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commit/galaxy-central: carlfeberhard: UI, multi-history view: allow drag and drop copy of collections
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/60fb187429eb/ Changeset: 60fb187429eb User: carlfeberhard Date: 2015-02-13 21:50:54+00:00 Summary: UI, multi-history view: allow drag and drop copy of collections Affected #: 9 files diff -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 -r 60fb187429eb0204eddbc5d6f7187236bd091c97 client/galaxy/scripts/mvc/history/hdca-model.js --- a/client/galaxy/scripts/mvc/history/hdca-model.js +++ b/client/galaxy/scripts/mvc/history/hdca-model.js @@ -23,6 +23,10 @@ var HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend( /** @lends HistoryListDatasetCollection.prototype */{ + defaults : _.extend( _.clone( ListDC.prototype.defaults ), { + model_class : 'HistoryDatasetCollectionAssociation' + }), + initialize : function( model, options ){ ListDC.prototype.initialize.call( this, model, options ); hcontentMixin.initialize.call( this, model, options ); @@ -42,6 +46,10 @@ var HistoryPairDatasetCollection = PairDC.extend( hcontentMixin ).extend( /** @lends HistoryPairDatasetCollection.prototype */{ + defaults : _.extend( _.clone( PairDC.prototype.defaults ), { + model_class : 'HistoryDatasetCollectionAssociation' + }), + initialize : function( model, options ){ PairDC.prototype.initialize.call( this, model, options ); hcontentMixin.initialize.call( this, model, options ); @@ -61,6 +69,10 @@ var HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend( /** @lends HistoryListPairedDatasetCollection.prototype */{ + defaults : _.extend( _.clone( ListPairedDC.prototype.defaults ), { + model_class : 'HistoryDatasetCollectionAssociation' + }), + initialize : function( model, options ){ ListPairedDC.prototype.initialize.call( this, model, options ); hcontentMixin.initialize.call( this, model, options ); diff -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 -r 60fb187429eb0204eddbc5d6f7187236bd091c97 client/galaxy/scripts/mvc/history/history-contents.js --- a/client/galaxy/scripts/mvc/history/history-contents.js +++ b/client/galaxy/scripts/mvc/history/history-contents.js @@ -186,20 +186,23 @@ }, /** copy an existing, accessible hda into this collection */ - copy : function( id ){ -//TODO: incorp collections - var collection = this, - xhr = jQuery.post( this.url(), { - source : 'hda', + copy : function( id, contentType ){ + contentType = contentType || 'hda'; + var type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ), + collection = this; + + var xhr = jQuery.post( this.url(), { + type : type, + source : contentType, content : id + }) + .done( function( json ){ + collection.add([ json ]); + }) + .fail( function( error, status, message ){ + collection.trigger( 'error', collection, xhr, {}, + 'Error copying contents', { type: type, id: id, source: contentType }); }); - xhr.done( function( json ){ - collection.add([ json ]); - }); - xhr.fail( function( error, status, message ){ -//TODO: better distinction btwn not-allowed and actual ajax error - collection.trigger( 'error', collection, xhr, {}, 'Error copying dataset' ); - }); return xhr; }, diff -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 -r 60fb187429eb0204eddbc5d6f7187236bd091c97 client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -666,7 +666,11 @@ /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */ setUpColumnListeners : function setUpColumnListeners( column ){ - var multipanel = this; + var multipanel = this, + modelClassToSource = { + 'HistoryDatasetAssociation' : 'hda', + 'HistoryDatasetCollectionAssociation' : 'hdca' + }; multipanel.listenTo( column, { //'all': function(){ console.info( 'column ' + column + ':', arguments ) }, 'in-view': multipanel.queueHdaFetch @@ -684,17 +688,20 @@ multipanel.currentColumnDropTargetOff(); }, 'droptarget:drop': function( ev, data, panel ){ + //note: this will bad copy sources fail silently var toCopy = multipanel._dropData.filter( function( json ){ - return ( _.isObject( json ) && json.id && json.model_class === 'HistoryDatasetAssociation' ); + return ( ( _.isObject( json ) && json.id ) + && ( _.contains( _.keys( modelClassToSource ), json.model_class ) ) ); }); multipanel._dropData = null; var queue = new ajaxQueue.NamedAjaxQueue(); - toCopy.forEach( function( hda ){ + toCopy.forEach( function( content ){ + var contentType = modelClassToSource[ content.model_class ]; queue.add({ - name : 'copy-' + hda.id, + name : 'copy-' + content.id, fn : function(){ - return panel.model.contents.copy( hda.id ); + return panel.model.contents.copy( content.id, contentType ); } }); }); diff -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 -r 60fb187429eb0204eddbc5d6f7187236bd091c97 static/scripts/mvc/history/hdca-model.js --- a/static/scripts/mvc/history/hdca-model.js +++ b/static/scripts/mvc/history/hdca-model.js @@ -23,6 +23,10 @@ var HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend( /** @lends HistoryListDatasetCollection.prototype */{ + defaults : _.extend( _.clone( ListDC.prototype.defaults ), { + model_class : 'HistoryDatasetCollectionAssociation' + }), + initialize : function( model, options ){ ListDC.prototype.initialize.call( this, model, options ); hcontentMixin.initialize.call( this, model, options ); @@ -42,6 +46,10 @@ var HistoryPairDatasetCollection = PairDC.extend( hcontentMixin ).extend( /** @lends HistoryPairDatasetCollection.prototype */{ + defaults : _.extend( _.clone( PairDC.prototype.defaults ), { + model_class : 'HistoryDatasetCollectionAssociation' + }), + initialize : function( model, options ){ PairDC.prototype.initialize.call( this, model, options ); hcontentMixin.initialize.call( this, model, options ); @@ -61,6 +69,10 @@ var HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend( /** @lends HistoryListPairedDatasetCollection.prototype */{ + defaults : _.extend( _.clone( ListPairedDC.prototype.defaults ), { + model_class : 'HistoryDatasetCollectionAssociation' + }), + initialize : function( model, options ){ ListPairedDC.prototype.initialize.call( this, model, options ); hcontentMixin.initialize.call( this, model, options ); diff -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 -r 60fb187429eb0204eddbc5d6f7187236bd091c97 static/scripts/mvc/history/history-contents.js --- a/static/scripts/mvc/history/history-contents.js +++ b/static/scripts/mvc/history/history-contents.js @@ -186,20 +186,23 @@ }, /** copy an existing, accessible hda into this collection */ - copy : function( id ){ -//TODO: incorp collections - var collection = this, - xhr = jQuery.post( this.url(), { - source : 'hda', + copy : function( id, contentType ){ + contentType = contentType || 'hda'; + var type = ( contentType === 'hdca'? 'dataset_collection' : 'dataset' ), + collection = this; + + var xhr = jQuery.post( this.url(), { + type : type, + source : contentType, content : id + }) + .done( function( json ){ + collection.add([ json ]); + }) + .fail( function( error, status, message ){ + collection.trigger( 'error', collection, xhr, {}, + 'Error copying contents', { type: type, id: id, source: contentType }); }); - xhr.done( function( json ){ - collection.add([ json ]); - }); - xhr.fail( function( error, status, message ){ -//TODO: better distinction btwn not-allowed and actual ajax error - collection.trigger( 'error', collection, xhr, {}, 'Error copying dataset' ); - }); return xhr; }, diff -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 -r 60fb187429eb0204eddbc5d6f7187236bd091c97 static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -666,7 +666,11 @@ /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */ setUpColumnListeners : function setUpColumnListeners( column ){ - var multipanel = this; + var multipanel = this, + modelClassToSource = { + 'HistoryDatasetAssociation' : 'hda', + 'HistoryDatasetCollectionAssociation' : 'hdca' + }; multipanel.listenTo( column, { //'all': function(){ console.info( 'column ' + column + ':', arguments ) }, 'in-view': multipanel.queueHdaFetch @@ -684,17 +688,20 @@ multipanel.currentColumnDropTargetOff(); }, 'droptarget:drop': function( ev, data, panel ){ + //note: this will bad copy sources fail silently var toCopy = multipanel._dropData.filter( function( json ){ - return ( _.isObject( json ) && json.id && json.model_class === 'HistoryDatasetAssociation' ); + return ( ( _.isObject( json ) && json.id ) + && ( _.contains( _.keys( modelClassToSource ), json.model_class ) ) ); }); multipanel._dropData = null; var queue = new ajaxQueue.NamedAjaxQueue(); - toCopy.forEach( function( hda ){ + toCopy.forEach( function( content ){ + var contentType = modelClassToSource[ content.model_class ]; queue.add({ - name : 'copy-' + hda.id, + name : 'copy-' + content.id, fn : function(){ - return panel.model.contents.copy( hda.id ); + return panel.model.contents.copy( content.id, contentType ); } }); }); diff -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 -r 60fb187429eb0204eddbc5d6f7187236bd091c97 static/scripts/packed/mvc/history/hdca-model.js --- a/static/scripts/packed/mvc/history/hdca-model.js +++ b/static/scripts/packed/mvc/history/hdca-model.js @@ -1,1 +1,1 @@ -define(["mvc/collection/collection-model","mvc/history/history-content-model","utils/localization"],function(c,i,a){var g=i.HistoryContentMixin,h=c.ListDatasetCollection,j=c.PairDatasetCollection,f=c.ListPairedDatasetCollection;var d=h.extend(g).extend({initialize:function(l,k){h.prototype.initialize.call(this,l,k);g.initialize.call(this,l,k)},toString:function(){return(["HistoryListDatasetCollection(",this.get("name"),")"].join(""))}});var e=j.extend(g).extend({initialize:function(l,k){j.prototype.initialize.call(this,l,k);g.initialize.call(this,l,k)},toString:function(){return(["HistoryPairDatasetCollection(",this.get("name"),")"].join(""))}});var b=f.extend(g).extend({initialize:function(l,k){f.prototype.initialize.call(this,l,k);g.initialize.call(this,l,k)},toString:function(){return(["HistoryListPairedDatasetCollection(",this.get("name"),")"].join(""))}});return{HistoryListDatasetCollection:d,HistoryPairDatasetCollection:e,HistoryListPairedDatasetCollection:b}}); \ No newline at end of file +define(["mvc/collection/collection-model","mvc/history/history-content-model","utils/localization"],function(c,i,a){var g=i.HistoryContentMixin,h=c.ListDatasetCollection,j=c.PairDatasetCollection,f=c.ListPairedDatasetCollection;var d=h.extend(g).extend({defaults:_.extend(_.clone(h.prototype.defaults),{model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(l,k){h.prototype.initialize.call(this,l,k);g.initialize.call(this,l,k)},toString:function(){return(["HistoryListDatasetCollection(",this.get("name"),")"].join(""))}});var e=j.extend(g).extend({defaults:_.extend(_.clone(j.prototype.defaults),{model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(l,k){j.prototype.initialize.call(this,l,k);g.initialize.call(this,l,k)},toString:function(){return(["HistoryPairDatasetCollection(",this.get("name"),")"].join(""))}});var b=f.extend(g).extend({defaults:_.extend(_.clone(f.prototype.defaults),{model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(l,k){f.prototype.initialize.call(this,l,k);g.initialize.call(this,l,k)},toString:function(){return(["HistoryListPairedDatasetCollection(",this.get("name"),")"].join(""))}});return{HistoryListDatasetCollection:d,HistoryPairDatasetCollection:e,HistoryListPairedDatasetCollection:b}}); \ No newline at end of file diff -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 -r 60fb187429eb0204eddbc5d6f7187236bd091c97 static/scripts/packed/mvc/history/history-contents.js --- a/static/scripts/packed/mvc/history/history-contents.js +++ b/static/scripts/packed/mvc/history/history-contents.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},copy:function(j){var i=this,h=jQuery.post(this.url(),{source:"hda",content:j});h.done(function(k){i.add([k])});h.fail(function(l,k,m){i.trigger("error",i,h,{},"Error copying dataset")});return h},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){this.debug("set:",j);var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=_.clone(o.attributes);_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},clone:function(){var h=Backbone.Collection.prototype.clone.call(this);h.historyId=this.historyId;return h},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file +define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},copy:function(l,k){k=k||"hda";var h=(k==="hdca"?"dataset_collection":"dataset"),j=this;var i=jQuery.post(this.url(),{type:h,source:k,content:l}).done(function(m){j.add([m])}).fail(function(n,m,o){j.trigger("error",j,i,{},"Error copying contents",{type:h,id:l,source:k})});return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){this.debug("set:",j);var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=_.clone(o.attributes);_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},clone:function(){var h=Backbone.Collection.prototype.clone.call(this);h.historyId=this.historyId;return h},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file diff -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 -r 60fb187429eb0204eddbc5d6f7187236bd091c97 static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(C),this.controlsRightTemplate(C),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"history"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"history"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-panel-history",initialize:function c(C){C=C||{};this.log(this+".init",C);this.$el.addClass(this.className);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);if(this.$(".more-options").is(":visible")){this.$(".open-more-options.btn").popover("show")}this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){return this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<button class="open-more-options btn btn-default">','<span class="fa fa-ellipsis-h" title="More options"></span>',"</button>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(C),this.controlsRightTemplate(C),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"history"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"history"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-panel-history",initialize:function c(C){C=C||{};this.log(this+".init",C);this.$el.addClass(this.className);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);if(this.$(".more-options").is(":visible")){this.$(".open-more-options.btn").popover("show")}this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(D){var E=this,C={HistoryDatasetAssociation:"hda",HistoryDatasetCollectionAssociation:"hdca"};E.listenTo(D,{"in-view":E.queueHdaFetch});E.listenTo(D.panel,{"view:draggable:dragstart":function(I,G,F,H){E._dropData=JSON.parse(I.dataTransfer.getData("text"));E.currentColumnDropTargetOn()},"view:draggable:dragend":function(I,G,F,H){E._dropData=null;E.currentColumnDropTargetOff()},"droptarget:drop":function(H,I,G){var J=E._dropData.filter(function(K){return((_.isObject(K)&&K.id)&&(_.contains(_.keys(C),K.model_class)))});E._dropData=null;var F=new a.NamedAjaxQueue();J.forEach(function(K){var L=C[K.model_class];F.add({name:"copy-"+K.id,fn:function(){return G.model.contents.copy(K.id,L)}})});F.start();F.done(function(K){G.