ case 'running':
+ // wait
+ chart.state('wait', 'Your job is running. You may close the browser window. The job will continue in the background.');
+ }
+
+ // wait and try again
+ if (!ready) {
+ setTimeout(function() {
+ self._wait(chart, success, error);
+ }, self.app.config.get('query_timeout'));
}
});
},
diff -r 96242495c567a287bdb4bc26e05b70403c732f24 -r 7c9b64b44298ceef9d5d9935ce5cd3736f9b36f6 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
@@ -173,19 +173,14 @@
// request data
if (self.chart_settings.execute) {
- if (chart.get('dataset_id_job') == '') {
- // submit job
- self.app.jobs.submit(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart),
- function() {
- view.draw(process_id, chart, self._defaultRequestDictionary(chart));
- },
- function() {
- chart.deferred.done(process_id);
- });
- } else {
- // load data into view
- view.draw(process_id, chart, self._defaultRequestDictionary(chart));
- }
+ self.app.jobs.request(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart),
+ function() {
+ view.draw(process_id, chart, self._defaultRequestDictionary(chart));
+ },
+ function() {
+ chart.deferred.done(process_id);
+ }
+ );
} else {
// load data into view
view.draw(process_id, chart, self._defaultRequestDictionary(chart));
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: pep 8, fixed decoding of folders again
by commits-noreply＠bitbucket.org 08 May '14
by commits-noreply＠bitbucket.org 08 May '14
08 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/96242495c567/
Changeset: 96242495c567
User: martenson
Date: 2014-05-09 00:55:57
Summary: pep 8, fixed decoding of folders again
Affected #: 2 files
diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 96242495c567a287bdb4bc26e05b70403c732f24 lib/galaxy/webapps/galaxy/api/folders.py
--- a/lib/galaxy/webapps/galaxy/api/folders.py
+++ b/lib/galaxy/webapps/galaxy/api/folders.py
@@ -136,7 +136,7 @@
def __cut_the_prefix(self, encoded_id):
- if ( ( len( encoded_id ) % 2 == 1 ) and encoded_id.startswith( 'F' ) ):
+ if ( ( len( encoded_id ) % 16 == 1 ) and encoded_id.startswith( 'F' ) ):
return encoded_id[ 1: ]
else:
raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_id ) )
diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 96242495c567a287bdb4bc26e05b70403c732f24 lib/galaxy/webapps/galaxy/api/library_contents.py
--- a/lib/galaxy/webapps/galaxy/api/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/library_contents.py
@@ -17,6 +17,7 @@
import logging
log = logging.getLogger( __name__ )
+
class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ):
@expose_api
@@ -26,7 +27,7 @@
* GET /api/libraries/{library_id}/contents:
Returns a list of library files and folders.
- .. note:: May be slow! Returns all content traversing recursively through all folders.
+ .. note:: May be slow! Returns all content traversing recursively through all folders.
.. seealso:: :class:`galaxy.webapps.galaxy.api.FolderContentsController.index` for a non-recursive solution
:param library_id: encoded id string of the library
@@ -78,7 +79,7 @@
except NoResultFound:
raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' )
except Exception, e:
- raise exceptions.InternalServerError( 'Error loading from the database.' + str(e))
+ raise exceptions.InternalServerError( 'Error loading from the database.' + str(e))
if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ):
raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' )
encoded_id = 'F' + trans.security.encode_id( library.root_folder.id )
@@ -122,7 +123,7 @@
class_name, content_id = self.__decode_library_content_id( trans, id )
if class_name == 'LibraryFolder':
content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True )
- rval = content.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id } )
+ rval = content.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
rval[ 'id' ] = 'F' + str( rval[ 'id' ] )
rval[ 'parent_id' ] = 'F' + str( trans.security.encode_id( rval[ 'parent_id' ] ) )
rval[ 'parent_library_id' ] = trans.security.encode_id( rval[ 'parent_library_id' ] )
@@ -236,9 +237,9 @@
encoded_id = trans.security.encode_id( v.id )
if create_type == 'folder':
encoded_id = 'F' + encoded_id
- rval.append( dict( id = encoded_id,
- name = v.name,
- url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) )
+ rval.append( dict( id=encoded_id,
+ name=v.name,
+ url=url_for( 'library_content', library_id=library_id, id=encoded_id ) ) )
return rval
def _scan_json_block(self, meta, prefix=""):
@@ -276,7 +277,7 @@
``library_contents.create`` will branch to this if called with 'from_hda_id'
in its payload.
"""
- log.debug( '_copy_hda_to_library_folder: %s' %( str(( from_hda_id, library_id, folder_id, ldda_message )) ) )
+ log.debug( '_copy_hda_to_library_folder: %s' % ( str(( from_hda_id, library_id, folder_id, ldda_message )) ) )
#PRECONDITION: folder_id has already been altered to remove the folder prefix ('F')
#TODO: allow name and other, editable ldda attrs?
if ldda_message:
@@ -287,14 +288,14 @@
# check permissions on (all three?) resources: hda, library, folder
#TODO: do we really need the library??
hda = self.get_dataset( trans, from_hda_id, check_ownership=True, check_accessible=True, check_state=True )
- library = self.get_library( trans, library_id, check_accessible=True )
+ # library = self.get_library( trans, library_id, check_accessible=True )
folder = self.get_library_folder( trans, folder_id, check_accessible=True )
# TOOD: refactor to use check_user_can_add_to_library_item, eliminate boolean
# can_current_user_add_to_library_item.
if not self.can_current_user_add_to_library_item( trans, folder ):
trans.response.status = 403
- return { 'error' : 'user has no permission to add to library folder (%s)' %( folder_id ) }
+ return { 'error': 'user has no permission to add to library folder (%s)' % ( folder_id ) }
ldda = self.copy_hda_to_library_folder( trans, hda, folder, ldda_message=ldda_message )
ldda_dict = ldda.to_dict()
@@ -304,11 +305,11 @@
#TODO: grrr...