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){return this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<button class="open-more-options btn btn-default">','<span class="fa fa-ellipsis-h" title="More options"></span>',"</button>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/74aa8a401390/ Changeset: 74aa8a401390 User: dannon Date: 2015-02-13 20:03:33+00:00 Summary: Change external display application reloading to use the internal queue and reflect appropriately to other processes. Affected #: 2 files diff -r 3fdbd1437678b2e3edd24b14a2658c5ec1a7dcb3 -r 74aa8a401390cd53ef04d836303c121d01a1f087 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -102,6 +102,12 @@ log.error("Reload tool invoked without tool id.") +def reload_display_application(app, **kwargs): + display_application_ids = kwargs.get('display_application_ids', None) + log.debug("Executing display application reload task for %s" % display_application_ids) + app.datatypes_registry.reload_display_applications( display_application_ids) + + def reload_tool_data_tables(app, **kwargs): params = util.Params(kwargs) log.debug("Executing tool data table reload for %s" % params.get('table_names', 'all tables')) @@ -118,5 +124,6 @@ % (job_lock, "not" if job_lock else "now")) control_message_to_task = { 'reload_tool': reload_tool, + 'reload_display_application': reload_display_application, 'reload_tool_data_tables': reload_tool_data_tables, 'admin_job_lock': admin_job_lock} diff -r 3fdbd1437678b2e3edd24b14a2658c5ec1a7dcb3 -r 74aa8a401390cd53ef04d836303c121d01a1f087 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -2,6 +2,7 @@ import logging import os +import galaxy.queue_worker import galaxy.util from galaxy import model from galaxy.model import tool_shed_install as install_model @@ -892,6 +893,10 @@ @web.expose @web.require_admin def reload_display_application( self, trans, **kwd ): + galaxy.queue_worker.send_control_task(trans, + 'reload_display_application', + noop_self=True, + kwargs={'display_application_ids': kwd.get( 'id' )} ) reloaded, failed = trans.app.datatypes_registry.reload_display_applications( kwd.get( 'id' ) ) if not reloaded and failed: return trans.show_error_message( 'Unable to reload any of the %i requested display applications ("%s").' % ( len( failed ), '", "'.join( failed ) ) ) https://bitbucket.org/galaxy/galaxy-central/commits/7179d35d2a99/ Changeset: 7179d35d2a99 User: dannon Date: 2015-02-13 20:03:44+00:00 Summary: Merge. Affected #: 2 files diff -r 74aa8a401390cd53ef04d836303c121d01a1f087 -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1414,7 +1414,7 @@ .ui-table tbody,.ui-table-plain tbody{cursor:pointer} .ui-table-plain{table-layout:fixed}.ui-table-plain tbody{cursor:auto !important}.ui-table-plain tbody td{padding:0px !important;border:none !important} .ui-table-plain .ui-table-section{border-left:solid 3px #ebd9b2;border-radius:5px !important;margin-bottom:5px;padding-left:10px} -.ui-table-form-element{margin-top:5px;margin-bottom:5px}.ui-table-form-element .ui-table-form-title-optional{font-weight:bold;text-decoration:underline;cursor:pointer} +.ui-table-form-element{margin-top:5px;margin-bottom:5px;overflow:hidden}.ui-table-form-element .ui-table-form-title-optional{font-weight:bold;text-decoration:underline;cursor:pointer} .ui-table-form-element .ui-table-form-field{margin-top:5px} .ui-table-form-title-strong{font-weight:bold} .ui-table-form-info{clear:both !important} @@ -1456,8 +1456,8 @@ .ui-color-picker .ui-color-picker-header{cursor:pointer} .ui-color-picker .ui-color-picker-value{float:left;border-radius:3px;border:solid 1px #000000;width:12px;height:12px;margin-bottom:10px;margin-right:5px} .ui-color-picker .ui-color-picker-label{float:left;line-height:1.2em} -.ui-color-picker .ui-color-picker-view{height:100%;overflow:auto;display:none;float:left}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel{height:100%;overflow:auto;width:230px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content{clear:both;margin-bottom:15px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .label{padding-bottom:2px} -.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line{clear:both}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box{cursor:pointer;float:left;margin-right:5px;border:solid 1px #c0c0c0;width:15px;height:15px;border-radius:2px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box .ui-color-picker-check{color:black;font-size:1.2em;position:relative;left:1px} +.ui-color-picker .ui-color-picker-view{display:none;float:left;overflow:auto;height:100%}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel{width:210px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content{margin-bottom:15px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .label{padding-bottom:2px} +.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box{cursor:pointer;float:left;margin-right:5px;border:solid 1px #c0c0c0;width:15px;height:15px;border-radius:2px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box .ui-color-picker-check{color:black;font-size:1.2em;position:relative;left:1px} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} diff -r 74aa8a401390cd53ef04d836303c121d01a1f087 -r 7179d35d2a998d960aeac03b3755ff1f64e118d7 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -152,6 +152,7 @@ } margin-top: @ui-margin-vertical; margin-bottom: @ui-margin-vertical; + overflow: hidden; } .ui-table-form-title-strong { @@ -465,17 +466,13 @@ display: none; float: left; .ui-color-picker-panel { - height: 100%; - overflow: auto; - width: 230px; + width: 210px; .ui-color-picker-content { - clear: both; margin-bottom: 15px; .label { padding-bottom: 2px; } .line { - clear: both; .ui-color-picker-box { cursor: pointer; float: left; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Ui: Adjust styles
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/960e7e1d2967/ Changeset: 960e7e1d2967 User: guerler Date: 2015-02-13 20:00:23+00:00 Summary: Ui: Adjust styles Affected #: 2 files diff -r 3fdbd1437678b2e3edd24b14a2658c5ec1a7dcb3 -r 960e7e1d2967b87950cd4cbb45b7956c38d0497c static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1414,7 +1414,7 @@ .ui-table tbody,.ui-table-plain tbody{cursor:pointer} .ui-table-plain{table-layout:fixed}.ui-table-plain tbody{cursor:auto !important}.ui-table-plain tbody td{padding:0px !important;border:none !important} .ui-table-plain .ui-table-section{border-left:solid 3px #ebd9b2;border-radius:5px !important;margin-bottom:5px;padding-left:10px} -.ui-table-form-element{margin-top:5px;margin-bottom:5px}.ui-table-form-element .ui-table-form-title-optional{font-weight:bold;text-decoration:underline;cursor:pointer} +.ui-table-form-element{margin-top:5px;margin-bottom:5px;overflow:hidden}.ui-table-form-element .ui-table-form-title-optional{font-weight:bold;text-decoration:underline;cursor:pointer} .ui-table-form-element .ui-table-form-field{margin-top:5px} .ui-table-form-title-strong{font-weight:bold} .ui-table-form-info{clear:both !important} @@ -1456,8 +1456,8 @@ .ui-color-picker .ui-color-picker-header{cursor:pointer} .ui-color-picker .ui-color-picker-value{float:left;border-radius:3px;border:solid 1px #000000;width:12px;height:12px;margin-bottom:10px;margin-right:5px} .ui-color-picker .ui-color-picker-label{float:left;line-height:1.2em} -.ui-color-picker .ui-color-picker-view{height:100%;overflow:auto;display:none;float:left}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel{height:100%;overflow:auto;width:230px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content{clear:both;margin-bottom:15px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .label{padding-bottom:2px} -.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line{clear:both}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box{cursor:pointer;float:left;margin-right:5px;border:solid 1px #c0c0c0;width:15px;height:15px;border-radius:2px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box .ui-color-picker-check{color:black;font-size:1.2em;position:relative;left:1px} +.ui-color-picker .ui-color-picker-view{display:none;float:left;overflow:auto;height:100%}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel{width:210px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content{margin-bottom:15px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .label{padding-bottom:2px} +.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box{cursor:pointer;float:left;margin-right:5px;border:solid 1px #c0c0c0;width:15px;height:15px;border-radius:2px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box .ui-color-picker-check{color:black;font-size:1.2em;position:relative;left:1px} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} diff -r 3fdbd1437678b2e3edd24b14a2658c5ec1a7dcb3 -r 960e7e1d2967b87950cd4cbb45b7956c38d0497c static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -152,6 +152,7 @@ } margin-top: @ui-margin-vertical; margin-bottom: @ui-margin-vertical; + overflow: hidden; } .ui-table-form-title-strong { @@ -465,17 +466,13 @@ display: none; float: left; .ui-color-picker-panel { - height: 100%; - overflow: auto; - width: 230px; + width: 210px; .ui-color-picker-content { - clear: both; margin-bottom: 15px; .label { padding-bottom: 2px; } .line { - clear: both; .ui-color-picker-box { cursor: pointer; float: left; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Mask password from connection log in queue worker.
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3fdbd1437678/ Changeset: 3fdbd1437678 User: dannon Date: 2015-02-13 19:15:22+00:00 Summary: Mask password from connection log in queue worker. Affected #: 1 file diff -r 586064ce6704b93685f93230dc788aeda0160d41 -r 3fdbd1437678b2e3edd24b14a2658c5ec1a7dcb3 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -20,7 +20,7 @@ from kombu.mixins import ConsumerMixin from kombu.pools import producers - +logging.getLogger('kombu').setLevel(logging.WARNING) log = logging.getLogger(__name__) @@ -32,7 +32,7 @@ """ def __init__(self, app, queue, task_mapping, connection=None): super(GalaxyQueueWorker, self).__init__() - log.info("Initalizing Galaxy Queue Worker on %s", app.config.amqp_internal_connection) + log.info("Initalizing Galaxy Queue Worker on %s", util.mask_password_from_url(app.config.amqp_internal_connection)) if connection: self.connection = connection else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: UI, multi-history: move styles from mako to less
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/586064ce6704/ Changeset: 586064ce6704 User: carlfeberhard Date: 2015-02-13 19:00:42+00:00 Summary: UI, multi-history: move styles from mako to less Affected #: 6 files diff -r 0f69ba9bccae59f5a8f204573bdd8a4a9749231c -r 586064ce6704b93685f93230dc788aeda0160d41 client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -37,7 +37,7 @@ .css( 'margin-top', '8px' ); Galaxy.modal.$( '.modal-body' ).append( $copyIndicator ); history.copy( true, name ) -//TODO: make this unneccessary with pub-sub error + //TODO: make this unneccessary with pub-sub error .fail( function(){ alert( _l( 'History could not be copied. Please contact a Galaxy administrator' ) ); }) @@ -329,7 +329,7 @@ controlsRightTemplate : _.template([ '<div class="pull-right">', '<% if( !history.purged ){ %>', - '<div class="panel-menu order btn-group">', + '<div class="panel-menu btn-group">', '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', '<span class="caret"></span>', '</button>', @@ -372,7 +372,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ //logger : console, - className : 'multi-history-columns', + className : 'multi-panel-history', // ------------------------------------------------------------------------ set up /** Set up internals, history collection, and columns to display the history */ @@ -380,6 +380,9 @@ options = options || {}; this.log( this + '.init', options ); + // add the className here (since we gen. pass the el in options) + this.$el.addClass( this.className ); + // --- instance vars if( !options.currentHistoryId ){ throw new Error( this + ' requires a currentHistoryId in the options' ); @@ -549,7 +552,11 @@ this.collection.comparator = function __comparator( a, b ){ return sortOrder.fn( a, b, currentHistoryId ); }; + // set the sort order text this.$( '.current-order' ).text( sortOrder.text ); + if( this.$( '.more-options' ).is( ':visible' ) ){ + this.$( '.open-more-options.btn' ).popover( 'show' ); + } //NOTE: auto fires 'sort' from collection this.collection.sort( options ); @@ -815,7 +822,7 @@ /** put a text msg in the header */ renderInfo : function( msg ){ - this.$( '.header .header-info' ).text( msg ); + return this.$( '.header .header-info' ).text( msg ); }, // ------------------------------------------------------------------------ events/behaviors @@ -1061,7 +1068,6 @@ optionsPopoverTemplate : _.template([ '<div class="more-options">', - '<div class="order btn-group">', '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', _l( 'Order histories by' ) + ' ', diff -r 0f69ba9bccae59f5a8f204573bdd8a4a9749231c -r 586064ce6704b93685f93230dc788aeda0160d41 static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -37,7 +37,7 @@ .css( 'margin-top', '8px' ); Galaxy.modal.$( '.modal-body' ).append( $copyIndicator ); history.copy( true, name ) -//TODO: make this unneccessary with pub-sub error + //TODO: make this unneccessary with pub-sub error .fail( function(){ alert( _l( 'History could not be copied. Please contact a Galaxy administrator' ) ); }) @@ -329,7 +329,7 @@ controlsRightTemplate : _.template([ '<div class="pull-right">', '<% if( !history.purged ){ %>', - '<div class="panel-menu order btn-group">', + '<div class="panel-menu btn-group">', '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', '<span class="caret"></span>', '</button>', @@ -372,7 +372,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ //logger : console, - className : 'multi-history-columns', + className : 'multi-panel-history', // ------------------------------------------------------------------------ set up /** Set up internals, history collection, and columns to display the history */ @@ -380,6 +380,9 @@ options = options || {}; this.log( this + '.init', options ); + // add the className here (since we gen. pass the el in options) + this.$el.addClass( this.className ); + // --- instance vars if( !options.currentHistoryId ){ throw new Error( this + ' requires a currentHistoryId in the options' ); @@ -549,7 +552,11 @@ this.collection.comparator = function __comparator( a, b ){ return sortOrder.fn( a, b, currentHistoryId ); }; + // set the sort order text this.$( '.current-order' ).text( sortOrder.text ); + if( this.$( '.more-options' ).is( ':visible' ) ){ + this.$( '.open-more-options.btn' ).popover( 'show' ); + } //NOTE: auto fires 'sort' from collection this.collection.sort( options ); @@ -815,7 +822,7 @@ /** put a text msg in the header */ renderInfo : function( msg ){ - this.$( '.header .header-info' ).text( msg ); + return this.$( '.header .header-info' ).text( msg ); }, // ------------------------------------------------------------------------ events/behaviors @@ -1061,7 +1068,6 @@ optionsPopoverTemplate : _.template([ '<div class="more-options">', - '<div class="order btn-group">', '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', _l( 'Order histories by' ) + ' ', diff -r 0f69ba9bccae59f5a8f204573bdd8a4a9749231c -r 586064ce6704b93685f93230dc788aeda0160d41 static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(C),this.controlsRightTemplate(C),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"history"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !history.purged ){ %>",'<div class="panel-menu order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"history"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-history-columns",initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<button class="open-more-options btn btn-default">','<span class="fa fa-ellipsis-h" title="More options"></span>',"</button>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(C),this.controlsRightTemplate(C),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"history"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"history"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-panel-history",initialize:function c(C){C=C||{};this.log(this+".init",C);this.$el.addClass(this.className);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);if(this.$(".more-options").is(":visible")){this.$(".open-more-options.btn").popover("show")}this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){return this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<button class="open-more-options btn btn-default">','<span class="fa fa-ellipsis-h" title="More options"></span>',"</button>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file diff -r 0f69ba9bccae59f5a8f204573bdd8a4a9749231c -r 586064ce6704b93685f93230dc788aeda0160d41 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2097,6 +2097,34 @@ .annotated-history-panel table.list-items>tbody>tr>td>.list-item{border:0px} .annotated-history-panel .empty-message{margin-top:8px} .current-history-panel .list-item.history-content.current-content{border-left:5px solid #4E5777} +.multi-panel-history{display:flex;flex-direction:column;}.multi-panel-history .flex-row-container,.multi-panel-history .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;min-width:0px;min-height:0px;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch;-webkit-justify-content:flex-start;-ms-flex-pack:start;justify-content:flex-start} +.multi-panel-history .flex-row-container{-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column} +.multi-panel-history .flex-column-container{-webkit-flex-direction:row;-ms-flex-direction:row;flex-direction:row} +.multi-panel-history .flex-row,.multi-panel-history .flex-column{-webkit-flex:1 1 auto;-ms-flex:1 1 auto;flex:1 1 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto} +.multi-panel-history .header,.multi-panel-history .footer{width:100%;background-color:lightgrey}.multi-panel-history .header .btn,.multi-panel-history .footer .btn{height:21px} +.multi-panel-history .header{min-height:29px;max-height:29px} +.multi-panel-history .footer{min-height:0;max-height:0} +.multi-panel-history .smaller-btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px} +.multi-panel-history .control-column{margin-top:4px}.multi-panel-history .control-column .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px} +.multi-panel-history .control-column .search-control{display:inline-block;width:40%}.multi-panel-history .control-column .search-control .search-clear,.multi-panel-history .control-column .search-control .search-loading{margin-top:-22px} +.multi-panel-history .control-column input.search-query{font-size:90%;height:21px;line-height:normal;padding:2px 2px 1px 2px} +.multi-panel-history .control-column .open-more-options{padding:2px 6px 2px 6px;font-size:100%} +.multi-panel-history .control-column .more-options input[type=checkbox]{margin-top:2px} +.multi-panel-history .control-column .header-info{display:inline-block;padding:2px 4px 2px 4px;color:grey} +.multi-panel-history .control-column.control-column-right,.multi-panel-history .control-column.control-column-left{margin-right:8px;margin-left:8px}.multi-panel-history .control-column.control-column-right>*,.multi-panel-history .control-column.control-column-left>*{margin:0px 4px 4px 0px} +.multi-panel-history .control-column.control-column-center{text-align:center;max-height:22px;-webkit-flex:0 1 auto;-ms-flex:0 1 auto;flex:0 1 auto;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;max-height:22px} +.multi-panel-history .control-column.control-column-right{text-align:right} +.multi-panel-history .outer-middle{overflow:auto} +.multi-panel-history .middle{min-width:100%;margin:0px 0px 0px 0px;background-color:white;padding:8px} +.multi-panel-history .history-column{width:312px;margin:0 8px 0 0}.multi-panel-history .history-column:first-child{position:fixed;z-index:2}.multi-panel-history .history-column:first-child .history-panel{border:1px solid black;box-shadow:4px 4px 4px rgba(96,96,96,0.3)} +.multi-panel-history .history-column:nth-child(2){margin-left:320px} +.multi-panel-history .history-column:last-child{margin-right:0px} +.multi-panel-history .history-column .panel-controls{width:100%;height:24px;border-radius:3px;background-color:white;text-align:center;flex:0 0 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}.multi-panel-history .history-column .panel-controls .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px} +.multi-panel-history .history-column .panel-controls .pull-left .btn{margin-right:4px} +.multi-panel-history .history-column .panel-controls .pull-right .btn{margin-left:4px} +.multi-panel-history .history-column .panel-controls .panel-menu{z-index:1}.multi-panel-history .history-column .panel-controls .panel-menu .dropdown-menu a{text-align:left} +.multi-panel-history .history-column .panel-controls .current-label{display:inline-block;color:grey;padding-left:2px;margin-top:2px} +.multi-panel-history .history-column .history-panel{width:100%;border:1px solid #808080;border-radius:3px;background-color:#DFE5F9;overflow:auto} body.historyPage{background:#dfe5f9;color:#000;margin:5px;border:0;padding:0} div.historyLinks{margin:5px 5px} div.historyItem{margin:0 -5px;padding:8px 10px;border-top:solid #bfbfbf 1px;border-right:none;word-wrap:break-word;background:#eee}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat} diff -r 0f69ba9bccae59f5a8f204573bdd8a4a9749231c -r 586064ce6704b93685f93230dc788aeda0160d41 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -579,6 +579,235 @@ } +// ---------------------------------------------------------------------------- multi-view / multi-panel +.multi-panel-history { + @mph-column_width: 312px; + @mph-border_width: 1px; + @mph-column_gap: 8px; + @mph-header_height: 29px; + @mph-footer_height: 0; + @mph-controls_height: 20px; + + // for some reason, .flex-row-container below won't be applied to multi-panel-history since it's the enclosing node + // re-apply here + display: flex; + flex-direction: column; + + .flex-row-container, + .flex-column-container { + display: -webkit-box; + display: -webkit-flex; + display: -ms-flexbox; + display: flex; + + /* force ff to squish beyond content: + https://developer.mozilla.org/en-US/Firefox/Releases/34/Site_Compatibility#… */ + min-width: 0px; + min-height: 0px; + + -webkit-align-items: stretch; + -ms-align-items: stretch; + align-items: stretch; + + -webkit-align-content: stretch; + -ms-align-content: stretch; + align-content: stretch; + + -webkit-justify-content: flex-start; + -ms-flex-pack: start; + justify-content: flex-start; + } + .flex-row-container { + -webkit-flex-direction: column; + -ms-flex-direction: column; + flex-direction: column; + } + .flex-column-container { + -webkit-flex-direction: row; + -ms-flex-direction: row; + flex-direction: row; + } + .flex-row, + .flex-column { + -webkit-flex: 1 1 auto; + -ms-flex: 1 1 auto; + flex: 1 1 auto; + + -webkit-align-self: auto; + -ms-flex-item-align: auto; + align-self: auto; + } + + /* ---------------------- header & footer */ + .header, + .footer { + width: 100%; + background-color: lightgrey; + .btn { + height: 21px; + } + } + .header { + min-height: @mph-header_height; + max-height: @mph-header_height; + } + .footer { + min-height: @mph-footer_height; + max-height: @mph-footer_height; + } + + // make the buttons in the header/footers and the panel controls slightly smaller + .smaller-btn { + height: 20px; + line-height: normal; + font-size: 90%; + padding-top: 0px; + padding-bottom: 0px; + } + + // the header/footers controls + .control-column { + margin-top: 4px; + + .btn { + .smaller-btn; + } + .search-control { + display: inline-block; + width: 40%; + + .search-clear, + .search-loading { + margin-top: -22px; + } + } + input.search-query { + font-size: 90%; + height: 21px; + line-height: normal; + padding: 2px 2px 1px 2px; + } + .open-more-options { + padding: 2px 6px 2px 6px; + font-size: 100%; + } + .more-options input[type=checkbox] { + margin-top: 2px; + } + .header-info { + display: inline-block; + padding: 2px 4px 2px 4px; + color: grey; + } + + &.control-column-right, + &.control-column-left { + margin-right: 8px; + margin-left: 8px; + & > * { + margin: 0px 4px 4px 0px; + } + } + &.control-column-center { + text-align: center; + max-height: 22px; + -webkit-flex: 0 1 auto; + -ms-flex: 0 1 auto; + flex: 0 1 auto; + + /* truncate */ + overflow: hidden; + text-overflow: ellipsis; + white-space: nowrap; + max-height: 22px; + } + &.control-column-right { + text-align: right; + } + } + + /* ---------------------- middle */ + .outer-middle { + overflow: auto; + } + .middle { + min-width: 100%; + margin: 0px 0px 0px 0px; + background-color: white; + padding: @mph-column_gap; + } + + .history-column { + width: @mph-column_width; + margin: 0px @mph-column_gap 0px 0px; + + // current history + &:first-child { + position: fixed; + z-index : 2; + + // visually differentiate the current history + .history-panel { + border: 1px solid black; + box-shadow: 4px 4px 4px rgba( 96, 96, 96, 0.3 ); + } + } + &:nth-child(2) { + // push the column after the current away from the left (since it's fixed) + margin-left: ( @mph-column_width + @mph-column_gap ); + } + &:last-child { + margin-right: 0px; + } + + .panel-controls { + width: 100%; + height: ( @mph-controls_height + 4 ); + border-radius: 3px; + background-color: white; + text-align: center; + + flex: 0 0 auto; + + -webkit-align-self: auto; + -ms-flex-item-align: auto; + align-self: auto; + + .btn { + .smaller-btn; + } + .pull-left .btn { + margin-right: 4px; + } + .pull-right .btn { + margin-left: 4px; + } + .panel-menu { + z-index: 1; + .dropdown-menu a { + text-align: left; + } + } + .current-label { + display: inline-block; + color: grey; + padding-left: 2px; + margin-top: 2px; + } + } + .history-panel { + width: 100%; + + border: @mph-border_width solid grey; + border-radius: 3px; + background-color: #DFE5F9; + + overflow: auto; + } + } +} + + // ---------------------------------------------------------------------------- older styles //TODO: these may still apply in mobile display, workflow stuff body.historyPage { diff -r 0f69ba9bccae59f5a8f204573bdd8a4a9749231c -r 586064ce6704b93685f93230dc788aeda0160d41 templates/webapps/galaxy/history/view_multiple.mako --- a/templates/webapps/galaxy/history/view_multiple.mako +++ b/templates/webapps/galaxy/history/view_multiple.mako @@ -6,250 +6,15 @@ </%def> ## ---------------------------------------------------------------------------- -<%! - column_width = 312 - border_width = 1 - column_gap = 8 - - header_height = 29 - footer_height = 0 - - controls_height = 20 -%> - -## ---------------------------------------------------------------------------- <%def name="stylesheets()"> ${parent.stylesheets()} <style type="text/css"> + /* reset */ html, body { margin: 0px; padding: 0px; } - - .flex-row-container, - .flex-column-container { - display: -webkit-box; - display: -webkit-flex; - display: -ms-flexbox; - display: flex; - - /* force ff to squish beyond content: - https://developer.mozilla.org/en-US/Firefox/Releases/34/Site_Compatibility#… */ - min-width: 0px; - min-height: 0px; - - -webkit-align-items: stretch; - -ms-align-items: stretch; - align-items: stretch; - - -webkit-align-content: stretch; - -ms-align-content: stretch; - align-content: stretch; - - -webkit-justify-content: flex-start; - -ms-flex-pack: start; - justify-content: flex-start; - } - .flex-row-container { - -webkit-flex-direction: column; - -ms-flex-direction: column; - flex-direction: column; - } - .flex-column-container { - -webkit-flex-direction: row; - -ms-flex-direction: row; - flex-direction: row; - } - .flex-row, - .flex-column { - -webkit-flex: 1 1 auto; - -ms-flex: 1 1 auto; - flex: 1 1 auto; - - -webkit-align-self: auto; - -ms-flex-item-align: auto; - align-self: auto; - } - .flex-row { - } - .flex-column { - } - - /* ---------------------- header & footer */ - .header, .footer { - width: 100%; - } - - /* ---------------------- header */ - .header { - background-color: lightgrey; - min-height: ${header_height}px; - max-height: ${header_height}px; - } - .control-column { - margin-top: 4px; - } - - .control-column-right, - .control-column-left { - margin-right: 8px; - margin-left: 8px; - /*background-color: green;*/ - } - - .control-column-left > * { - margin: 0px 4px 4px 0px; - } - .more-options input[type=checkbox] { - margin-top: 3px; - } - - .control-column-center { - text-align: center; - max-height: 22px; - -webkit-flex: 0 1 auto; - -ms-flex: 0 1 auto; - flex: 0 1 auto; - - /* truncate */ - overflow: hidden; - text-overflow: ellipsis; - white-space: nowrap; - max-height: 22px; - } - .header-info { - display: inline-block; - padding: 2px 4px 2px 4px; - color: grey; - - } - - .control-column-right { - text-align: right; - } - .control-column-right > * { - margin: 0px 0px 4px 4px; - } - - .search-control { - display: inline-block; - width: 40%; - } - .search-control .search-clear, - .search-control .search-loading { - margin-top: -22px; - } - .footer input.search-query, - .header input.search-query { - font-size: 90%; - height: 21px; - line-height: normal; - padding: 2px 2px 1px 2px; - } - - .open-more-options { - padding: 2px 6px 2px 6px; - font-size: 150%; - } - - /* ---------------------- middle */ - .outer-middle { - overflow: auto; - } - .middle { - min-width: 100%; - margin: 0px 0px 0px 0px; - background-color: white; - padding: ${column_gap}px; - } - - .history-column { - width: ${column_width}px; - margin: 0px ${column_gap}px 0px 0px; - } - .history-column:last-child { - margin-right: 0px; - } - - .panel-controls { - width: 100%; - height: ${controls_height + 4}px; - border-radius: 3px; - background-color: white; - text-align: center; - - flex: 0 0 auto; - - -webkit-align-self: auto; - -ms-flex-item-align: auto; - align-self: auto; - } - .header .btn, - .footer .btn, - .panel-controls .btn { - height: 20px; - /*line-height: ${controls_height - 2}px;*/ - line-height: normal; - font-size: 90%; - padding-top: 0px; - padding-bottom: 0px; - } - .header .btn { - height: 21px; - } - .panel-controls .pull-left .btn { - margin-right: 4px; - } - .panel-controls .pull-right .btn { - margin-left: 4px; - } - .panel-controls .panel-menu { - z-index: 1; - } - .panel-controls .panel-menu .dropdown-menu a { - text-align: left; - } - - - /* ---------------------- footer */ - .footer { - min-height: ${footer_height}px; - max-height: ${footer_height}px; - background-color: lightgrey; - } - - /* ---------------------- columns */ - .history-panel { - width: 100%; - - border: ${border_width}px solid grey; - border-radius: 3px; - background-color: #DFE5F9; - - overflow: auto; - } - - .history-column:first-child { - position: fixed; - z-index : 2; - } - .history-column:first-child .history-panel { - border: 1px solid black; - box-shadow: 4px 4px 4px rgba( 96, 96, 96, 0.3 ); - } - - .history-column:nth-child(2) { - margin-left: ${( column_width + column_gap )}px; - } - - .current-label { - display: inline-block; - color: grey; - padding-left: 2px; - margin-top: 2px; - } </style> - </%def> @@ -264,7 +29,6 @@ 'mvc/history/multi-panel' ], function( HISTORY_MODEL, MULTI_PANEL ){ $(function(){ - $( '#center' ).addClass( 'flex-row-container' ); window.historyJSONArray = bootstrapped.historyJSONArray; var historyModels = []; @@ -277,7 +41,7 @@ includeDeleted : bootstrapped.includingDeleted }); multipanel = new MULTI_PANEL.MultiPanelColumns({ - el : $( '#center' ), + el : $( '#center' ).get(0), histories : histories, //historiesJSON : historiesJSON, order : bootstrapped.order, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/17bb0bc8b488/ Changeset: 17bb0bc8b488 User: dannon Date: 2015-02-13 14:39:49+00:00 Summary: Cleanup in util. Affected #: 1 file diff -r 63def64e9ed027e48b9ff257d384b8907bc661d5 -r 17bb0bc8b488c7b8bbe9d3c03e72a1fe0abfe6c6 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -12,7 +12,6 @@ import grp import logging import os -import pickle import random import re import shutil @@ -340,7 +339,7 @@ return value -def pretty_print_time_interval( time = False, precise = False ): +def pretty_print_time_interval( time=False, precise=False ): """ Get a datetime object or a int() Epoch timestamp and return a pretty string like 'an hour ago', 'Yesterday', '3 months ago', @@ -441,6 +440,7 @@ text = smart_str( text ) return _sanitize_text_helper( text, valid_characters=valid_characters, character_map=character_map ) + def _sanitize_text_helper( text, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X' ): """Restricts the characters that are allowed in a string""" @@ -459,7 +459,10 @@ if isinstance( values, list ): rval = [] for value in values: - rval.append( sanitize_lists_to_string( value, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character ) ) + rval.append( sanitize_lists_to_string( value, + valid_characters=valid_characters, + character_map=character_map, + invalid_character=invalid_character ) ) values = ",".join( rval ) else: values = sanitize_text( values, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character ) @@ -614,7 +617,12 @@ def __init__( self, params, sanitize=True ): if sanitize: for key, value in params.items(): - if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: # sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed. + # sanitize check both ungrouped and grouped parameters by + # name. Anything relying on NEVER_SANITIZE should be + # changed to not require this and NEVER_SANITIZE should be + # removed. + if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for + nonsanitize_parameter in self.NEVER_SANITIZE ]: self.__dict__[ key ] = sanitize_param( value ) else: self.