if 'not accessible to the current user' in str( exc ):
trans.response.status = 403
- return { 'error' : str( exc ) }
+ return { 'error': str( exc ) }
else:
log.exception( exc )
trans.response.status = 500
- return { 'error' : str( exc ) }
+ return { 'error': str( exc ) }
return rval
@@ -335,10 +336,10 @@
converted_id = payload.pop( 'converted_dataset_id' )
content = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=False )
content_conv = self.get_library_dataset( trans, converted_id, check_ownership=False, check_accessible=False )
- assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = content.library_dataset_dataset_association,
- dataset = content_conv.library_dataset_dataset_association,
- file_type = content_conv.library_dataset_dataset_association.extension,
- metadata_safe = True )
+ assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent=content.library_dataset_dataset_association,
+ dataset=content_conv.library_dataset_dataset_association,
+ file_type=content_conv.library_dataset_dataset_association.extension,
+ metadata_safe=True )
trans.sa_session.add( assoc )
trans.sa_session.flush()
@@ -346,11 +347,10 @@
if ( len( content_id ) % 16 == 0 ):
return 'LibraryDataset', content_id
elif ( content_id.startswith( 'F' ) ):
- return 'LibraryFolder', content_id[1:]
+ return 'LibraryFolder', content_id[ 1: ]
else:
raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) )
-
@web.expose_api
def delete( self, trans, library_id, id, **kwd ):
"""
@@ -377,7 +377,7 @@
if kwd.get( 'payload', None ):
purge = util.string_as_bool( kwd['payload'].get( 'purge', False ) )
- rval = { 'id' : id }
+ rval = { 'id': id }
try:
ld = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=True )
user_is_admin = trans.user_is_admin()
@@ -424,5 +424,3 @@
trans.response.status = 500
rval.update({ 'error': str( exc ) })
return rval
-
-
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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5 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b7d43f49b239/
Changeset: b7d43f49b239
User: jmchilton
Date: 2014-05-08 23:12:07
Summary: Doc fix in Galaxy's tool shed repositories API.
Affected #: 1 file
diff -r 521fead562531f96564c0e08f2c3ac523a92c6e5 -r b7d43f49b239e99fdb65e4b049bc2b633aafff98 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -107,7 +107,7 @@
@web.expose_api
def import_workflows( self, trans, **kwd ):
"""
- POST /api/tool_shed_repositories/import_workflow
+ POST /api/tool_shed_repositories/import_workflows
Import all of the exported workflows contained in the specified installed tool shed repository into Galaxy.
https://bitbucket.org/galaxy/galaxy-central/commits/7c302d65be90/
Changeset: 7c302d65be90
User: jmchilton
Date: 2014-05-08 23:12:07
Summary: Reduce polling frequency of API tests, seems to help prevent sqlite locks.
Affected #: 1 file
diff -r b7d43f49b239e99fdb65e4b049bc2b633aafff98 -r 7c302d65be90f414cff9bf067cf426f5ea3b3207 test/api/helpers.py
--- a/test/api/helpers.py
+++ b/test/api/helpers.py
@@ -312,7 +312,7 @@
def wait_on_state( state_func, assert_ok=False, timeout=5 ):
- delta = .1
+ delta = .25
iteration = 0
while True:
if (delta * iteration) > timeout:
https://bitbucket.org/galaxy/galaxy-central/commits/376d5e107a58/
Changeset: 376d5e107a58
User: jmchilton
Date: 2014-05-08 23:12:07
Summary: Refactor API assertions for reuse outside explicit TestCase classes.
Affected #: 2 files
diff -r 7c302d65be90f414cff9bf067cf426f5ea3b3207 -r 376d5e107a584ac32e5f827b47cd962b79e4248c test/base/api.py
--- a/test/base/api.py
+++ b/test/base/api.py
@@ -8,6 +8,11 @@
from .api_util import get_master_api_key
from .api_util import get_user_api_key
+from .api_asserts import (
+ assert_status_code_is,
+ assert_has_keys,
+ assert_error_code_is,
+)
from urllib import urlencode
@@ -73,25 +78,13 @@
return self.galaxy_interactor.post( *args, **kwds )
def _assert_status_code_is( self, response, expected_status_code ):
- response_status_code = response.status_code
- if expected_status_code != response_status_code:
- try:
- body = response.json()
- except Exception:
- body = "INVALID JSON RESPONSE <%s>" % response.content
- assertion_message_template = "Request status code (%d) was not expected value %d. Body was %s"
- assertion_message = assertion_message_template % ( response_status_code, expected_status_code, body )
- raise AssertionError( assertion_message )
+ assert_status_code_is( response, expected_status_code )
def _assert_has_keys( self, response, *keys ):
- for key in keys:
- assert key in response, "Response [%s] does not contain key [%s]" % ( response, key )
+ assert_has_keys( response, *keys )
def _assert_error_code_is( self, response, error_code ):
- if hasattr( response, "json" ):
- response = response.json()
- self._assert_has_keys( response, "err_code" )
- self.assertEquals( response[ "err_code" ], int( error_code ) )
+ assert_error_code_is( response, error_code )
def _random_key( self ): # Used for invalid request testing...
return "1234567890123456"
diff -r 7c302d65be90f414cff9bf067cf426f5ea3b3207 -r 376d5e107a584ac32e5f827b47cd962b79e4248c test/base/api_asserts.py
--- /dev/null
+++ b/test/base/api_asserts.py
@@ -0,0 +1,30 @@
+""" Utility methods for making assertions about Galaxy API responses, etc...
+"""
+ASSERT_FAIL_ERROR_CODE = "Expected Galaxy error code %d, obtained %d"
+ASSERT_FAIL_STATUS_CODE = "Request status code (%d) was not expected value %d. Body was %s"
+
+
+def assert_status_code_is( response, expected_status_code ):
+ response_status_code = response.status_code
+ if expected_status_code != response_status_code:
+ try:
+ body = response.json()
+ except Exception:
+ body = "INVALID JSON RESPONSE <%s>" % response.content
+ assertion_message = ASSERT_FAIL_STATUS_CODE % ( response_status_code, expected_status_code, body )
+ raise AssertionError( assertion_message )
+
+
+def assert_has_keys( response, *keys ):
+ for key in keys:
+ assert key in response, "Response [%s] does not contain key [%s]" % ( response, key )
+
+
+def assert_error_code_is( response, error_code ):
+ if hasattr( response, "json" ):
+ response = response.json()
+ assert_has_keys( response, "err_code" )
+ err_code = response[ "err_code" ]
+ assert err_code == int( error_code ), ASSERT_FAIL_ERROR_CODE % ( err_code, int( error_code ) )
+
+assert_has_key = assert_has_keys
https://bitbucket.org/galaxy/galaxy-central/commits/a314a3464b08/
Changeset: a314a3464b08
User: jmchilton
Date: 2014-05-08 23:12:07
Summary: Add simple collection mapping workflow extraction functional test.