__dict__[ key ] = value @@ -664,7 +672,9 @@ log.warn( str ) return unicodify( docutils.core.publish_string( s, writer=docutils.writers.html4css1.Writer(), - settings_overrides={ "embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream() } ) ) + settings_overrides={ "embed_stylesheet": False, + "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), + "warning_stream": FakeStream() } ) ) def xml_text(root, name=None): @@ -761,7 +771,7 @@ if len(amount) <= sfs: return amount else: - return amount[0:sfs] + '0'*(len(amount) - sfs) + return amount[0:sfs] + '0' * (len(amount) - sfs) def unicodify( value, encoding=DEFAULT_ENCODING, error='replace', default=None ): @@ -912,7 +922,7 @@ except Exception, e: print "ERROR: Unable to read builds file:", e if len(db_names) < 1: - db_names = DBNames( [( db_names.default_value, db_names.default_name )] ) + db_names = DBNames( [( db_names.default_value, db_names.default_name )] ) return db_names @@ -1109,11 +1119,11 @@ size = float( size_match.group(1) ) multiple = size_match.group(2) if multiple.startswith( 't' ): - return int( size * 1024**4 ) + return int( size * 1024 ** 4 ) elif multiple.startswith( 'g' ): - return int( size * 1024**3 ) + return int( size * 1024 ** 3 ) elif multiple.startswith( 'm' ): - return int( size * 1024**2 ) + return int( size * 1024 ** 2 ) elif multiple.startswith( 'k' ): return int( size * 1024 ) elif multiple.startswith( 'b' ): https://bitbucket.org/galaxy/galaxy-central/commits/0f69ba9bccae/ Changeset: 0f69ba9bccae User: dannon Date: 2015-02-13 18:05:24+00:00 Summary: Add utility method for masking passwords from urls. Affected #: 1 file diff -r 17bb0bc8b488c7b8bbe9d3c03e72a1fe0abfe6c6 -r 0f69ba9bccae59f5a8f204573bdd8a4a9749231c lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -21,6 +21,7 @@ import sys import tempfile import threading +import urlparse from galaxy.util import json from datetime import datetime @@ -31,8 +32,6 @@ from hashlib import md5 from itertools import izip -from urlparse import urlparse - from galaxy import eggs eggs.require( 'docutils' ) @@ -501,6 +500,30 @@ return out +def mask_password_from_url( url ): + """ + Masks out passwords from connection urls like the database connection in galaxy.ini + + >>> mask_password_from_url( 'sqlite+postgresql://user:password@localhost/' ) + 'sqlite+postgresql://user:********@localhost/' + >>> mask_password_from_url( 'amqp://user:amqp@localhost' ) + 'amqp://user:********@localhost' + >>> mask_password_from_url( 'amqp://localhost') + 'amqp://localhost' + """ + split = urlparse.urlsplit(url) + if split.password: + if url.count(split.password) == 1: + url = url.replace(split.password, "********") + else: + # This can manipulate the input other than just masking password, + # so the previous string replace method is preferred when the + # password doesn't appear twice in the url + split._replace(netloc=split.netloc.replace("%s:%s" % (split.username, split.password), '%s:********' % split.username)) + url = urlparse.urlunsplit(split) + return url + + def ready_name_for_url( raw_name ): """ General method to convert a string (i.e. object name) to a URL-ready slug. @@ -856,8 +879,8 @@ def compare_urls( url1, url2, compare_scheme=True, compare_hostname=True, compare_path=True ): - url1 = urlparse( url1 ) - url2 = urlparse( url2 ) + url1 = urlparse.urlparse( url1 ) + url2 = urlparse.urlparse( url2 ) if compare_scheme and url1.scheme and url2.scheme and url1.scheme != url2.scheme: return False if compare_hostname and url1.hostname and url2.hostname and url1.hostname != url2.hostname: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] a46802: prod mutable configs update
by GitHub 13 Feb '15

13 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a46802f99af926d92be8aaa3de88c523c86c7086 https://github.com/galaxyproject/usegalaxy-playbook/commit/a46802f99af926d9… Author: martenson <cech.marten(a)gmail.com> Date: 2015-02-13 (Fri, 13 Feb 2015) Changed paths: M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- prod mutable configs update

1 0

commit/galaxy-central: natefoo: Update tag latest_2015.01.13 for changeset a6e9a1d72674
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cc6774fcfed1/ Changeset: cc6774fcfed1 Branch: stable User: natefoo Date: 2015-02-13 14:00:30+00:00 Summary: Update tag latest_2015.01.13 for changeset a6e9a1d72674 Affected #: 1 file diff -r a6e9a1d7267410f697f30102ed78317b08274026 -r cc6774fcfed18076b0bc0b3a671b696a8a7d7a87 .hgtags --- a/.hgtags +++ b/.hgtags @@ -22,4 +22,4 @@ 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -577b270034b48d90e58ffbea296e700d229545c9 latest_2015.01.13 +a6e9a1d7267410f697f30102ed78317b08274026 latest_2015.01.13 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ColorPicker: Use fade out
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/63def64e9ed0/ Changeset: 63def64e9ed0 User: guerler Date: 2015-02-13 02:15:03+00:00 Summary: ColorPicker: Use fade out Affected #: 3 files diff -r f171cd70001a4566c82b7d19d1235562e5a5b3a9 -r 63def64e9ed027e48b9ff257d384b8907bc661d5 client/galaxy/scripts/mvc/ui/ui-color-picker.js --- a/client/galaxy/scripts/mvc/ui/ui-color-picker.js +++ b/client/galaxy/scripts/mvc/ui/ui-color-picker.js @@ -52,7 +52,7 @@ if (self.visible) { self.$view.fadeIn('fast'); } else { - self.$view.hide(); + self.$view.fadeOut('fast'); } }); }, diff -r f171cd70001a4566c82b7d19d1235562e5a5b3a9 -r 63def64e9ed027e48b9ff257d384b8907bc661d5 static/scripts/mvc/ui/ui-color-picker.js --- a/static/scripts/mvc/ui/ui-color-picker.js +++ b/static/scripts/mvc/ui/ui-color-picker.js @@ -52,7 +52,7 @@ if (self.visible) { self.$view.fadeIn('fast'); } else { - self.$view.hide(); + self.$view.fadeOut('fast'); } }); }, diff -r f171cd70001a4566c82b7d19d1235562e5a5b3a9 -r 63def64e9ed027e48b9ff257d384b8907bc661d5 static/scripts/packed/mvc/ui/ui-color-picker.js --- a/static/scripts/packed/mvc/ui/ui-color-picker.js +++ b/static/scripts/packed/mvc/ui/ui-color-picker.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc"],function(a,b){return Backbone.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},optionsDefault:{},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template());this.$panel=this.$(".ui-color-picker-panel");this.$view=this.$(".ui-color-picker-view");this.$value=this.$(".ui-color-picker-value");this.$header=this.$(".ui-color-picker-header");this._build();this.visible=false;this.value(this.options.value);this.$boxes=this.$(".ui-color-picker-box");var c=this;this.$boxes.on("click",function(){c.value($(this).css("background-color"));c.$header.trigger("click")});this.$header.on("click",function(){c.visible=!c.visible;if(c.visible){c.$view.fadeIn("fast")}else{c.$view.hide()}})},value:function(c){if(c!==undefined){if(c!==null){this.$value.css("background-color",c);this.$(".ui-color-picker-box").empty();this.$(this._getValue()).html(this._templateCheck());this.options.onchange&&this.options.onchange(c)}}return this._getValue()},_getValue:function(){var c=this.$value.css("background-color");c=c.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/);if(c){function d(e){return("0"+parseInt(e).toString(16)).slice(-2)}return"#"+d(c[1])+d(c[2])+d(c[3])}else{return null}},_build:function(){var d=this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var e in this.colors.theme){var c={};if(e==0){c.bottom=true}else{if(e!=this.colors.theme.length-1){c.top=true;c.bottom=true}else{c.top=true;c.padding=5}}c.colors=this.colors.theme[e];this._content(c)}this._content({label:"Standard Colors",colors:this.colors.standard,padding:5})},_content:function(n){var l=n.label;var d=n.colors;var k=n.padding;var h=n.top;var c=n.bottom;var f=$(this._templateContent());var j=f.find(".label");if(n.label){j.html(n.label)}else{j.hide()}var m=f.find(".line");this.$panel.append(f);for(var g in d){var e=$(this._templateBox(d[g]));if(h){e.css("border-top","none");e.css("border-top-left-radius","0px");e.css("border-top-right-radius","0px")}if(c){e.css("border-bottom","none");e.css("border-bottom-left-radius","0px");e.css("border-bottom-right-radius","0px")}m.append(e)}if(k){m.css("padding-bottom",k)}return f},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(c){return'<div id="'+c+'" class="ui-color-picker-box" style="background-color: #'+c+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>';"</div>"}})}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc"],function(a,b){return Backbone.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},optionsDefault:{},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template());this.$panel=this.$(".ui-color-picker-panel");this.$view=this.$(".ui-color-picker-view");this.$value=this.$(".ui-color-picker-value");this.$header=this.$(".ui-color-picker-header");this._build();this.visible=false;this.value(this.options.value);this.$boxes=this.$(".ui-color-picker-box");var c=this;this.$boxes.on("click",function(){c.value($(this).css("background-color"));c.$header.trigger("click")});this.$header.on("click",function(){c.visible=!c.visible;if(c.visible){c.$view.fadeIn("fast")}else{c.$view.fadeOut("fast")}})},value:function(c){if(c!==undefined){if(c!==null){this.$value.css("background-color",c);this.$(".ui-color-picker-box").empty();this.$(this._getValue()).html(this._templateCheck());this.options.onchange&&this.options.onchange(c)}}return this._getValue()},_getValue:function(){var c=this.$value.css("background-color");c=c.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/);if(c){function d(e){return("0"+parseInt(e).toString(16)).slice(-2)}return"#"+d(c[1])+d(c[2])+d(c[3])}else{return null}},_build:function(){var d=this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var e in this.colors.theme){var c={};if(e==0){c.bottom=true}else{if(e!=this.colors.theme.length-1){c.top=true;c.bottom=true}else{c.top=true;c.padding=5}}c.colors=this.colors.theme[e];this._content(c)}this._content({label:"Standard Colors",colors:this.colors.standard,padding:5})},_content:function(n){var l=n.label;var d=n.colors;var k=n.padding;var h=n.top;var c=n.bottom;var f=$(this._templateContent());var j=f.find(".label");if(n.label){j.html(n.label)}else{j.hide()}var m=f.find(".line");this.$panel.append(f);for(var g in d){var e=$(this._templateBox(d[g]));if(h){e.css("border-top","none");e.css("border-top-left-radius","0px");e.css("border-top-right-radius","0px")}if(c){e.css("border-bottom","none");e.css("border-bottom-left-radius","0px");e.css("border-bottom-right-radius","0px")}m.append(e)}if(k){m.css("padding-bottom",k)}return f},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(c){return'<div id="'+c+'" class="ui-color-picker-box" style="background-color: #'+c+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>';"</div>"}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ColorPicker: Hide on selection
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f171cd70001a/ Changeset: f171cd70001a User: guerler Date: 2015-02-13 02:12:13+00:00 Summary: ColorPicker: Hide on selection Affected #: 3 files diff -r 4b024e277fc5d89a93cc6a7919b8baf0bf5d094a -r f171cd70001a4566c82b7d19d1235562e5a5b3a9 client/galaxy/scripts/mvc/ui/ui-color-picker.js --- a/client/galaxy/scripts/mvc/ui/ui-color-picker.js +++ b/client/galaxy/scripts/mvc/ui/ui-color-picker.js @@ -45,7 +45,7 @@ var self = this; this.$boxes.on('click', function() { self.value($(this).css('background-color')); - //self.$header.trigger('click'); + self.$header.trigger('click'); }); this.$header.on('click', function() { self.visible = !self.visible; diff -r 4b024e277fc5d89a93cc6a7919b8baf0bf5d094a -r f171cd70001a4566c82b7d19d1235562e5a5b3a9 static/scripts/mvc/ui/ui-color-picker.js --- a/static/scripts/mvc/ui/ui-color-picker.js +++ b/static/scripts/mvc/ui/ui-color-picker.js @@ -45,7 +45,7 @@ var self = this; this.$boxes.on('click', function() { self.value($(this).css('background-color')); - //self.$header.trigger('click'); + self.$header.trigger('click'); }); this.$header.on('click', function() { self.visible = !self.visible; diff -r 4b024e277fc5d89a93cc6a7919b8baf0bf5d094a -r f171cd70001a4566c82b7d19d1235562e5a5b3a9 static/scripts/packed/mvc/ui/ui-color-picker.js --- a/static/scripts/packed/mvc/ui/ui-color-picker.js +++ b/static/scripts/packed/mvc/ui/ui-color-picker.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc"],function(a,b){return Backbone.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},optionsDefault:{},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template());this.$panel=this.$(".ui-color-picker-panel");this.$view=this.$(".ui-color-picker-view");this.$value=this.$(".ui-color-picker-value");this.$header=this.$(".ui-color-picker-header");this._build();this.visible=false;this.value(this.options.value);this.$boxes=this.$(".ui-color-picker-box");var c=this;this.$boxes.on("click",function(){c.value($(this).css("background-color"))});this.$header.on("click",function(){c.visible=!c.visible;if(c.visible){c.$view.fadeIn("fast")}else{c.$view.hide()}})},value:function(c){if(c!==undefined){if(c!==null){this.$value.css("background-color",c);this.$(".ui-color-picker-box").empty();this.$(this._getValue()).html(this._templateCheck());this.options.onchange&&this.options.onchange(c)}}return this._getValue()},_getValue:function(){var c=this.$value.css("background-color");c=c.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/);if(c){function d(e){return("0"+parseInt(e).toString(16)).slice(-2)}return"#"+d(c[1])+d(c[2])+d(c[3])}else{return null}},_build:function(){var d=this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var e in this.colors.theme){var c={};if(e==0){c.bottom=true}else{if(e!=this.colors.theme.length-1){c.top=true;c.bottom=true}else{c.top=true;c.padding=5}}c.colors=this.colors.theme[e];this._content(c)}this._content({label:"Standard Colors",colors:this.colors.standard,padding:5})},_content:function(n){var l=n.label;var d=n.colors;var k=n.padding;var h=n.top;var c=n.bottom;var f=$(this._templateContent());var j=f.find(".label");if(n.label){j.html(n.label)}else{j.hide()}var m=f.find(".line");this.$panel.append(f);for(var g in d){var e=$(this._templateBox(d[g]));if(h){e.css("border-top","none");e.css("border-top-left-radius","0px");e.css("border-top-right-radius","0px")}if(c){e.css("border-bottom","none");e.css("border-bottom-left-radius","0px");e.css("border-bottom-right-radius","0px")}m.append(e)}if(k){m.css("padding-bottom",k)}return f},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(c){return'<div id="'+c+'" class="ui-color-picker-box" style="background-color: #'+c+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>';"</div>"}})}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc"],function(a,b){return Backbone.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},optionsDefault:{},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template());this.$panel=this.$(".ui-color-picker-panel");this.$view=this.$(".ui-color-picker-view");this.$value=this.$(".ui-color-picker-value");this.$header=this.$(".ui-color-picker-header");this._build();this.visible=false;this.value(this.options.value);this.$boxes=this.$(".ui-color-picker-box");var c=this;this.$boxes.on("click",function(){c.value($(this).css("background-color"));c.$header.trigger("click")});this.$header.on("click",function(){c.visible=!c.visible;if(c.visible){c.$view.fadeIn("fast")}else{c.$view.hide()}})},value:function(c){if(c!==undefined){if(c!==null){this.$value.css("background-color",c);this.$(".ui-color-picker-box").empty();this.$(this._getValue()).html(this._templateCheck());this.options.onchange&&this.options.onchange(c)}}return this._getValue()},_getValue:function(){var c=this.$value.css("background-color");c=c.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/);if(c){function d(e){return("0"+parseInt(e).toString(16)).slice(-2)}return"#"+d(c[1])+d(c[2])+d(c[3])}else{return null}},_build:function(){var d=this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var e in this.colors.theme){var c={};if(e==0){c.bottom=true}else{if(e!=this.colors.theme.length-1){c.top=true;c.bottom=true}else{c.top=true;c.padding=5}}c.colors=this.colors.theme[e];this._content(c)}this._content({label:"Standard Colors",colors:this.colors.standard,padding:5})},_content:function(n){var l=n.label;var d=n.colors;var k=n.padding;var h=n.top;var c=n.bottom;var f=$(this._templateContent());var j=f.find(".label");if(n.label){j.html(n.label)}else{j.hide()}var m=f.find(".line");this.$panel.append(f);for(var g in d){var e=$(this._templateBox(d[g]));if(h){e.css("border-top","none");e.css("border-top-left-radius","0px");e.css("border-top-right-radius","0px")}if(c){e.css("border-bottom","none");e.css("border-bottom-left-radius","0px");e.css("border-bottom-right-radius","0px")}m.append(e)}if(k){m.css("padding-bottom",k)}return f},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(c){return'<div id="'+c+'" class="ui-color-picker-box" style="background-color: #'+c+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>';"</div>"}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ColorPicker: Use lower case values
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4b024e277fc5/ Changeset: 4b024e277fc5 User: guerler Date: 2015-02-13 01:42:56+00:00 Summary: ColorPicker: Use lower case values Affected #: 1 file diff -r a48be42539e27d35476ebaf8bea9f30fe09d65bc -r 4b024e277fc5d89a93cc6a7919b8baf0bf5d094a lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -661,7 +661,7 @@ return form_builder.HiddenField( self.name, self.value ) def get_initial_value( self, trans, context, history=None ): - return self.value + return self.value.lower(); ## This is clearly a HACK, parameters should only be used for things the user ## can change, there needs to be a different way to specify this. I'm leaving Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ColorPicker: Fix event handler