Affected #: 3 files
diff -r 376d5e107a584ac32e5f827b47cd962b79e4248c -r a314a3464b0806c5f7cb92379ce0788260637ba4 lib/galaxy/workflow/extract.py
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -93,7 +93,9 @@
steps.append( step )
# Tool steps
for job_id in job_ids:
- assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
+ if job_id not in jobs_by_id:
+ log.warn( "job_id %s not found in jobs_by_id %s" % ( job_id, jobs_by_id ) )
+ raise AssertionError( "Attempt to create workflow with job not connected to current history" )
job = jobs_by_id[ job_id ]
tool_inputs, associations = step_inputs( trans, job )
step = model.WorkflowStep()
diff -r 376d5e107a584ac32e5f827b47cd962b79e4248c -r a314a3464b0806c5f7cb92379ce0788260637ba4 test/api/helpers.py
--- a/test/api/helpers.py
+++ b/test/api/helpers.py
@@ -1,3 +1,4 @@
+from base import api_asserts
from operator import itemgetter
import time
@@ -111,6 +112,12 @@
**kwds
)
+ def run_tool( self, tool_id, inputs, history_id, **kwds ):
+ payload = self.run_tool_payload( tool_id, inputs, history_id, **kwds )
+ tool_response = self.galaxy_interactor.post( "tools", data=payload )
+ api_asserts.assert_status_code_is( tool_response, 200 )
+ return tool_response.json()
+
class WorkflowPopulator( object ):
# Impulse is to make this a Mixin, but probably better as an object.
diff -r 376d5e107a584ac32e5f827b47cd962b79e4248c -r a314a3464b0806c5f7cb92379ce0788260637ba4 test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -115,35 +115,81 @@
inputs = {
"f1": dict( src="hdca", id=hdca_id )
}
- payload = self.dataset_populator.run_tool_payload(
+ run_output = self.dataset_populator.run_tool(
tool_id="collection_paired_test",
inputs=inputs,
history_id=history_id,
)
- tool_response = self._post( "tools", data=payload )
- self._assert_status_code_is( tool_response, 200 )
- job_id = tool_response.json()[ "jobs" ][ 0 ][ "id" ]
+ job_id = run_output[ "jobs" ][ 0 ][ "id" ]
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
- create_from_data = dict(
+ downloaded_workflow = self._extract_and_download_workflow(
from_history_id=history_id,
dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
job_ids=dumps( [ job_id ] ),
workflow_name="test import from history",
)
- create_workflow_response = self._post( "workflows", data=create_from_data )
+ collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 )
+ collection_step = collection_steps[ 0 ]
+ collection_step_state = loads( collection_step[ "tool_state" ] )
+ self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
+
+ @skip_without_tool( "random_lines1" )
+ def test_extract_mapping_workflow_from_history( self ):
+ history_id = self.dataset_populator.new_history()
+ hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json()
+ hdca_id = hdca[ "id" ]
+ inputs1 = {
+ "input|__collection_multirun__": hdca_id,
+ "num_lines": 2
+ }
+ run_output1 = self.dataset_populator.run_tool(
+ tool_id="random_lines1",
+ inputs=inputs1,
+ history_id=history_id,
+ )
+ implicit_hdca1 = run_output1[ "implicit_collections" ][ 0 ]
+ job_id1 = run_output1[ "jobs" ][ 0 ][ "id" ]
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 )
+ inputs2 = {
+ "input|__collection_multirun__": implicit_hdca1[ "id" ],
+ "num_lines": 1
+ }
+ run_output2 = self.dataset_populator.run_tool(
+ tool_id="random_lines1",
+ inputs=inputs2,
+ history_id=history_id,
+ )
+ # implicit_hdca2 = run_output2[ "implicit_collections" ][ 0 ]
+ job_id2 = run_output2[ "jobs" ][ 0 ][ "id" ]
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 )
+ downloaded_workflow = self._extract_and_download_workflow(
+ from_history_id=history_id,
+ dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
+ job_ids=dumps( [ job_id1, job_id2 ] ),
+ workflow_name="test import from mapping history",
+ )
+ assert len( downloaded_workflow[ "steps" ] ) == 3
+ collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 )
+ collection_step = collection_steps[ 0 ]
+ collection_step_state = loads( collection_step[ "tool_state" ] )
+ self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
+ self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 )
+
+ def _extract_and_download_workflow( self, **extract_payload ):
+ create_workflow_response = self._post( "workflows", data=extract_payload )
self._assert_status_code_is( create_workflow_response, 200 )
- create_workflow_response.json()[ "id" ]
new_workflow_id = create_workflow_response.json()[ "id" ]
download_response = self._get( "workflows/%s/download" % new_workflow_id )
self._assert_status_code_is( download_response, 200 )
downloaded_workflow = download_response.json()
- assert len( downloaded_workflow[ "steps" ] ) == 2
- collection_steps = [ s for s in downloaded_workflow[ "steps" ].values() if s[ "type" ] == "data_collection_input" ]
- assert len( collection_steps ) == 1
- collection_step = collection_steps[ 0 ]
- collection_step_state = loads( collection_step[ "tool_state" ] )
- self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
+ return downloaded_workflow
+
+ def _get_steps_of_type( self, downloaded_workflow, type, expected_len=None ):
+ steps = [ s for s in downloaded_workflow[ "steps" ].values() if s[ "type" ] == type ]
+ if expected_len is not None:
+ assert len( steps ) == expected_len
+ return steps
@skip_without_tool( "random_lines1" )
def test_run_replace_params_by_tool( self ):
https://bitbucket.org/galaxy/galaxy-central/commits/f2f32d8b8a06/
Changeset: f2f32d8b8a06
User: jmchilton
Date: 2014-05-08 23:12:07
Summary: Bugfix: (For bf60fa7) Only initial mapping steps in map reduce workflows were being connected correctly.
With expanded test case that checks such a connection. This takes care of of subsequent connections by iteratively updating hid_to_output_pair correctly (... I think, test works with at least two).
Affected #: 2 files
diff -r a314a3464b0806c5f7cb92379ce0788260637ba4 -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 lib/galaxy/workflow/extract.py
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -123,7 +123,18 @@
steps_by_job_id[ job_id ] = step
# Store created dataset hids
for assoc in job.output_datasets:
- hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name )
+ if job in summary.implicit_map_jobs:
+ hid = None
+ for implicit_pair in jobs[ job ]:
+ query_assoc_name, dataset_collection = implicit_pair
+ if query_assoc_name == assoc.name:
+ hid = dataset_collection.hid
+ if hid is None:
+ log.warn("Failed to find matching implicit job.")
+ raise Exception( "Failed to extract job." )
+ else:
+ hid = assoc.dataset.hid
+ hid_to_output_pair[ hid ] = ( step, assoc.name )
return steps
diff -r a314a3464b0806c5f7cb92379ce0788260637ba4 -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -173,7 +173,19 @@
collection_step = collection_steps[ 0 ]
collection_step_state = loads( collection_step[ "tool_state" ] )
self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
- self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 )
+ collect_step_idx = collection_step[ "id" ]
+ tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 )
+ tool_step_idxs = []
+ tool_input_step_idxs = []
+ for tool_step in tool_steps:
+ self._assert_has_key( tool_step[ "input_connections" ], "input" )
+ input_step_idx = tool_step[ "input_connections" ][ "input" ][ "id" ]
+ tool_step_idxs.append( tool_step[ "id" ] )
+ tool_input_step_idxs.append( input_step_idx )
+
+ assert collect_step_idx not in tool_step_idxs
+ assert tool_input_step_idxs[ 0 ] == collect_step_idx
+ assert tool_input_step_idxs[ 1 ] == tool_step_idxs[ 0 ]
def _extract_and_download_workflow( self, **extract_payload ):
create_workflow_response = self._post( "workflows", data=extract_payload )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Update authenticate/baseauth doc with sample usage.
by commits-noreply＠bitbucket.org 08 May '14
by commits-noreply＠bitbucket.org 08 May '14
08 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/521fead56253/
Changeset: 521fead56253
User: dannon
Date: 2014-05-08 17:47:24
Summary: Update authenticate/baseauth doc with sample usage.