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a48be42539e2/ Changeset: a48be42539e2 User: guerler Date: 2015-02-13 01:11:11+00:00 Summary: ColorPicker: Fix event handler Affected #: 3 files diff -r d34fb2d38b99ca9f5d4db79edf9a0cd01dc4c7f4 -r a48be42539e27d35476ebaf8bea9f30fe09d65bc client/galaxy/scripts/mvc/tools/tools-parameters.js --- a/client/galaxy/scripts/mvc/tools/tools-parameters.js +++ b/client/galaxy/scripts/mvc/tools/tools-parameters.js @@ -248,7 +248,7 @@ */ _fieldColor : function(input_def) { var self = this; - return new ColorPicker(this.app, { + return new ColorPicker({ id : 'field-' + input_def.id, onchange : function() { self.app.trigger('refresh'); diff -r d34fb2d38b99ca9f5d4db79edf9a0cd01dc4c7f4 -r a48be42539e27d35476ebaf8bea9f30fe09d65bc static/scripts/mvc/tools/tools-parameters.js --- a/static/scripts/mvc/tools/tools-parameters.js +++ b/static/scripts/mvc/tools/tools-parameters.js @@ -248,7 +248,7 @@ */ _fieldColor : function(input_def) { var self = this; - return new ColorPicker(this.app, { + return new ColorPicker({ id : 'field-' + input_def.id, onchange : function() { self.app.trigger('refresh'); diff -r d34fb2d38b99ca9f5d4db79edf9a0cd01dc4c7f4 -r a48be42539e27d35476ebaf8bea9f30fe09d65bc static/scripts/packed/mvc/tools/tools-parameters.js --- a/static/scripts/packed/mvc/tools/tools-parameters.js +++ b/static/scripts/packed/mvc/tools/tools-parameters.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-select-content","mvc/ui/ui-color-picker"],function(c,d,a,b){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",},initialize:function(f,e){this.app=f},create:function(e){if(e.value===undefined){e.value=null}if(e.default_value===undefined){e.default_value=e.value}var g=null;var f=this.types[e.type];if(f&&typeof(this[f])==="function"){g=this[f].call(this,e)}if(!g){this.app.incompatible=true;if(e.options){g=this._fieldSelect(e)}else{g=this._fieldText(e)}console.debug("tools-form::_addRow() : Auto matched field type ("+e.type+").")}if(e.value!==undefined){g.value(e.value)}return g},_fieldData:function(e){if(!this.app.options.is_dynamic){e.info="Data input '"+e.name+"' ("+c.textify(e.extensions.toString())+")";e.value=null;return this._fieldHidden(e)}var f=this;return new a.View(this.app,{id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,data:e.options,onchange:function(){f.app.trigger("refresh")}})},_fieldSelect:function(e){if(!this.app.options.is_dynamic&&e.is_dynamic){return this._fieldText(e)}if(e.type=="data_column"){e.error_text="Missing columns in referenced dataset."}if(e.type=="genomebuild"){e.searchable=true}var g=[];for(var h in e.options){var j=e.options[h];g.push({label:j[0],value:j[1]})}var k=d.Select;switch(e.display){case"checkboxes":k=d.Checkbox;break;case"radio":k=d.Radio;break}var f=this;return new k.View({id:"field-"+e.id,data:g,error_text:e.error_text||"No options available",multiple:e.multiple,searchable:e.searchable,onchange:function(){f.app.trigger("refresh")}})},_fieldDrilldown:function(e){if(!this.app.options.is_dynamic&&e.is_dynamic){return this._fieldText(e)}var f=this;return new d.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,onchange:function(){f.app.trigger("refresh")}})},_fieldText:function(e){if(e.options){e.area=e.multiple;if(!c.validate(e.value)){e.value=""}else{if(e.value instanceof Array){e.value=value.toString()}else{e.value=String(e.value).replace(/[\[\]'"\s]/g,"");if(e.multiple){e.value=e.value.replace(/,/g,"\n")}}}}var f=this;return new d.Input({id:"field-"+e.id,area:e.area,onchange:function(){f.app.trigger("refresh")}})},_fieldSlider:function(e){var f=this;return new d.Slider.View({id:"field-"+e.id,precise:e.type=="float",min:e.min,max:e.max,onchange:function(){f.app.trigger("refresh")}})},_fieldHidden:function(e){return new d.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){var f=this;return new d.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){f.app.trigger("refresh")}})},_fieldColor:function(e){var f=this;return new b(this.app,{id:"field-"+e.id,onchange:function(){f.app.trigger("refresh")}})}});return{View:View}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-select-content","mvc/ui/ui-color-picker"],function(c,d,a,b){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",},initialize:function(f,e){this.app=f},create:function(e){if(e.value===undefined){e.value=null}if(e.default_value===undefined){e.default_value=e.value}var g=null;var f=this.types[e.type];if(f&&typeof(this[f])==="function"){g=this[f].call(this,e)}if(!g){this.app.incompatible=true;if(e.options){g=this._fieldSelect(e)}else{g=this._fieldText(e)}console.debug("tools-form::_addRow() : Auto matched field type ("+e.type+").")}if(e.value!==undefined){g.value(e.value)}return g},_fieldData:function(e){if(!this.app.options.is_dynamic){e.info="Data input '"+e.name+"' ("+c.textify(e.extensions.toString())+")";e.value=null;return this._fieldHidden(e)}var f=this;return new a.View(this.app,{id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,data:e.options,onchange:function(){f.app.trigger("refresh")}})},_fieldSelect:function(e){if(!this.app.options.is_dynamic&&e.is_dynamic){return this._fieldText(e)}if(e.type=="data_column"){e.error_text="Missing columns in referenced dataset."}if(e.type=="genomebuild"){e.searchable=true}var g=[];for(var h in e.options){var j=e.options[h];g.push({label:j[0],value:j[1]})}var k=d.Select;switch(e.display){case"checkboxes":k=d.Checkbox;break;case"radio":k=d.Radio;break}var f=this;return new k.View({id:"field-"+e.id,data:g,error_text:e.error_text||"No options available",multiple:e.multiple,searchable:e.searchable,onchange:function(){f.app.trigger("refresh")}})},_fieldDrilldown:function(e){if(!this.app.options.is_dynamic&&e.is_dynamic){return this._fieldText(e)}var f=this;return new d.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,onchange:function(){f.app.trigger("refresh")}})},_fieldText:function(e){if(e.options){e.area=e.multiple;if(!c.validate(e.value)){e.value=""}else{if(e.value instanceof Array){e.value=value.toString()}else{e.value=String(e.value).replace(/[\[\]'"\s]/g,"");if(e.multiple){e.value=e.value.replace(/,/g,"\n")}}}}var f=this;return new d.Input({id:"field-"+e.id,area:e.area,onchange:function(){f.app.trigger("refresh")}})},_fieldSlider:function(e){var f=this;return new d.Slider.View({id:"field-"+e.id,precise:e.type=="float",min:e.min,max:e.max,onchange:function(){f.app.trigger("refresh")}})},_fieldHidden:function(e){return new d.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){var f=this;return new d.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){f.app.trigger("refresh")}})},_fieldColor:function(e){var f=this;return new b({id:"field-"+e.id,onchange:function(){f.app.trigger("refresh")}})}});return{View:View}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Ui: Add default color
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d34fb2d38b99/ Changeset: d34fb2d38b99 User: guerler Date: 2015-02-13 01:02:59+00:00 Summary: Ui: Add default color Affected #: 4 files diff -r bcb29996bd53620fcb724e1ac25c17f01ee568b8 -r d34fb2d38b99ca9f5d4db79edf9a0cd01dc4c7f4 client/galaxy/scripts/mvc/ui/ui-color-picker.js --- a/client/galaxy/scripts/mvc/ui/ui-color-picker.js +++ b/client/galaxy/scripts/mvc/ui/ui-color-picker.js @@ -15,7 +15,6 @@ // default options optionsDefault: { - default_color: '#fdeada' }, // initialize @@ -62,19 +61,17 @@ value : function (new_val) { if (new_val !== undefined) { // set default value - if (new_val === null) { - new_val = this.options.default_color; + if (new_val !== null) { + // update color value + this.$value.css('background-color', new_val); + + // check selected color in panel + this.$('.ui-color-picker-box').empty(); + this.$(this._getValue()).html(this._templateCheck()); + + // trigger custom event + this.options.onchange && this.options.onchange(new_val); } - - // update color value - this.$value.css('background-color', new_val); - - // check selected color in panel - this.$('.ui-color-picker-box').empty(); - this.$(this._getValue()).html(this._templateCheck()); - - // trigger custom event - this.options.onchange && this.options.onchange(new_val); } // return current value diff -r bcb29996bd53620fcb724e1ac25c17f01ee568b8 -r d34fb2d38b99ca9f5d4db79edf9a0cd01dc4c7f4 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -655,7 +655,7 @@ def __init__( self, tool, input_source ): input_source = ensure_input_source( input_source ) ToolParameter.__init__( self, tool, input_source ) - self.value = input_source.get( 'value' ) + self.value = input_source.get( 'value', '#fdeada' ) def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.HiddenField( self.name, self.value ) diff -r bcb29996bd53620fcb724e1ac25c17f01ee568b8 -r d34fb2d38b99ca9f5d4db79edf9a0cd01dc4c7f4 static/scripts/mvc/ui/ui-color-picker.js --- a/static/scripts/mvc/ui/ui-color-picker.js +++ b/static/scripts/mvc/ui/ui-color-picker.js @@ -15,7 +15,6 @@ // default options optionsDefault: { - default_color: '#fdeada' }, // initialize @@ -62,19 +61,17 @@ value : function (new_val) { if (new_val !== undefined) { // set default value - if (new_val === null) { - new_val = this.options.default_color; + if (new_val !== null) { + // update color value + this.$value.css('background-color', new_val); + + // check selected color in panel + this.$('.ui-color-picker-box').empty(); + this.$(this._getValue()).html(this._templateCheck()); + + // trigger custom event + this.options.onchange && this.options.onchange(new_val); } - - // update color value - this.$value.css('background-color', new_val); - - // check selected color in panel - this.$('.ui-color-picker-box').empty(); - this.$(this._getValue()).html(this._templateCheck()); - - // trigger custom event - this.options.onchange && this.options.onchange(new_val); } // return current value diff -r bcb29996bd53620fcb724e1ac25c17f01ee568b8 -r d34fb2d38b99ca9f5d4db79edf9a0cd01dc4c7f4 static/scripts/packed/mvc/ui/ui-color-picker.js --- a/static/scripts/packed/mvc/ui/ui-color-picker.js +++ b/static/scripts/packed/mvc/ui/ui-color-picker.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc"],function(a,b){return Backbone.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},optionsDefault:{default_color:"#fdeada"},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template());this.$panel=this.$(".ui-color-picker-panel");this.$view=this.$(".ui-color-picker-view");this.$value=this.$(".ui-color-picker-value");this.$header=this.$(".ui-color-picker-header");this._build();this.visible=false;this.value(this.options.value);this.$boxes=this.$(".ui-color-picker-box");var c=this;this.$boxes.on("click",function(){c.value($(this).css("background-color"))});this.$header.on("click",function(){c.visible=!c.visible;if(c.visible){c.$view.fadeIn("fast")}else{c.$view.hide()}})},value:function(c){if(c!==undefined){if(c===null){c=this.options.default_color}this.$value.css("background-color",c);this.$(".ui-color-picker-box").empty();this.$(this._getValue()).html(this._templateCheck());this.options.onchange&&this.options.onchange(c)}return this._getValue()},_getValue:function(){var c=this.$value.css("background-color");c=c.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/);if(c){function d(e){return("0"+parseInt(e).toString(16)).slice(-2)}return"#"+d(c[1])+d(c[2])+d(c[3])}else{return null}},_build:function(){var d=this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var e in this.colors.theme){var c={};if(e==0){c.bottom=true}else{if(e!=this.colors.theme.length-1){c.top=true;c.bottom=true}else{c.top=true;c.padding=5}}c.colors=this.colors.theme[e];this._content(c)}this._content({label:"Standard Colors",colors:this.colors.standard,padding:5})},_content:function(n){var l=n.label;var d=n.colors;var k=n.padding;var h=n.top;var c=n.bottom;var f=$(this._templateContent());var j=f.find(".label");if(n.label){j.html(n.label)}else{j.hide()}var m=f.find(".line");this.$panel.append(f);for(var g in d){var e=$(this._templateBox(d[g]));if(h){e.css("border-top","none");e.css("border-top-left-radius","0px");e.css("border-top-right-radius","0px")}if(c){e.css("border-bottom","none");e.css("border-bottom-left-radius","0px");e.css("border-bottom-right-radius","0px")}m.append(e)}if(k){m.css("padding-bottom",k)}return f},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(c){return'<div id="'+c+'" class="ui-color-picker-box" style="background-color: #'+c+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>';"</div>"}})}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc"],function(a,b){return Backbone.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},optionsDefault:{},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template());this.$panel=this.$(".ui-color-picker-panel");this.$view=this.$(".ui-color-picker-view");this.$value=this.$(".ui-color-picker-value");this.$header=this.$(".ui-color-picker-header");this._build();this.visible=false;this.value(this.options.value);this.$boxes=this.$(".ui-color-picker-box");var c=this;this.$boxes.on("click",function(){c.value($(this).css("background-color"))});this.$header.on("click",function(){c.visible=!c.visible;if(c.visible){c.$view.fadeIn("fast")}else{c.$view.hide()}})},value:function(c){if(c!==undefined){if(c!==null){this.$value.css("background-color",c);this.$(".ui-color-picker-box").empty();this.$(this._getValue()).html(this._templateCheck());this.options.onchange&&this.options.onchange(c)}}return this._getValue()},_getValue:function(){var c=this.$value.css("background-color");c=c.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/);if(c){function d(e){return("0"+parseInt(e).toString(16)).slice(-2)}return"#"+d(c[1])+d(c[2])+d(c[3])}else{return null}},_build:function(){var d=this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var e in this.colors.theme){var c={};if(e==0){c.bottom=true}else{if(e!=this.colors.theme.length-1){c.top=true;c.bottom=true}else{c.top=true;c.padding=5}}c.colors=this.colors.theme[e];this._content(c)}this._content({label:"Standard Colors",colors:this.colors.standard,padding:5})},_content:function(n){var l=n.label;var d=n.colors;var k=n.padding;var h=n.top;var c=n.bottom;var f=$(this._templateContent());var j=f.find(".label");if(n.label){j.html(n.label)}else{j.hide()}var m=f.find(".line");this.$panel.append(f);for(var g in d){var e=$(this._templateBox(d[g]));if(h){e.css("border-top","none");e.css("border-top-left-radius","0px");e.css("border-top-right-radius","0px")}if(c){e.css("border-bottom","none");e.css("border-bottom-left-radius","0px");e.css("border-bottom-right-radius","0px")}m.append(e)}if(k){m.css("padding-bottom",k)}return f},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(c){return'<div id="'+c+'" class="ui-color-picker-box" style="background-color: #'+c+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>';"</div>"}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Change color
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bcb29996bd53/ Changeset: bcb29996bd53 User: guerler Date: 2015-02-13 00:46:08+00:00 Summary: Change color Affected #: 3 files diff -r 32b5ad88cd9baf12cd0776c54437b445a0561abf -r bcb29996bd53620fcb724e1ac25c17f01ee568b8 client/galaxy/scripts/mvc/ui/ui-color-picker.js --- a/client/galaxy/scripts/mvc/ui/ui-color-picker.js +++ b/client/galaxy/scripts/mvc/ui/ui-color-picker.js @@ -10,7 +10,7 @@ ['d8d8d8','595959','c4bd97','8db3e2','b8cce4','e5b9b7','d7e3bc','ccc1d9','b7dde8','fbd5b5'], ['bfbfbf','3f3f3f','938953','548dd4','95b3d7','d99694','c3d69b','b2a2c7','92cddc','fac08f'], ['a5a5a5','262626','494429','17365d','366092','953734','76923c','5f497a','31859b','e36c09'], - ['7f7f7f','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']] + ['7f7f7e','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']] }, // default options diff -r 32b5ad88cd9baf12cd0776c54437b445a0561abf -r bcb29996bd53620fcb724e1ac25c17f01ee568b8 static/scripts/mvc/ui/ui-color-picker.js --- a/static/scripts/mvc/ui/ui-color-picker.js +++ b/static/scripts/mvc/ui/ui-color-picker.js @@ -10,7 +10,7 @@ ['d8d8d8','595959','c4bd97','8db3e2','b8cce4','e5b9b7','d7e3bc','ccc1d9','b7dde8','fbd5b5'], ['bfbfbf','3f3f3f','938953','548dd4','95b3d7','d99694','c3d69b','b2a2c7','92cddc','fac08f'], ['a5a5a5','262626','494429','17365d','366092','953734','76923c','5f497a','31859b','e36c09'], - ['7f7f7f','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']] + ['7f7f7e','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']] }, // default options diff -r 32b5ad88cd9baf12cd0776c54437b445a0561abf -r bcb29996bd53620fcb724e1ac25c17f01ee568b8 static/scripts/packed/mvc/ui/ui-color-picker.js --- a/static/scripts/packed/mvc/ui/ui-color-picker.js +++ b/static/scripts/packed/mvc/ui/ui-color-picker.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc"],function(a,b){return Backbone.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7f","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},optionsDefault:{default_color:"#fdeada"},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template());this.$panel=this.$(".ui-color-picker-panel");this.$view=this.$(".ui-color-picker-view");this.$value=this.$(".ui-color-picker-value");this.$header=this.$(".ui-color-picker-header");this._build();this.visible=false;this.value(this.options.value);this.$boxes=this.$(".ui-color-picker-box");var c=this;this.$boxes.on("click",function(){c.value($(this).css("background-color"))});this.$header.on("click",function(){c.visible=!c.visible;if(c.visible){c.$view.fadeIn("fast")}else{c.$view.hide()}})},value:function(c){if(c!==undefined){if(c===null){c=this.options.default_color}this.$value.css("background-color",c);this.$(".ui-color-picker-box").empty();this.$(this._getValue()).html(this._templateCheck());this.options.onchange&&this.options.onchange(c)}return this._getValue()},_getValue:function(){var c=this.$value.css("background-color");c=c.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/);if(c){function d(e){return("0"+parseInt(e).toString(16)).slice(-2)}return"#"+d(c[1])+d(c[2])+d(c[3])}else{return null}},_build:function(){var d=this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var e in this.colors.theme){var c={};if(e==0){c.bottom=true}else{if(e!=this.colors.theme.length-1){c.top=true;c.bottom=true}else{c.top=true;c.padding=5}}c.colors=this.colors.theme[e];this._content(c)}this._content({label:"Standard Colors",colors:this.colors.standard,padding:5})},_content:function(n){var l=n.label;var d=n.colors;var k=n.padding;var h=n.top;var c=n.bottom;var f=$(this._templateContent());var j=f.find(".label");if(n.label){j.html(n.label)}else{j.hide()}var m=f.find(".line");this.$panel.append(f);for(var g in d){var e=$(this._templateBox(d[g]));if(h){e.css("border-top","none");e.css("border-top-left-radius","0px");e.css("border-top-right-radius","0px")}if(c){e.css("border-bottom","none");e.css("border-bottom-left-radius","0px");e.css("border-bottom-right-radius","0px")}m.append(e)}if(k){m.css("padding-bottom",k)}return f},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(c){return'<div id="'+c+'" class="ui-color-picker-box" style="background-color: #'+c+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>';"</div>"}})}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc"],function(a,b){return Backbone.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},optionsDefault:{default_color:"#fdeada"},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template());this.$panel=this.$(".ui-color-picker-panel");this.$view=this.$(".ui-color-picker-view");this.$value=this.$(".ui-color-picker-value");this.$header=this.$(".ui-color-picker-header");this._build();this.visible=false;this.value(this.options.value);this.$boxes=this.$(".ui-color-picker-box");var c=this;this.$boxes.on("click",function(){c.value($(this).css("background-color"))});this.$header.on("click",function(){c.visible=!c.visible;if(c.visible){c.$view.fadeIn("fast")}else{c.$view.hide()}})},value:function(c){if(c!==undefined){if(c===null){c=this.options.default_color}this.$value.css("background-color",c);this.$(".ui-color-picker-box").empty();this.$(this._getValue()).html(this._templateCheck());this.options.onchange&&this.options.onchange(c)}return this._getValue()},_getValue:function(){var c=this.$value.css("background-color");c=c.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/);if(c){function d(e){return("0"+parseInt(e).toString(16)).slice(-2)}return"#"+d(c[1])+d(c[2])+d(c[3])}else{return null}},_build:function(){var d=this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var e in this.colors.theme){var c={};if(e==0){c.bottom=true}else{if(e!=this.colors.theme.length-1){c.top=true;c.bottom=true}else{c.top=true;c.padding=5}}c.colors=this.colors.theme[e];this._content(c)}this._content({label:"Standard Colors",colors:this.colors.standard,padding:5})},_content:function(n){var l=n.label;var d=n.colors;var k=n.padding;var h=n.top;var c=n.bottom;var f=$(this._templateContent());var j=f.find(".label");if(n.label){j.html(n.label)}else{j.hide()}var m=f.find(".line");this.$panel.append(f);for(var g in d){var e=$(this._templateBox(d[g]));if(h){e.css("border-top","none");e.css("border-top-left-radius","0px");e.css("border-top-right-radius","0px")}if(c){e.css("border-bottom","none");e.css("border-bottom-left-radius","0px");e.css("border-bottom-right-radius","0px")}m.append(e)}if(k){m.css("padding-bottom",k)}return f},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(c){return'<div id="'+c+'" class="ui-color-picker-box" style="background-color: #'+c+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>';"</div>"}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Ui: Add simple color picker
by commits-noreply＠bitbucket.org 13 Feb '15

13 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/32b5ad88cd9b/ Changeset: 32b5ad88cd9b User: guerler Date: 2015-02-13 00:24:56+00:00 Summary: Ui: Add simple color picker Affected #: 9 files diff -r 8563e5b33300a733344a165dff13a1877bccde79 -r 32b5ad88cd9baf12cd0776c54437b445a0561abf client/galaxy/scripts/mvc/tools/tools-parameters.js --- a/client/galaxy/scripts/mvc/tools/tools-parameters.js +++ b/client/galaxy/scripts/mvc/tools/tools-parameters.js @@ -1,8 +1,11 @@ /** This class creates input elements. New input parameter types should be added to the types dictionary. */ -define(['utils/utils','mvc/ui/ui-misc', 'mvc/tools/tools-select-content'], - function(Utils, Ui, SelectContent) { +define(['utils/utils', + 'mvc/ui/ui-misc', + 'mvc/tools/tools-select-content', + 'mvc/ui/ui-color-picker'], + function(Utils, Ui, SelectContent, ColorPicker) { // create form view return Backbone.Model.extend({ @@ -18,9 +21,10 @@ 'float' : '_fieldSlider', 'boolean' : '_fieldBoolean', 'drill_down' : '_fieldDrilldown', + 'color' : '_fieldColor', 'hidden' : '_fieldHidden', 'hidden_data' : '_fieldHidden', - 'baseurl' : '_fieldHidden' + 'baseurl' : '_fieldHidden', }, // initialize @@ -238,6 +242,18 @@ self.app.trigger('refresh'); } }); + }, + + /** Color picker field + */ + _fieldColor : function(input_def) { + var self = this; + return new ColorPicker(this.app, { + id : 'field-' + input_def.id, + onchange : function() { + self.app.trigger('refresh'); + } + }); } }); diff -r 8563e5b33300a733344a165dff13a1877bccde79 -r 32b5ad88cd9baf12cd0776c54437b445a0561abf client/galaxy/scripts/mvc/ui/ui-color-picker.js --- /dev/null +++ b/client/galaxy/scripts/mvc/ui/ui-color-picker.js @@ -0,0 +1,202 @@ +// dependencies +define(['utils/utils', 'mvc/ui/ui-misc'], function(Utils, Ui) { + +// plugin +return Backbone.View.extend({ + colors: { + standard: ['c00000','ff0000','ffc000','ffff00','92d050','00b050','00b0f0','0070c0','002060','7030a0'], + base : ['ffffff','000000','eeece1','1f497d','4f81bd','c0504d','9bbb59','8064a2','4bacc6','f79646'], + theme :[['f2f2f2','7f7f7f','ddd9c3','c6d9f0','dbe5f1','f2dcdb','ebf1dd','e5e0ec','dbeef3','fdeada'], + ['d8d8d8','595959','c4bd97','8db3e2','b8cce4','e5b9b7','d7e3bc','ccc1d9','b7dde8','fbd5b5'], + ['bfbfbf','3f3f3f','938953','548dd4','95b3d7','d99694','c3d69b','b2a2c7','92cddc','fac08f'], + ['a5a5a5','262626','494429','17365d','366092','953734','76923c','5f497a','31859b','e36c09'], + ['7f7f7f','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']] + }, + + // default options + optionsDefault: { + default_color: '#fdeada' + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template()); + this.$panel = this.$('.ui-color-picker-panel'); + this.$view = this.$('.ui-color-picker-view'); + this.$value = this.$('.ui-color-picker-value'); + this.$header = this.$('.ui-color-picker-header'); + + // build panel + this._build(); + + // hide panel on start up + this.visible = false; + + // set initial value + this.value(this.options.value); + + // link boxes + this.$boxes = this.$('.ui-color-picker-box'); + + // add event handler + var self = this; + this.$boxes.on('click', function() { + self.value($(this).css('background-color')); + //self.$header.trigger('click'); + }); + this.$header.on('click', function() { + self.visible = !self.visible; + if (self.visible) { + self.$view.fadeIn('fast'); + } else { + self.$view.hide(); + } + }); + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + // set default value + if (new_val === null) { + new_val = this.options.default_color; + } + + // update color value + this.$value.css('background-color', new_val); + + // check selected color in panel + this.$('.ui-color-picker-box').empty(); + this.$(this._getValue()).html(this._templateCheck()); + + // trigger custom event + this.options.onchange && this.options.onchange(new_val); + } + + // return current value + return this._getValue(); + }, + + // get value from dom + _getValue: function() { + var rgb = this.$value.css('background-color'); + rgb = rgb.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/); + if (rgb) { + function hex(x) { + return ('0' + parseInt(x).toString(16)).slice(-2); + } + return '#' + hex(rgb[1]) + hex(rgb[2]) + hex(rgb[3]); + } else { + return null; + } + }, + + // build panel + _build: function() { + var $content = this._content({ + label : 'Theme Colors', + colors : this.colors.base, + padding : 10 + }); + for (var i in this.colors.theme) { + var line_def = {}; + if (i == 0) { + line_def['bottom'] = true; + } else { + if (i != this.colors.theme.length - 1) { + line_def['top'] = true; + line_def['bottom'] = true; + } else { + line_def['top'] = true; + line_def['padding'] = 5; + } + } + line_def['colors'] = this.colors.theme[i]; + this._content(line_def); + } + this._content({ + label : 'Standard Colors', + colors : this.colors.standard, + padding : 5 + }); + }, + + // create content + _content: function(options) { + // get parameters + var label = options.label; + var colors = options.colors; + var padding = options.padding; + var top = options.top; + var bottom = options.bottom; + + // create lines + var $content = $(this._templateContent()); + + // set label + var $label = $content.find('.label'); + if (options.label) { + $label.html(options.label); + } else { + $label.hide(); + } + + // build line + var $line = $content.find('.line'); + this.$panel.append($content); + for (var i in colors) { + var $box = $(this._templateBox(colors[i])); + if (top) { + $box.css('border-top', 'none'); + $box.css('border-top-left-radius', '0px'); + $box.css('border-top-right-radius', '0px'); + } + if (bottom) { + $box.css('border-bottom', 'none'); + $box.css('border-bottom-left-radius', '0px'); + $box.css('border-bottom-right-radius', '0px'); + } + $line.append($box); + } + if (padding) { + $line.css('padding-bottom', padding); + } + return $content; + }, + + // check icon + _templateCheck: function() { + return '<div class="ui-color-picker-check fa fa-check"/>'; + }, + + // content template + _templateContent: function() { + return '<div class="ui-color-picker-content">' + + '<div class="label"/>' + + '<div class="line"/>' + + '</div>'; + }, + + // box template + _templateBox: function(color) { + return '<div id="' + color + '" class="ui-color-picker-box" style="background-color: #' + color + ';"/>'; + }, + + // template + _template: function() { + return '<div class="ui-color-picker">' + + '<div class="ui-color-picker-header">' + + '<div class="ui-color-picker-value"/>' + + '<div class="ui-color-picker-label">Select a color</div>' + + '</div>' + + '<div class="ui-color-picker-view ui-input">' + + '<div class="ui-color-picker-panel"/>' + + '</div>' + '</div>'; + } +}); +}); \ No newline at end of file diff -r 8563e5b33300a733344a165dff13a1877bccde79 -r 32b5ad88cd9baf12cd0776c54437b445a0561abf lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -644,6 +644,25 @@ def get_label( self ): return None +class ColorToolParameter( ToolParameter ): + """ + Parameter that stores a color. + + >>> p = ColorToolParameter( None, XML( '<param name="blah" type="color" value="#ffffff"/>' ) ) + >>> print p.name + blah + """ + def __init__( self, tool, input_source ): + input_source = ensure_input_source( input_source ) + ToolParameter.__init__( self, tool, input_source ) + self.value = input_source.get( 'value' ) + + def get_html_field( self, trans=None, value=None, other_values={} ): + return form_builder.HiddenField( self.name, self.value ) + + def get_initial_value( self, trans, context, history=None ): + return self.value + ## This is clearly a HACK, parameters should only be used for things the user ## can change, there needs to be a different way to specify this. I'm leaving ## it for now to avoid breaking any tools. @@ -2514,6 +2533,7 @@ boolean=BooleanToolParameter, genomebuild=GenomeBuildParameter, select=SelectToolParameter, + color=ColorToolParameter, data_column=ColumnListParameter, hidden=HiddenToolParameter, hidden_data=HiddenDataToolParameter, diff -r 8563e5b33300a733344a165dff13a1877bccde79 -r 32b5ad88cd9baf12cd0776c54437b445a0561abf static/scripts/mvc/tools/tools-parameters.js --- a/static/scripts/mvc/tools/tools-parameters.js +++ b/static/scripts/mvc/tools/tools-parameters.js @@ -1,8 +1,11 @@ /** This class creates input elements. New input parameter types should be added to the types dictionary. */ -define(['utils/utils','mvc/ui/ui-misc', 'mvc/tools/tools-select-content'], - function(Utils, Ui, SelectContent) { +define(['utils/utils', + 'mvc/ui/ui-misc', + 'mvc/tools/tools-select-content', + 'mvc/ui/ui-color-picker'], + function(Utils, Ui, SelectContent, ColorPicker) { // create form view return Backbone.Model.extend({ @@ -18,9 +21,10 @@ 'float' : '_fieldSlider', 'boolean' : '_fieldBoolean', 'drill_down' : '_fieldDrilldown', + 'color' : '_fieldColor', 'hidden' : '_fieldHidden', 'hidden_data' : '_fieldHidden', - 'baseurl' : '_fieldHidden' + 'baseurl' : '_fieldHidden', }, // initialize @@ -238,6 +242,18 @@ self.app.trigger('refresh'); } }); + }, + + /** Color picker field + */ + _fieldColor : function(input_def) { + var self = this; + return new ColorPicker(this.app, { + id : 'field-' + input_def.id, + onchange : function() { + self.app.trigger('refresh'); + } + }); } }); diff -r 8563e5b33300a733344a165dff13a1877bccde79 -r 32b5ad88cd9baf12cd0776c54437b445a0561abf static/scripts/mvc/ui/ui-color-picker.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-color-picker.js @@ -0,0 +1,202 @@ +// dependencies +define(['utils/utils', 'mvc/ui/ui-misc'], function(Utils, Ui) { + +// plugin +return Backbone.View.extend({ + colors: { + standard: ['c00000','ff0000','ffc000','ffff00','92d050','00b050','00b0f0','0070c0','002060','7030a0'], + base : ['ffffff','000000','eeece1','1f497d','4f81bd','c0504d','9bbb59','8064a2','4bacc6','f79646'], + theme :[['f2f2f2','7f7f7f','ddd9c3','c6d9f0','dbe5f1','f2dcdb','ebf1dd','e5e0ec','dbeef3','fdeada'], + ['d8d8d8','595959','c4bd97','8db3e2','b8cce4','e5b9b7','d7e3bc','ccc1d9','b7dde8','fbd5b5'], + ['bfbfbf','3f3f3f','938953','548dd4','95b3d7','d99694','c3d69b','b2a2c7','92cddc','fac08f'], + ['a5a5a5','262626','494429','17365d','366092','953734','76923c','5f497a','31859b','e36c09'], + ['7f7f7f','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']] + }, + + // default options + optionsDefault: { + default_color: '#fdeada' + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template()); + this.$panel = this.$('.ui-color-picker-panel'); + this.$view = this.$('.ui-color-picker-view'); + this.$value = this.$('.ui-color-picker-value'); + this.$header = this.$('.ui-color-picker-header'); + + // build panel + this._build(); + + // hide panel on start up + this.visible = false; + + // set initial value + this.value(this.options.value); + + // link boxes + this.$boxes = this.$('.ui-color-picker-box'); + + // add event handler + var self = this; + this.$boxes.on('click', function() { + self.value($(this).css('background-color')); + //self.$header.trigger('click'); + }); + this.$header.on('click', function() { + self.visible = !self.visible; + if (self.visible) { + self.$view.fadeIn('fast'); + } else { + self.$view.hide(); + } + }); + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + // set default value + if (new_val === null) { + new_val = this.options.default_color; + } + + // update color value + this.