Affected #: 1 file
diff -r fc7de175ea2f59b0389a74f30e1152ff4563ad0e -r 521fead562531f96564c0e08f2c3ac523a92c6e5 lib/galaxy/webapps/galaxy/api/authenticate.py
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -1,5 +1,14 @@
"""
API key retrieval through BaseAuth
+Sample usage:
+
+curl --user zipzap@foo.com:password http://localhost:8080/api/authenticate/baseauth
+
+Returns:
+
+{
+ "api_key": "baa4d6e3a156d3033f05736255f195f9"
+}
"""
from base64 import b64decode
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Added the ability for /api/authenticate/baseauth to create an API key for a user if one is not set. Misc cleanup, using mappings instead of raw queries.
by commits-noreply＠bitbucket.org 08 May '14
by commits-noreply＠bitbucket.org 08 May '14
08 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fc7de175ea2f/
Changeset: fc7de175ea2f
User: dannon
Date: 2014-05-08 17:33:55
Summary: Added the ability for /api/authenticate/baseauth to create an API key for a user if one is not set. Misc cleanup, using mappings instead of raw queries.
Affected #: 1 file
diff -r d6826c29e15a1f17553ae2fe2b149ef65ac4da9d -r fc7de175ea2f59b0389a74f30e1152ff4563ad0e lib/galaxy/webapps/galaxy/api/authenticate.py
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -2,18 +2,19 @@
API key retrieval through BaseAuth
"""
-from galaxy import util, web
-from pprint import pprint
-from galaxy.web.base.controller import BaseAPIController
-from base64 import b64decode, b64encode
-from urllib import quote, unquote
+from base64 import b64decode
+from paste.httpexceptions import HTTPBadRequest
+from urllib import unquote
+
+from galaxy import web
from galaxy.exceptions import ObjectNotFound
-from paste.httpexceptions import HTTPBadRequest
+from galaxy.web.base.controller import BaseAPIController, CreatesApiKeysMixin
import logging
log = logging.getLogger( __name__ )
-class AuthenticationController( BaseAPIController ):
+
+class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ):
@web.expose_api_anonymous
def get_api_key( self, trans, **kwd ):
@@ -37,15 +38,15 @@
else:
user = user[0]
is_valid_user = user.check_password( password )
-
if ( is_valid_user ):
- user_id = user.id
- api_key_row = trans.sa_session.query( trans.app.model.APIKeys ).filter( trans.app.model.APIKeys.table.c.user_id == user_id ).first()
+ if user.api_keys:
+ key = user.api_keys[0].key
+ else:
+ key = self.create_api_key( trans, user )
+ return dict( api_key=key )
else:
trans.response.status = 500
- return "invalid password"
-
- return dict( api_key= api_key_row.key )
+ return "invalid password"
def _decode_baseauth( self, encoded_str ):
"""
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Add some documentation to job_conf.xml.sample_advanced about LWR caching.
by commits-noreply＠bitbucket.org 08 May '14
by commits-noreply＠bitbucket.org 08 May '14
08 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d6826c29e15a/
Changeset: d6826c29e15a
User: jmchilton
Date: 2014-05-08 16:14:24
Summary: Add some documentation to job_conf.xml.sample_advanced about LWR caching.
Affected #: 1 file
diff -r 56d4cb37d62700e5baa94cc63e56041556844c43 -r d6826c29e15a1f17553ae2fe2b149ef65ac4da9d job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -28,6 +28,14 @@
file actions are remote executable. --><!-- <param id="url">amqp://guest:guest@localhost:5672//</param> --><!-- <param id="manager">_default_</param> -->
+ <!-- *Experimental Caching*: Uncomment next parameters to enable
+ caching and specify the number of caching threads to enable on Galaxy
+ side. Likely will not work with newer features such as MQ support.
+ If this is enabled be sure to specify a `file_cache_dir` in the remote
+ LWR's main configuration file.
+ -->
+ <!-- <param id="cache">True</param> -->
+ <!-- <param id="transfer_threads">2</param> --></plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: data libraries: introduced three visible share states for datasets in libraries private(only the current users private role has access)/restricted(not private and not non-restricted)/non-restricted(there is not a single role in the access set of roles)
by commits-noreply＠bitbucket.org 07 May '14
by commits-noreply＠bitbucket.org 07 May '14
07 May '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/56d4cb37d627/
Changeset: 56d4cb37d627
User: martenson
Date: 2014-05-07 22:51:36
Summary: data libraries: introduced three visible share states for datasets in libraries private(only the current users private role has access)/restricted(not private and not non-restricted)/non-restricted(there is not a single role in the access set of roles)
also callback on modal hide() to call router and modify URL, some other minor fixes, pep8
Affected #: 14 files
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 lib/galaxy/security/__init__.py
--- a/lib/galaxy/security/__init__.py
+++ b/lib/galaxy/security/__init__.py
@@ -969,11 +969,37 @@
self.make_dataset_public( dataset )
def dataset_is_public( self, dataset ):
- # A dataset is considered public if there are no "access" actions associated with it. Any
- # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant.
- # SM: Accessing dataset.actions will cause a query to be emitted.
+ """
+ A dataset is considered public if there are no "access" actions
+ associated with it. Any other actions ( 'manage permissions',
+ 'edit metadata' ) are irrelevant. Accessing dataset.actions
+ will cause a query to be emitted.
+ """
return self.permitted_actions.DATASET_ACCESS.action not in [ a.action for a in dataset.actions ]
+ def dataset_is_unrestricted( self, trans, dataset):
+ """
+ Different implementation of the method above with signature:
+ def dataset_is_public( self, dataset )
+ """
+ return len( dataset.library_dataset_dataset_association.get_access_roles( trans ) ) == 0
+
+ def dataset_is_private_to_user( self, trans, dataset ):
+ """
+ If the dataset object has exactly one access role and that is the
+ current user's private role then we consider the dataset private.