$value.css('background-color', new_val); + + // check selected color in panel + this.$('.ui-color-picker-box').empty(); + this.$(this._getValue()).html(this._templateCheck()); + + // trigger custom event + this.options.onchange && this.options.onchange(new_val); + } + + // return current value + return this._getValue(); + }, + + // get value from dom + _getValue: function() { + var rgb = this.$value.css('background-color'); + rgb = rgb.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/); + if (rgb) { + function hex(x) { + return ('0' + parseInt(x).toString(16)).slice(-2); + } + return '#' + hex(rgb[1]) + hex(rgb[2]) + hex(rgb[3]); + } else { + return null; + } + }, + + // build panel + _build: function() { + var $content = this._content({ + label : 'Theme Colors', + colors : this.colors.base, + padding : 10 + }); + for (var i in this.colors.theme) { + var line_def = {}; + if (i == 0) { + line_def['bottom'] = true; + } else { + if (i != this.colors.theme.length - 1) { + line_def['top'] = true; + line_def['bottom'] = true; + } else { + line_def['top'] = true; + line_def['padding'] = 5; + } + } + line_def['colors'] = this.colors.theme[i]; + this._content(line_def); + } + this._content({ + label : 'Standard Colors', + colors : this.colors.standard, + padding : 5 + }); + }, + + // create content + _content: function(options) { + // get parameters + var label = options.label; + var colors = options.colors; + var padding = options.padding; + var top = options.top; + var bottom = options.bottom; + + // create lines + var $content = $(this._templateContent()); + + // set label + var $label = $content.find('.label'); + if (options.label) { + $label.html(options.label); + } else { + $label.hide(); + } + + // build line + var $line = $content.find('.line'); + this.$panel.append($content); + for (var i in colors) { + var $box = $(this._templateBox(colors[i])); + if (top) { + $box.css('border-top', 'none'); + $box.css('border-top-left-radius', '0px'); + $box.css('border-top-right-radius', '0px'); + } + if (bottom) { + $box.css('border-bottom', 'none'); + $box.css('border-bottom-left-radius', '0px'); + $box.css('border-bottom-right-radius', '0px'); + } + $line.append($box); + } + if (padding) { + $line.css('padding-bottom', padding); + } + return $content; + }, + + // check icon + _templateCheck: function() { + return '<div class="ui-color-picker-check fa fa-check"/>'; + }, + + // content template + _templateContent: function() { + return '<div class="ui-color-picker-content">' + + '<div class="label"/>' + + '<div class="line"/>' + + '</div>'; + }, + + // box template + _templateBox: function(color) { + return '<div id="' + color + '" class="ui-color-picker-box" style="background-color: #' + color + ';"/>'; + }, + + // template + _template: function() { + return '<div class="ui-color-picker">' + + '<div class="ui-color-picker-header">' + + '<div class="ui-color-picker-value"/>' + + '<div class="ui-color-picker-label">Select a color</div>' + + '</div>' + + '<div class="ui-color-picker-view ui-input">' + + '<div class="ui-color-picker-panel"/>' + + '</div>' + '</div>'; + } +}); +}); \ No newline at end of file diff -r 8563e5b33300a733344a165dff13a1877bccde79 -r 32b5ad88cd9baf12cd0776c54437b445a0561abf static/scripts/packed/mvc/tools/tools-parameters.js --- a/static/scripts/packed/mvc/tools/tools-parameters.js +++ b/static/scripts/packed/mvc/tools/tools-parameters.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-select-content"],function(b,c,a){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden"},initialize:function(e,d){this.app=e},create:function(d){if(d.value===undefined){d.value=null}if(d.default_value===undefined){d.default_value=d.value}var f=null;var e=this.types[d.type];if(e&&typeof(this[e])==="function"){f=this[e].call(this,d)}if(!f){this.app.incompatible=true;if(d.options){f=this._fieldSelect(d)}else{f=this._fieldText(d)}console.debug("tools-form::_addRow() : Auto matched field type ("+d.type+").")}if(d.value!==undefined){f.value(d.value)}return f},_fieldData:function(d){if(!this.app.options.is_dynamic){d.info="Data input '"+d.name+"' ("+b.textify(d.extensions.toString())+")";d.value=null;return this._fieldHidden(d)}var e=this;return new a.View(this.app,{id:"field-"+d.id,extensions:d.extensions,optional:d.optional,multiple:d.multiple,type:d.type,data:d.options,onchange:function(){e.app.trigger("refresh")}})},_fieldSelect:function(d){if(!this.app.options.is_dynamic&&d.is_dynamic){return this._fieldText(d)}if(d.type=="data_column"){d.error_text="Missing columns in referenced dataset."}if(d.type=="genomebuild"){d.searchable=true}var f=[];for(var g in d.options){var h=d.options[g];f.push({label:h[0],value:h[1]})}var j=c.Select;switch(d.display){case"checkboxes":j=c.Checkbox;break;case"radio":j=c.Radio;break}var e=this;return new j.View({id:"field-"+d.id,data:f,error_text:d.error_text||"No options available",multiple:d.multiple,searchable:d.searchable,onchange:function(){e.app.trigger("refresh")}})},_fieldDrilldown:function(d){if(!this.app.options.is_dynamic&&d.is_dynamic){return this._fieldText(d)}var e=this;return new c.Drilldown.View({id:"field-"+d.id,data:d.options,display:d.display,onchange:function(){e.app.trigger("refresh")}})},_fieldText:function(d){if(d.options){d.area=d.multiple;if(!b.validate(d.value)){d.value=""}else{if(d.value instanceof Array){d.value=value.toString()}else{d.value=String(d.value).replace(/[\[\]'"\s]/g,"");if(d.multiple){d.value=d.value.replace(/,/g,"\n")}}}}var e=this;return new c.Input({id:"field-"+d.id,area:d.area,onchange:function(){e.app.trigger("refresh")}})},_fieldSlider:function(d){var e=this;return new c.Slider.View({id:"field-"+d.id,precise:d.type=="float",min:d.min,max:d.max,onchange:function(){e.app.trigger("refresh")}})},_fieldHidden:function(d){return new c.Hidden({id:"field-"+d.id,info:d.info})},_fieldBoolean:function(d){var e=this;return new c.RadioButton.View({id:"field-"+d.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){e.app.trigger("refresh")}})}});return{View:View}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-select-content","mvc/ui/ui-color-picker"],function(c,d,a,b){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",},initialize:function(f,e){this.app=f},create:function(e){if(e.value===undefined){e.value=null}if(e.default_value===undefined){e.default_value=e.value}var g=null;var f=this.types[e.type];if(f&&typeof(this[f])==="function"){g=this[f].call(this,e)}if(!g){this.app.incompatible=true;if(e.options){g=this._fieldSelect(e)}else{g=this._fieldText(e)}console.debug("tools-form::_addRow() : Auto matched field type ("+e.type+").")}if(e.value!==undefined){g.value(e.value)}return g},_fieldData:function(e){if(!this.app.options.is_dynamic){e.info="Data input '"+e.name+"' ("+c.textify(e.extensions.toString())+")";e.value=null;return this._fieldHidden(e)}var f=this;return new a.View(this.app,{id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,data:e.options,onchange:function(){f.app.trigger("refresh")}})},_fieldSelect:function(e){if(!this.app.options.is_dynamic&&e.is_dynamic){return this._fieldText(e)}if(e.type=="data_column"){e.error_text="Missing columns in referenced dataset."}if(e.type=="genomebuild"){e.searchable=true}var g=[];for(var h in e.options){var j=e.options[h];g.push({label:j[0],value:j[1]})}var k=d.Select;switch(e.display){case"checkboxes":k=d.Checkbox;break;case"radio":k=d.Radio;break}var f=this;return new k.View({id:"field-"+e.id,data:g,error_text:e.error_text||"No options available",multiple:e.multiple,searchable:e.searchable,onchange:function(){f.app.trigger("refresh")}})},_fieldDrilldown:function(e){if(!this.app.options.is_dynamic&&e.is_dynamic){return this._fieldText(e)}var f=this;return new d.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,onchange:function(){f.app.trigger("refresh")}})},_fieldText:function(e){if(e.options){e.area=e.multiple;if(!c.validate(e.value)){e.value=""}else{if(e.value instanceof Array){e.value=value.toString()}else{e.value=String(e.value).replace(/[\[\]'"\s]/g,"");if(e.multiple){e.value=e.value.replace(/,/g,"\n")}}}}var f=this;return new d.Input({id:"field-"+e.id,area:e.area,onchange:function(){f.app.trigger("refresh")}})},_fieldSlider:function(e){var f=this;return new d.Slider.View({id:"field-"+e.id,precise:e.type=="float",min:e.min,max:e.max,onchange:function(){f.app.trigger("refresh")}})},_fieldHidden:function(e){return new d.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){var f=this;return new d.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){f.app.trigger("refresh")}})},_fieldColor:function(e){var f=this;return new b(this.app,{id:"field-"+e.id,onchange:function(){f.app.trigger("refresh")}})}});return{View:View}}); \ No newline at end of file diff -r 8563e5b33300a733344a165dff13a1877bccde79 -r 32b5ad88cd9baf12cd0776c54437b445a0561abf static/scripts/packed/mvc/ui/ui-color-picker.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-color-picker.js @@ -0,0 +1,1 @@ +define(["utils/utils","mvc/ui/ui-misc"],function(a,b){return Backbone.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7f","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},optionsDefault:{default_color:"#fdeada"},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template());this.$panel=this.$(".ui-color-picker-panel");this.$view=this.$(".ui-color-picker-view");this.$value=this.$(".ui-color-picker-value");this.$header=this.$(".ui-color-picker-header");this._build();this.visible=false;this.value(this.options.value);this.$boxes=this.$(".ui-color-picker-box");var c=this;this.$boxes.on("click",function(){c.value($(this).css("background-color"))});this.$header.on("click",function(){c.visible=!c.visible;if(c.visible){c.$view.fadeIn("fast")}else{c.$view.hide()}})},value:function(c){if(c!==undefined){if(c===null){c=this.options.default_color}this.$value.css("background-color",c);this.$(".ui-color-picker-box").empty();this.$(this._getValue()).html(this._templateCheck());this.options.onchange&&this.options.onchange(c)}return this._getValue()},_getValue:function(){var c=this.$value.css("background-color");c=c.match(/^rgb$(\d+),\s*(\d+),\s*(\d+)$$/);if(c){function d(e){return("0"+parseInt(e).toString(16)).slice(-2)}return"#"+d(c[1])+d(c[2])+d(c[3])}else{return null}},_build:function(){var d=this._content({label:"Theme Colors",colors:this.colors.base,padding:10});for(var e in this.colors.theme){var c={};if(e==0){c.bottom=true}else{if(e!=this.colors.theme.length-1){c.top=true;c.bottom=true}else{c.top=true;c.padding=5}}c.colors=this.colors.theme[e];this._content(c)}this._content({label:"Standard Colors",colors:this.colors.standard,padding:5})},_content:function(n){var l=n.label;var d=n.colors;var k=n.padding;var h=n.top;var c=n.bottom;var f=$(this._templateContent());var j=f.find(".label");if(n.label){j.html(n.label)}else{j.hide()}var m=f.find(".line");this.$panel.append(f);for(var g in d){var e=$(this._templateBox(d[g]));if(h){e.css("border-top","none");e.css("border-top-left-radius","0px");e.css("border-top-right-radius","0px")}if(c){e.css("border-bottom","none");e.css("border-bottom-left-radius","0px");e.css("border-bottom-right-radius","0px")}m.append(e)}if(k){m.css("padding-bottom",k)}return f},_templateCheck:function(){return'<div class="ui-color-picker-check fa fa-check"/>'},_templateContent:function(){return'<div class="ui-color-picker-content"><div class="label"/><div class="line"/></div>'},_templateBox:function(c){return'<div id="'+c+'" class="ui-color-picker-box" style="background-color: #'+c+';"/>'},_template:function(){return'<div class="ui-color-picker"><div class="ui-color-picker-header"><div class="ui-color-picker-value"/><div class="ui-color-picker-label">Select a color</div></div><div class="ui-color-picker-view ui-input"><div class="ui-color-picker-panel"/></div>';"</div>"}})}); \ No newline at end of file diff -r 8563e5b33300a733344a165dff13a1877bccde79 -r 32b5ad88cd9baf12cd0776c54437b445a0561abf static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1453,6 +1453,11 @@ .ui-select .select2-container{width:100%} .ui-select select{position:relative;top:0px;height:27px;width:100%;padding-left:5px;padding-right:20px;cursor:pointer;background:transparent;-webkit-appearance:none;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px} .ui-select-content .ui-options{float:left;padding-top:2px} +.ui-color-picker .ui-color-picker-header{cursor:pointer} +.ui-color-picker .ui-color-picker-value{float:left;border-radius:3px;border:solid 1px #000000;width:12px;height:12px;margin-bottom:10px;margin-right:5px} +.ui-color-picker .ui-color-picker-label{float:left;line-height:1.2em} +.ui-color-picker .ui-color-picker-view{height:100%;overflow:auto;display:none;float:left}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel{height:100%;overflow:auto;width:230px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content{clear:both;margin-bottom:15px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .label{padding-bottom:2px} +.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line{clear:both}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box{cursor:pointer;float:left;margin-right:5px;border:solid 1px #c0c0c0;width:15px;height:15px;border-radius:2px}.ui-color-picker .ui-color-picker-view .ui-color-picker-panel .ui-color-picker-content .line .ui-color-picker-box .ui-color-picker-check{color:black;font-size:1.2em;position:relative;left:1px} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} diff -r 8563e5b33300a733344a165dff13a1877bccde79 -r 32b5ad88cd9baf12cd0776c54437b445a0561abf static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -440,4 +440,59 @@ float: left; padding-top: 2px; } +} + +.ui-color-picker { + .ui-color-picker-header { + cursor: pointer; + } + .ui-color-picker-value { + float: left; + border-radius: 3px; + border: solid 1px #000000; + width: 12px; + height: 12px; + margin-bottom: 10px; + margin-right: 5px; + } + .ui-color-picker-label { + float: left; + line-height: 1.2em; + } + .ui-color-picker-view { + height: 100%; + overflow: auto; + display: none; + float: left; + .ui-color-picker-panel { + height: 100%; + overflow: auto; + width: 230px; + .ui-color-picker-content { + clear: both; + margin-bottom: 15px; + .label { + padding-bottom: 2px; + } + .line { + clear: both; + .ui-color-picker-box { + cursor: pointer; + float: left; + margin-right: 5px; + border: solid 1px #c0c0c0; + width: 15px; + height: 15px; + border-radius: 2px; + .ui-color-picker-check { + color: black; + font-size: 1.2em; + position: relative; + left: 1px; + } + } + } + } + } + } } \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: UI, history multi-view: fix size sorting, add more orders, rework UI for orders