+ """
+ private_role = self.get_private_user_role( trans.user )
+ access_roles = dataset.library_dataset_dataset_association.get_access_roles( trans )
+
+ if len(access_roles) != 1:
+ return False
+ else:
+ if access_roles[0].id == private_role.id:
+ return True
+ else:
+ return False
+
def datasets_are_public( self, trans, datasets ):
'''
Given a transaction object and a list of Datasets, return
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 lib/galaxy/webapps/galaxy/api/lda_datasets.py
--- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
@@ -12,12 +12,13 @@
import urllib
import urllib2
import zipfile
+from galaxy import web
+from galaxy import util
from galaxy import exceptions
-from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound
+from galaxy.exceptions import ObjectNotFound
+from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
from galaxy.web import _future_expose_api as expose_api
from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
-from galaxy import util
-from galaxy import web
from galaxy.security import Action
from galaxy.util.streamball import StreamBall
from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin
@@ -25,6 +26,7 @@
import logging
log = logging.getLogger( __name__ )
+
class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
@expose_api_anonymous
@@ -42,28 +44,25 @@
.. seealso:: :attr:`galaxy.web.base.controller.UsesLibraryMixinItems.get_library_dataset`
"""
try:
- dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True )
- except Exception, e:
+ dataset = self.get_library_dataset( trans, id=id, check_ownership=False, check_accessible=True )
+ except Exception:
raise exceptions.ObjectNotFound( 'Requested dataset was not found.' )
- rval = dataset.to_dict()
- rval['deleted'] = dataset.deleted
- rval['id'] = trans.security.encode_id(rval['id'])
- rval['ldda_id'] = trans.security.encode_id(rval['ldda_id'])
- rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id'])
- rval['folder_id'] = 'F' + trans.security.encode_id(rval['folder_id'])
+ rval = trans.security.encode_all_ids( dataset.to_dict() )
+ rval[ 'deleted' ] = dataset.deleted
+ rval[ 'folder_id' ] = 'F' + rval[ 'folder_id' ]
return rval
-
@expose_api
def delete( self, trans, encoded_dataset_id, **kwd ):
"""
delete( self, trans, encoded_dataset_id, **kwd ):
* DELETE /api/libraries/datasets/{encoded_dataset_id}
- Marks the dataset deleted.
+ Marks the dataset deleted or undeletes it based on the value
+ of the undelete flag (if present).
"""
undelete = util.string_as_bool( kwd.get( 'undelete', False ) )
try:
- dataset = self.get_library_dataset( trans, id = encoded_dataset_id, check_ownership=False, check_accessible=False )
+ dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False )
except Exception, e:
raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) )
current_user_roles = trans.get_current_user_roles()
@@ -79,21 +78,18 @@
trans.sa_session.add( dataset )
trans.sa_session.flush()
- rval = dataset.to_dict()
- rval['update_time'] = dataset.update_time.strftime( "%Y-%m-%d %I:%M %p" )
- rval['deleted'] = dataset.deleted
- rval['id'] = trans.security.encode_id(rval['id'])
- rval['ldda_id'] = trans.security.encode_id(rval['ldda_id'])
- rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id'])
- rval['folder_id'] = 'F' + trans.security.encode_id(rval['folder_id'])
+ rval = trans.security.encode_all_ids( dataset.to_dict() )
+ rval[ 'update_time' ] = dataset.update_time.strftime( "%Y-%m-%d %I:%M %p" )
+ rval[ 'deleted' ] = dataset.deleted
+ rval[ 'folder_id' ] = 'F' + rval[ 'folder_id' ]
return rval
-
@web.expose
def download( self, trans, format, **kwd ):
"""
download( self, trans, format, **kwd )
* GET /api/libraries/datasets/download/{format}
+ * POST /api/libraries/datasets/download/{format}
Downloads requested datasets (identified by encoded IDs) in requested format.
example: ``GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828``
@@ -111,33 +107,25 @@
:raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound
"""
lddas = []
- datasets_to_download = kwd['ldda_ids%5B%5D']
+ datasets_to_download = kwd[ 'ldda_ids%5B%5D' ]
- if ( datasets_to_download != None ):
+ if ( datasets_to_download is not None ):
datasets_to_download = util.listify( datasets_to_download )
for dataset_id in datasets_to_download:
try:
ldda = self.get_hda_or_ldda( trans, hda_ldda='ldda', dataset_id=dataset_id )
lddas.append( ldda )
- except ItemAccessibilityException:
- trans.response.status = 403
- return 'Insufficient rights to access library dataset with id: (%s)' % str( dataset_id )
- except MessageException:
- trans.response.status = 400
- return 'Wrong library dataset id: (%s)' % str( dataset_id )
- except ItemDeletionException:
- trans.response.status = 400
- return 'The item with library dataset id: (%s) is deleted' % str( dataset_id )
except HTTPBadRequest, e:
- return 'http bad request' + str( e.err_msg )
+ raise exceptions.RequestParameterInvalidException( 'Bad Request. ' + str( e.err_msg ) )
+ except HTTPInternalServerError, e:
+ raise exceptions.InternalServerError( 'Internal error. ' + str( e.err_msg ) )
except Exception, e:
- trans.response.status = 500
- return 'error of unknown kind' + str( e )
+ raise exceptions.InternalServerError( 'Unknown error. ' + str( e ) )
- if format in [ 'zip','tgz','tbz' ]:
+ if format in [ 'zip', 'tgz', 'tbz' ]:
# error = False
killme = string.punctuation + string.whitespace
- trantab = string.maketrans(killme,'_'*len(killme))
+ trantab = string.maketrans( killme, '_'*len( killme ) )
try:
outext = 'zip'
if format == 'zip':
@@ -149,7 +137,7 @@
archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True )
else:
archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
- archive.add = lambda x, y: archive.write( x, y.encode('CP437') )
+ archive.add = lambda x, y: archive.write( x, y.encode( 'CP437' ) )
elif format == 'tgz':
if trans.app.config.upstream_gzip:
archive = StreamBall( 'w|' )
@@ -162,12 +150,10 @@
outext = 'tbz2'
except ( OSError, zipfile.BadZipfile ):
log.exception( "Unable to create archive for download" )
- trans.response.status = 500
- return "Unable to create archive for download, please report this error"
- except:
- log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] )
- trans.response.status = 500
- return "Unable to create archive for download, please report - %s" % sys.exc_info()[0]
+ raise exceptions.InternalServerError( "Unable to create archive for download." )
+ except Exception:
+ log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[ 0 ] )
+ raise exceptions.InternalServerError( "Unable to create archive for download." )
composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
seen = []
for ldda in lddas:
@@ -178,7 +164,7 @@
while parent_folder is not None:
# Exclude the now-hidden "root folder"
if parent_folder.parent is None:
- path = os.path.join( parent_folder.library_root[0].name, path )
+ path = os.path.join( parent_folder.library_root[ 0 ].name, path )
break
path = os.path.join( parent_folder.name, path )
parent_folder = parent_folder.parent
@@ -186,87 +172,83 @@
while path in seen:
path += '_'
seen.append( path )
- zpath = os.path.split(path)[-1] # comes as base_name/fname
- outfname,zpathext = os.path.splitext(zpath)
- if is_composite: # need to add all the components from the extra_files_path to the zip
+ zpath = os.path.split(path)[ -1 ] # comes as base_name/fname
+ outfname, zpathext = os.path.splitext( zpath )
+
+ if is_composite: # need to add all the components from the extra_files_path to the zip
if zpathext == '':
- zpath = '%s.html' % zpath # fake the real nature of the html file
+ zpath = '%s.html' % zpath # fake the real nature of the html file
try:
- if format=='zip':
- archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set
- else:
- archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set
+ if format == 'zip':
+ archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set
+ else:
+ archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set
except IOError:
- log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name)
- trans.response.status = 500
- return "Unable to create archive for download, please report this error"
+ log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name )
+ raise exceptions.InternalServerError( "Unable to create archive for download." )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
- trans.response.status = 500
- return "Requested dataset does not exist on the host."
- except:
- trans.response.status = 500
- return "Unknown error, please report this error"
- flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths
+ raise exceptions.ObjectNotFound( "Requested dataset not found. " )
+ except Exception, e:
+ log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name )
+ raise exceptions.InternalServerError( "Unable to add composite parent to temporary library download archive. " + str( e ) )
+
+ flist = glob.glob(os.path.join(ldda.dataset.extra_files_path, '*.*')) # glob returns full paths
for fpath in flist:
- efp,fname = os.path.split(fpath)
+ efp, fname = os.path.split(fpath)
if fname > '':
fname = fname.translate(trantab)
try:
- if format=='zip':
- archive.add( fpath,fname )
+ if format == 'zip':
+ archive.add( fpath, fname )
else:
- archive.add( fpath,fname, check_file=True )
+ archive.add( fpath, fname, check_file=True )
except IOError:
- log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname))
- trans.response.status = 500
- return "Unable to create archive for download, please report this error"
+ log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname) )
+ raise exceptions.InternalServerError( "Unable to create archive for download." )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % fpath )
- trans.response.status = 500
- return "Requested dataset does not exist on the host."
- except:
- trans.response.status = 500
- return "Unknown error, please report this error"
- else: # simple case
+ raise exceptions.ObjectNotFound( "Requested dataset not found." )
+ except Exception, e:
+ log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname ) )
+ raise exceptions.InternalServerError( "Unable to add dataset to temporary library download archive . " + str( e ) )
+
+ else: # simple case
try:
- if format=='zip':
+ if format == 'zip':
archive.add( ldda.dataset.file_name, path )
else:
- archive.add( ldda.dataset.file_name, path, check_file=True )
+ archive.add( ldda.dataset.file_name, path, check_file=True )
except IOError:
- log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name)
- trans.response.status = 500
- return "Unable to create archive for download, please report this error"
+ log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name )
+ raise exceptions.InternalServerError( "Unable to create archive for download" )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
- trans.response.status = 500
- return "Requested dataset does not exist on the host."
- except:
- trans.response.status = 500
- return "Unknown error, please report this error"
+ raise exceptions.ObjectNotFound( "Requested dataset not found." )
+ except Exception, e:
+ log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname ) )
+ raise exceptions.InternalServerError( "Unknown error. " + str( e ) )
lname = 'selected_dataset'
fname = lname.replace( ' ', '_' ) + '_files'
if format == 'zip':
archive.close()
trans.response.set_content_type( "application/octet-stream" )
- trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext)
- archive = util.streamball.ZipBall(tmpf, tmpd)
+ trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % ( fname, outext )
+ archive = util.streamball.ZipBall( tmpf, tmpd )
archive.wsgi_status = trans.response.wsgi_status()
archive.wsgi_headeritems = trans.response.wsgi_headeritems()
return archive.stream
else:
trans.response.set_content_type( "application/x-tar" )
- trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext)
+ trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % ( fname, outext )
archive.wsgi_status = trans.response.wsgi_status()
archive.wsgi_headeritems = trans.response.wsgi_headeritems()
return archive.stream
elif format == 'uncompressed':
if len(lddas) != 1:
- trans.response.status = 400
- return 'Wrong request'
+ raise exceptions.RequestParameterInvalidException( "You can download only one uncompressed file at once." )
else:
- single_dataset = lddas[0]
+ single_dataset = lddas[ 0 ]
trans.response.set_content_type( single_dataset.get_mime() )
fStat = os.stat( ldda.file_name )
trans.response.headers[ 'Content-Length' ] = int( fStat.st_size )
@@ -277,8 +259,6 @@
try:
return open( single_dataset.file_name )
except:
- trans.response.status = 500
- return 'This dataset contains no content'
+ raise exceptions.InternalServerError( "This dataset contains no content." )
else:
- trans.response.status = 400
- return 'Wrong format parameter specified';
+ raise exceptions.RequestParameterInvalidException( "Wrong format parameter specified" )
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/galaxy.library.js
--- a/static/scripts/galaxy.library.js
+++ b/static/scripts/galaxy.library.js
@@ -106,12 +106,12 @@
});
this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){
- if (Galaxy.libraries.folderToolbarView){
- Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id, dataset_id: dataset_id});
- } else {
+ // if (Galaxy.libraries.folderToolbarView){
+ // Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id, dataset_id: dataset_id});
+ // } else {
Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id});
Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id, dataset_id: dataset_id});
- }
+ // }
});
Backbone.history.start({pushState: false});
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/mvc/library/library-folderlist-view.js
--- a/static/scripts/mvc/library/library-folderlist-view.js
+++ b/static/scripts/mvc/library/library-folderlist-view.js
@@ -283,21 +283,15 @@
},
makeDarkRow: function($row){
- $row.removeClass('light');
- $row.find('a').removeClass('light');
- $row.addClass('dark');
- $row.find('a').addClass('dark');
- $row.find('span').removeClass('fa-file-o');
- $row.find('span').addClass('fa-file');
+ $row.removeClass('light').addClass('dark');
+ $row.find('a').removeClass('light').addClass('dark');
+ $row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file');
},
makeWhiteRow: function($row){
- $row.removeClass('dark');
- $row.find('a').removeClass('dark');
- $row.addClass('light');
- $row.find('a').addClass('light');
- $row.find('span').addClass('fa-file-o');
- $row.find('span').removeClass('fa-file');
+ $row.removeClass('dark').addClass('light');
+ $row.find('a').removeClass('dark').addClass('light');
+ $row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o');
},
// MMMMMMMMMMMMMMMMMM
@@ -324,11 +318,11 @@
tmpl_array.push(' <thead>');
tmpl_array.push(' <th class="button_heading"></th>');
tmpl_array.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
- tmpl_array.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
- tmpl_array.push(' <th>data type</th>');
- tmpl_array.push(' <th>size</th>');
- tmpl_array.push(' <th>time updated (UTC)</th>');
- tmpl_array.push(' <th style="width:15%;"></th> ');
+ tmpl_array.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
+ tmpl_array.push(' <th style="width:5%;">data type</th>');
+ tmpl_array.push(' <th style="width:5%;">size</th>');
+ tmpl_array.push(' <th style="width:160px;">time updated (UTC)</th>');
+ tmpl_array.push(' <th style="width:10%;"></th> ');
tmpl_array.push(' </thead>');
tmpl_array.push(' <tbody id="folder_list_body">');
tmpl_array.push(' <tr id="first_folder_item">');
@@ -343,7 +337,7 @@
tmpl_array.push(' </tbody>');
tmpl_array.push('</table>');
- tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>');
+ tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');
return _.template(tmpl_array.join(''));
}
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/mvc/library/library-folderrow-view.js
--- a/static/scripts/mvc/library/library-folderrow-view.js
+++ b/static/scripts/mvc/library/library-folderrow-view.js
@@ -15,7 +15,6 @@
lastSelectedHistory: '',
events: {
- // 'click .library-dataset' : 'showDatasetDetails',
'click .undelete_dataset_btn' : 'undelete_dataset'
},
@@ -102,6 +101,10 @@
'Import' : function() { self.importCurrentIntoHistory(); },
'Download' : function() { self.downloadCurrent(); },
'Close' : function() { self.modal.hide(); }
+ },
+ closing_callback : function(){
+ var path_to_folder = Backbone.history.fragment.split('/datasets')[0];
+ Galaxy.libraries.library_router.navigate('#' + path_to_folder, {trigger:true, replace:true});
}
});
@@ -221,7 +224,7 @@
* bug in tooltip
*/
$(".tooltip").hide();
-
+ var that = this;
var dataset_id = $(event.target).closest('tr')[0].id;
var dataset = Galaxy.libraries.folderListView.collection.get(dataset_id);
dataset.url = dataset.urlRoot + dataset.id + '?undelete=true';
@@ -230,7 +233,7 @@
Galaxy.libraries.folderListView.collection.remove(dataset_id);
var updated_dataset = new mod_library_model.Item(response);
Galaxy.libraries.folderListView.collection.add(updated_dataset)
- mod_toastr.success('Dataset undeleted');
+ mod_toastr.success('Dataset undeleted. Click this to see it.', '', {onclick: function() {that.showDatasetDetails()}});
},
error : function(model, response){
if (typeof response.responseJSON !== "undefined"){
@@ -252,9 +255,9 @@
tmpl_array.push(' <td></td>');
tmpl_array.push(' <td>');
tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');
- tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder
- tmpl_array.push(' <span>(empty folder)</span>');
- tmpl_array.push(' <% } %>');
+ // tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder
+ // tmpl_array.push(' <span>(empty folder)</span>');
+ // tmpl_array.push(' <% } %>');
tmpl_array.push(' </td>');
tmpl_array.push(' <td>folder</td>');
tmpl_array.push(' <td></td>');
@@ -279,7 +282,12 @@
tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type
tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size
tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated
- tmpl_array.push(' <td></td>');
+ tmpl_array.push(' <td>');
+ tmpl_array.push(' <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');
+ tmpl_array.push(' <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');
+ tmpl_array.push(' <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-group fa-lg"></span>');
+ tmpl_array.push(' <% } %>');
+ tmpl_array.push(' </td>');
tmpl_array.push('</tr>');
return _.template(tmpl_array.join(''));
@@ -292,12 +300,12 @@
tmpl_array.push(' <td>');
tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');
tmpl_array.push(' </td>');
- tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span></td>');
+ tmpl_array.push(' <td></td>');
tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>'); // dataset
tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type
tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size
tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated
- tmpl_array.push(' <td class="right-center"><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button></td>');
+ tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');
tmpl_array.push('</tr>');
return _.template(tmpl_array.join(''));
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/mvc/library/library-librarylist-view.js
--- a/static/scripts/mvc/library/library-librarylist-view.js
+++ b/static/scripts/mvc/library/library-librarylist-view.js
@@ -149,7 +149,7 @@
tmpl_array.push('<div class="library_container table-responsive">');
tmpl_array.push('<% if(length === 0) { %>');
- tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');
+ tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');
tmpl_array.push('<% } else{ %>');
tmpl_array.push('<table class="grid table table-condensed">');
tmpl_array.push(' <thead>');
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/mvc/library/library-libraryrow-view.js
--- a/static/scripts/mvc/library/library-libraryrow-view.js
+++ b/static/scripts/mvc/library/library-libraryrow-view.js
@@ -245,7 +245,7 @@
tmpl_array.push(' <% } %>');
tmpl_array.push(' <td class="right-center">');
tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');
- tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');
+ tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');
tmpl_array.push(' <% }%>');
tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');
tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/mvc/library/library-librarytoolbar-view.js
--- a/static/scripts/mvc/library/library-librarytoolbar-view.js
+++ b/static/scripts/mvc/library/library-librarytoolbar-view.js
@@ -116,7 +116,6 @@
tmpl_array.push('<div class="library_style_container">');
// TOOLBAR
tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');
- tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');
tmpl_array.push(' <% if(admin_user === true) { %>');
tmpl_array.push(' <div id="library_toolbar">');
tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/packed/galaxy.library.js
--- a/static/scripts/packed/galaxy.library.js
+++ b/static/scripts/packed/galaxy.library.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#folder_list_body").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(n,m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderListView=new a.FolderListView({id:n,dataset_id:m})}else{Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:n});Galaxy.libraries.folderListView=new a.FolderListView({id:n,dataset_id:m})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#folder_list_body").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(n,m){Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:n});Galaxy.libraries.folderListView=new a.FolderListView({id:n,dataset_id:m})});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}});
\ No newline at end of file
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/packed/mvc/library/library-folderlist-view.js
--- a/static/scripts/packed/mvc/library/library-folderlist-view.js
+++ b/static/scripts/packed/mvc/library/library-folderlist-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},rowViews:{},initialize:function(g){this.options=_.defaults(this.options||{},g);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models);if(h.options.dataset_id){_.findWhere(h.rowViews,{id:h.options.dataset_id}).showDatasetDetails()}},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{f.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(g){this.options=_.defaults(this.options,g);var h=this.templateFolder();var i=this.folderContainer.attributes.metadata.full_path;var j;if(i.length===1){j=0}else{j=i[i.length-2][0]}this.$el.html(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:j,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var g=this.folderContainer.attributes.metadata;g.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(g);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});this.postRender()},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}h.set("folder_id",this.id);var g=new a.FolderRowView(h);this.rowViews[h.get("id")]=g;this.$el.find("#first_folder_item").after(g.el);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(g){this.$el.find("#"+g.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(' <th style="width:15%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>');return _.template(g.join(""))}});return{FolderListView:b}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},rowViews:{},initialize:function(g){this.options=_.defaults(this.options||{},g);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models);if(h.options.dataset_id){_.findWhere(h.rowViews,{id:h.options.dataset_id}).showDatasetDetails()}},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{f.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(g){this.options=_.defaults(this.options,g);var h=this.templateFolder();var i=this.folderContainer.attributes.metadata.full_path;var j;if(i.length===1){j=0}else{j=i[i.length-2][0]}this.$el.html(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:j,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var g=this.folderContainer.attributes.metadata;g.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(g);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});this.postRender()},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}h.set("folder_id",this.id);var g=new a.FolderRowView(h);this.rowViews[h.get("id")]=g;this.$el.find("#first_folder_item").after(g.el);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(g){this.$el.find("#"+g.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light").addClass("dark");g.find("a").removeClass("light").addClass("dark");g.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark").addClass("light");g.find("a").removeClass("dark").addClass("light");g.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(' <th style="width:5%;">data type</th>');g.push(' <th style="width:5%;">size</th>');g.push(' <th style="width:160px;">time updated (UTC)</th>');g.push(' <th style="width:10%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');return _.template(g.join(""))}});return{FolderListView:b}});
\ No newline at end of file
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/packed/mvc/library/library-folderrow-view.js
--- a/static/scripts/packed/mvc/library/library-folderrow-view.js
+++ b/static/scripts/packed/mvc/library/library-folderrow-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";if(f.get("deleted")){g=this.templateRowDeletedFile()}else{g=this.templateRowFile()}}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(){var i=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=i;var f=this;h.fetch({success:function(j){g.fetch({success:function(k){f.renderModalAfterFetch(j,k)},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error(k.responseJSON.err_msg)}else{e.error("An error occured during fetching histories:(")}f.renderModalAfterFetch(j)}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error occured during loading dataset details :(")}}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:k.get("name"),body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var i=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=i;var g=$("#id_row").attr("data-id");var j=new c.HistoryItem();var h=this;j.url=j.urlRoot+i+"/contents";var f="/api/histories/"+i+"/set_as_current";$.ajax({url:f,type:"PUT"});j.save({content:g,source:"library"},{success:function(){e.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}});h.modal.enableButton("Import");h.modal.enableButton("Download")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error("Dataset not imported. "+k.responseJSON.err_msg)}else{e.error("An error occured! Dataset not imported. Please try again.")}h.modal.enableButton("Import");h.modal.enableButton("Download")}})},undelete_dataset:function(g){$(".tooltip").hide();var f=$(g.target).closest("tr")[0].id;var h=Galaxy.libraries.folderListView.collection.get(f);h.url=h.urlRoot+h.id+"?undelete=true";h.destroy({success:function(j,i){Galaxy.libraries.folderListView.collection.remove(f);var k=new c.Item(i);Galaxy.libraries.folderListView.collection.add(k);e.success("Dataset undeleted")},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error("Dataset was not undeleted. "+i.responseJSON.err_msg)}else{e.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>');tmpl_array.push(" <span>(empty folder)</span>");tmpl_array.push(" <% } %>");tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span></td>');tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td class="right-center"><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")}});return{FolderRowView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";if(f.get("deleted")){g=this.templateRowDeletedFile()}else{g=this.templateRowFile()}}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(){var i=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=i;var f=this;h.fetch({success:function(j){g.fetch({success:function(k){f.renderModalAfterFetch(j,k)},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error(k.responseJSON.err_msg)}else{e.error("An error occured during fetching histories:(")}f.renderModalAfterFetch(j)}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error occured during loading dataset details :(")}}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:k.get("name"),body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}},closing_callback:function(){var l=Backbone.history.fragment.split("/datasets")[0];Galaxy.libraries.library_router.navigate("#"+l,{trigger:true,replace:true})}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var i=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=i;var g=$("#id_row").attr("data-id");var j=new c.HistoryItem();var h=this;j.url=j.urlRoot+i+"/contents";var f="/api/histories/"+i+"/set_as_current";$.ajax({url:f,type:"PUT"});j.save({content:g,source:"library"},{success:function(){e.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}});h.modal.enableButton("Import");h.modal.enableButton("Download")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error("Dataset not imported. "+k.responseJSON.err_msg)}else{e.error("An error occured! Dataset not imported. Please try again.")}h.modal.enableButton("Import");h.modal.enableButton("Download")}})},undelete_dataset:function(h){$(".tooltip").hide();var g=this;var f=$(h.target).closest("tr")[0].id;var i=Galaxy.libraries.folderListView.collection.get(f);i.url=i.urlRoot+i.id+"?undelete=true";i.destroy({success:function(k,j){Galaxy.libraries.folderListView.collection.remove(f);var l=new c.Item(j);Galaxy.libraries.folderListView.collection.add(l);e.success("Dataset undeleted. Click this to see it.","",{onclick:function(){g.showDatasetDetails()}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error("Dataset was not undeleted. "+j.responseJSON.err_msg)}else{e.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');tmpl_array.push(' <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-group fa-lg"></span>');tmpl_array.push(" <% } %>");tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")}});return{FolderRowView:a}});
\ No newline at end of file
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/packed/mvc/library/library-librarylist-view.js
--- a/static/scripts/packed/mvc/library/library-librarylist-view.js
+++ b/static/scripts/packed/mvc/library/library-librarylist-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){h.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);if(j.prepend){this.$el.find("#library_list_body").prepend(h.el)}else{this.$el.find("#library_list_body").append(h.el)}this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},});return{LibraryListView:f}});
\ No newline at end of file
+define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){h.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);if(j.prepend){this.$el.find("#library_list_body").prepend(h.el)}else{this.$el.find("#library_list_body").append(h.el)}this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},});return{LibraryListView:f}});
\ No newline at end of file
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/packed/mvc/library/library-libraryrow-view.js
--- a/static/scripts/packed/mvc/library/library-libraryrow-view.js
+++ b/static/scripts/packed/mvc/library/library-libraryrow-view.js
@@ -1,1 +1,1 @@
-define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},permissions_on_library:function(){d.info("Coming soon. Stay tuned.")},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){d.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}});
\ No newline at end of file
+define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},permissions_on_library:function(){d.info("Coming soon. Stay tuned.")},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){d.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}});
\ No newline at end of file
diff -r f09f01f2b21ed47f3dca5104ea6c00dfb6c77210 -r 56d4cb37d62700e5baa94cc63e56041556844c43 static/scripts/packed/mvc/library/library-librarytoolbar-view.js
--- a/static/scripts/packed/mvc/library/library-librarytoolbar-view.js
+++ b/static/scripts/packed/mvc/library/library-librarytoolbar-view.js
@@ -1,1 +1,1 @@
-define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured :(")}}})}else{b.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(d){return d.name!==""},check_include_deleted:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');tmpl_array.push(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}});
\ No newline at end of file
+define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured :(")}}})}else{b.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(d){return d.name!==""},check_include_deleted:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');tmpl_array.push(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}});
\ No newline at end of file
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