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8563e5b33300/ Changeset: 8563e5b33300 User: carlfeberhard Date: 2015-02-12 22:51:45+00:00 Summary: UI, history multi-view: fix size sorting, add more orders, rework UI for orders Affected #: 3 files diff -r 658eb245347822b95722b4a679d1aeb93da39890 -r 8563e5b33300a733344a165dff13a1877bccde79 client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -400,6 +400,7 @@ /** the order that the collection is rendered in */ this.order = options.order || 'update'; + this._initSortOrders(); /** named ajax queue for loading hdas */ this.hdaQueue = new ajaxQueue.NamedAjaxQueue( [], false ); @@ -416,6 +417,47 @@ this.setUpListeners(); }, + _initSortOrders : function(){ + function _comparator( getter, options ){ + return function __comparator( a, b, currentHistoryId ){ + // current always first + if( a.id === currentHistoryId ){ return -1; } + if( b.id === currentHistoryId ){ return 1; } + // then compare by an attribute + a = getter( a ); + b = getter( b ); + return options.asc? + ( ( a === b )?( 0 ):( a > b ? 1 : -1 ) ): + ( ( a === b )?( 0 ):( a > b ? -1 : 1 ) ); + }; + } + + this.sortOrders = { + // default + update : { + text: _l( 'most recent first' ), + fn: _comparator( function( h ){ return Date( h.get( 'update_time' ) ); }, { asc : false }) + }, + 'name' : { + text: _l( 'name, a to z' ), + fn: _comparator( function( h ){ return h.get( 'name' ); }, { asc : true }) + }, + 'name-dsc' : { + text: _l( 'name, z to a' ), + fn: _comparator( function( h ){ return h.get( 'name' ); }, { asc : false }) + }, + 'size' : { + text: _l( 'size, large to small' ), + fn: _comparator( function( h ){ return h.get( 'size' ); }, { asc : false }) + }, + 'size-dsc' : { + text: _l( 'size, small to large' ), + fn: _comparator( function( h ){ return h.get( 'size' ); }, { asc : true }) + } + }; + return this.sortOrders; + }, + /** Set up reflexive listeners */ setUpListeners : function setUpListeners(){ //var multipanel = this; @@ -497,46 +539,23 @@ * (sorting the collection will re-render the panel) */ sortCollection : function( order, options ){ - order = order || this.order; - var currentHistoryId = this.currentHistoryId; + if( !( order in this.sortOrders ) ){ + order = 'update'; + } + this.order = order; + var currentHistoryId = this.currentHistoryId, + sortOrder = this.sortOrders[ order ]; - //note: h.id !== currentHistoryId allows the sort to put the current history first - switch( order ){ - case 'name': - //TODO: we can use a 2 arg version and return 1/0/-1 - //this.collection.comparator = function( h1, h2 ){ - this.collection.comparator = function( h ){ - //TODO: this won't do reverse order well - return [ h.id !== currentHistoryId, h.get( 'name' ).toLowerCase() ]; - }; - break; - case 'size': - this.collection.comparator = function( h ){ - return [ h.id !== currentHistoryId, h.get( 'size' ) ]; - }; - break; - default: - this.collection.comparator = function( h ){ - return [ h.id !== currentHistoryId, Date( h.get( 'update_time' ) ) ]; - }; - } + this.collection.comparator = function __comparator( a, b ){ + return sortOrder.fn( a, b, currentHistoryId ); + }; + this.$( '.current-order' ).text( sortOrder.text ); + //NOTE: auto fires 'sort' from collection this.collection.sort( options ); return this.collection; }, - /** Set the sort order and re-sort */ - setOrder : function( order ){ - if( [ 'update', 'name', 'size' ].indexOf( order ) === -1 ){ - order = 'update'; - } - this.order = order; - this.trigger( 'order:change', order, this ); - this.$( '.current-order' ).text( order ); - this.sortCollection(); - return this; - }, - /** create a new history and set it to current */ create : function( ev ){ return this.collection.create({ current: true }); @@ -806,13 +825,9 @@ 'click .done.btn' : 'close', // creates a new empty history and makes it current 'click .create-new.btn' : 'create', - 'click #include-deleted' : '_clickToggleDeletedHistories', // these change the collection and column sort order - 'click .order .order-update' : function( e ){ this.setOrder( 'update' ); }, - 'click .order .order-name' : function( e ){ this.setOrder( 'name' ); }, - 'click .order .order-size' : function( e ){ this.setOrder( 'size' ); }, - + 'click .order .set-order' : '_chooseOrder', 'click #toggle-deleted' : '_clickToggleDeletedDatasets', 'click #toggle-hidden' : '_clickToggleHiddenDatasets' @@ -868,6 +883,11 @@ }); }, + _chooseOrder : function( ev ){ + var orderKey = $( ev.currentTarget ).data( 'order' ); + this.sortCollection( orderKey ); + }, + /** Set up any view plugins */ setUpBehaviors : function(){ var multipanel = this; @@ -1041,29 +1061,28 @@ optionsPopoverTemplate : _.template([ '<div class="more-options">', + + '<div class="order btn-group">', + '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', + _l( 'Order histories by' ) + ' ', + '<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ', + '<span class="caret"></span>', + '</button>', + '<ul class="dropdown-menu" role="menu">', + '<% _.each( view.sortOrders, function( order, key ){ %>', + '<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">', + '<%= order.text %>', + '</a></li>', + '<% }); %>', + '</ul>', + '</div>', + '<div class="checkbox"><label><input id="include-deleted" type="checkbox"', '<%= view.collection.includeDeleted? " checked" : "" %>>', _l( 'Include deleted histories' ), '</label></div>', - '<div class="order btn-group">', - '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', - _l( 'Order histories by' ) + ' ', - '<span class="current-order"><%= view.order %></span> ', - '<span class="caret"></span>', - '</button>', - '<ul class="dropdown-menu" role="menu">', - '<li><a href="javascript:void(0);" class="order-update">', - _l( 'Time of last update' ), - '</a></li>', - '<li><a href="javascript:void(0);" class="order-name">', - _l( 'Name' ), - '</a></li>', - '<li><a href="javascript:void(0);" class="order-size">', - _l( 'Size' ), - '</a></li>', - '</ul>', - '</div>', + '<hr />', '<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">', _l( 'Include deleted datasets' ), diff -r 658eb245347822b95722b4a679d1aeb93da39890 -r 8563e5b33300a733344a165dff13a1877bccde79 static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -400,6 +400,7 @@ /** the order that the collection is rendered in */ this.order = options.order || 'update'; + this._initSortOrders(); /** named ajax queue for loading hdas */ this.hdaQueue = new ajaxQueue.NamedAjaxQueue( [], false ); @@ -416,6 +417,47 @@ this.setUpListeners(); }, + _initSortOrders : function(){ + function _comparator( getter, options ){ + return function __comparator( a, b, currentHistoryId ){ + // current always first + if( a.id === currentHistoryId ){ return -1; } + if( b.id === currentHistoryId ){ return 1; } + // then compare by an attribute + a = getter( a ); + b = getter( b ); + return options.asc? + ( ( a === b )?( 0 ):( a > b ? 1 : -1 ) ): + ( ( a === b )?( 0 ):( a > b ? -1 : 1 ) ); + }; + } + + this.sortOrders = { + // default + update : { + text: _l( 'most recent first' ), + fn: _comparator( function( h ){ return Date( h.get( 'update_time' ) ); }, { asc : false }) + }, + 'name' : { + text: _l( 'name, a to z' ), + fn: _comparator( function( h ){ return h.get( 'name' ); }, { asc : true }) + }, + 'name-dsc' : { + text: _l( 'name, z to a' ), + fn: _comparator( function( h ){ return h.get( 'name' ); }, { asc : false }) + }, + 'size' : { + text: _l( 'size, large to small' ), + fn: _comparator( function( h ){ return h.get( 'size' ); }, { asc : false }) + }, + 'size-dsc' : { + text: _l( 'size, small to large' ), + fn: _comparator( function( h ){ return h.get( 'size' ); }, { asc : true }) + } + }; + return this.sortOrders; + }, + /** Set up reflexive listeners */ setUpListeners : function setUpListeners(){ //var multipanel = this; @@ -497,46 +539,23 @@ * (sorting the collection will re-render the panel) */ sortCollection : function( order, options ){ - order = order || this.order; - var currentHistoryId = this.currentHistoryId; + if( !( order in this.sortOrders ) ){ + order = 'update'; + } + this.order = order; + var currentHistoryId = this.currentHistoryId, + sortOrder = this.sortOrders[ order ]; - //note: h.id !== currentHistoryId allows the sort to put the current history first - switch( order ){ - case 'name': - //TODO: we can use a 2 arg version and return 1/0/-1 - //this.collection.comparator = function( h1, h2 ){ - this.collection.comparator = function( h ){ - //TODO: this won't do reverse order well - return [ h.id !== currentHistoryId, h.get( 'name' ).toLowerCase() ]; - }; - break; - case 'size': - this.collection.comparator = function( h ){ - return [ h.id !== currentHistoryId, h.get( 'size' ) ]; - }; - break; - default: - this.collection.comparator = function( h ){ - return [ h.id !== currentHistoryId, Date( h.get( 'update_time' ) ) ]; - }; - } + this.collection.comparator = function __comparator( a, b ){ + return sortOrder.fn( a, b, currentHistoryId ); + }; + this.$( '.current-order' ).text( sortOrder.text ); + //NOTE: auto fires 'sort' from collection this.collection.sort( options ); return this.collection; }, - /** Set the sort order and re-sort */ - setOrder : function( order ){ - if( [ 'update', 'name', 'size' ].indexOf( order ) === -1 ){ - order = 'update'; - } - this.order = order; - this.trigger( 'order:change', order, this ); - this.$( '.current-order' ).text( order ); - this.sortCollection(); - return this; - }, - /** create a new history and set it to current */ create : function( ev ){ return this.collection.create({ current: true }); @@ -806,13 +825,9 @@ 'click .done.btn' : 'close', // creates a new empty history and makes it current 'click .create-new.btn' : 'create', - 'click #include-deleted' : '_clickToggleDeletedHistories', // these change the collection and column sort order - 'click .order .order-update' : function( e ){ this.setOrder( 'update' ); }, - 'click .order .order-name' : function( e ){ this.setOrder( 'name' ); }, - 'click .order .order-size' : function( e ){ this.setOrder( 'size' ); }, - + 'click .order .set-order' : '_chooseOrder', 'click #toggle-deleted' : '_clickToggleDeletedDatasets', 'click #toggle-hidden' : '_clickToggleHiddenDatasets' @@ -868,6 +883,11 @@ }); }, + _chooseOrder : function( ev ){ + var orderKey = $( ev.currentTarget ).data( 'order' ); + this.sortCollection( orderKey ); + }, + /** Set up any view plugins */ setUpBehaviors : function(){ var multipanel = this; @@ -1041,29 +1061,28 @@ optionsPopoverTemplate : _.template([ '<div class="more-options">', + + '<div class="order btn-group">', + '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', + _l( 'Order histories by' ) + ' ', + '<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ', + '<span class="caret"></span>', + '</button>', + '<ul class="dropdown-menu" role="menu">', + '<% _.each( view.sortOrders, function( order, key ){ %>', + '<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">', + '<%= order.text %>', + '</a></li>', + '<% }); %>', + '</ul>', + '</div>', + '<div class="checkbox"><label><input id="include-deleted" type="checkbox"', '<%= view.collection.includeDeleted? " checked" : "" %>>', _l( 'Include deleted histories' ), '</label></div>', - '<div class="order btn-group">', - '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', - _l( 'Order histories by' ) + ' ', - '<span class="current-order"><%= view.order %></span> ', - '<span class="caret"></span>', - '</button>', - '<ul class="dropdown-menu" role="menu">', - '<li><a href="javascript:void(0);" class="order-update">', - _l( 'Time of last update' ), - '</a></li>', - '<li><a href="javascript:void(0);" class="order-name">', - _l( 'Name' ), - '</a></li>', - '<li><a href="javascript:void(0);" class="order-size">', - _l( 'Size' ), - '</a></li>', - '</ul>', - '</div>', + '<hr />', '<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">', _l( 'Include deleted datasets' ), diff -r 658eb245347822b95722b4a679d1aeb93da39890 -r 8563e5b33300a733344a165dff13a1877bccde79 static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(C),this.controlsRightTemplate(C),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"history"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !history.purged ){ %>",'<div class="panel-menu order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"history"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-history-columns",initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.trigger("order:change",C,this);this.$(".current-order").text(C);this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")},"click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<button class="open-more-options btn btn-default">','<span class="fa fa-ellipsis-h" title="More options"></span>',"</button>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>",'<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.order %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(C),this.controlsRightTemplate(C),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"history"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !history.purged ){ %>",'<div class="panel-menu order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"history"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-history-columns",initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this._initSortOrders();this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},_initSortOrders:function(){function C(D,E){return function F(H,G,I){if(H.id===I){return -1}if(G.id===I){return 1}H=D(H);G=D(G);return E.asc?((H===G)?(0):(H>G?1:-1)):((H===G)?(0):(H>G?-1:1))}}this.sortOrders={update:{text:_l("most recent first"),fn:C(function(D){return Date(D.get("update_time"))},{asc:false})},name:{text:_l("name, a to z"),fn:C(function(D){return D.get("name")},{asc:true})},"name-dsc":{text:_l("name, z to a"),fn:C(function(D){return D.get("name")},{asc:false})},size:{text:_l("size, large to small"),fn:C(function(D){return D.get("size")},{asc:false})},"size-dsc":{text:_l("size, small to large"),fn:C(function(D){return D.get("size")},{asc:true})}};return this.sortOrders},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){if(!(C in this.sortOrders)){C="update"}this.order=C;var G=this.currentHistoryId,F=this.sortOrders[C];this.collection.comparator=function E(I,H){return F.fn(I,H,G)};this.$(".current-order").text(F.text);this.collection.sort(D);return this.collection},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},_chooseOrder:function(D){var C=$(D.currentTarget).data("order");this.sortCollection(C)},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<button class="open-more-options btn btn-default">','<span class="fa fa-ellipsis-h" title="More options"></span>',"</button>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: martenson: fix for 'add datasets to folder' button in data libraries
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/658eb2453478/ Changeset: 658eb2453478 User: martenson Date: 2015-02-12 21:09:18+00:00 Summary: fix for 'add datasets to folder' button in data libraries when no library import configuration is set; thanks to Carl for reporting this Affected #: 3 files diff -r 916aee1b2e3d74015a727133cd7f4a2ef9c1a447 -r 658eb245347822b95722b4a679d1aeb93da39890 client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -1039,7 +1039,7 @@ tmpl_array.push(' </ul>'); tmpl_array.push(' </div>'); tmpl_array.push('<% } else { %>'); - tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); + tmpl_array.push(' <a data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></a>'); tmpl_array.push('<% } %>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>'); diff -r 916aee1b2e3d74015a727133cd7f4a2ef9c1a447 -r 658eb245347822b95722b4a679d1aeb93da39890 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -1039,7 +1039,7 @@ tmpl_array.push(' </ul>'); tmpl_array.push(' </div>'); tmpl_array.push('<% } else { %>'); - tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); + tmpl_array.push(' <a data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></a>'); tmpl_array.push('<% } %>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>'); diff -r 916aee1b2e3d74015a727133cd7f4a2ef9c1a447 -r 658eb245347822b95722b4a679d1aeb93da39890 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(Galaxy.config.user_library_import_dir!==null||Galaxy.config.allow_library_path_paste!==false||Galaxy.config.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},renderPaginator:function(h){this.options=_.extend(this.options,h);var g=this.templatePaginator();this.$el.find("#folder_paginator").html(g({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)}});e.get({url:galaxy_config.root+"api/genomes",success:function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})}})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"library-genome-select",data:g.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"});this.select_extension=new a.View({css:"library-extension-select",data:g.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(g){var i=this;var h=this.templateBrowserModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Please select folders or files",body:h({}),buttons:{Import:function(){i.importFromJstreePath(i,g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+i.id,{trigger:true})}});this.renderSelectBoxes();g.disabled_jstree_element="folders";this.renderJstree(g);$("input[type=radio]").change(function(j){if(j.target.value==="jstree-disable-folders"){g.disabled_jstree_element="folders";i.renderJstree(g);$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(j.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.disabled_jstree_element="files";i.renderJstree(g)}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var j=g.source||"userdir";var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target="+j+"&format=jstree&disable="+h;this.jstree.fetch({success:function(l,k){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(m){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:l},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error(k.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromJstreePath:function(n,r){var g=$("#jstree_browser").jstree().get_selected(true);var m=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var j=this.select_extension.value();var p=this.select_genome.value();var k=g[0].type;var q=[];if(g.length<1){f.info("Please select some items first.")}else{this.modal.disableButton("Import");for(var l=g.length-1;l>=0;l--){if(g[l].li_attr.full_path!==undefined){q.push(g[l].li_attr.full_path)}}this.initChainCallControl({length:q.length,action:"adding_datasets"});if(k==="folder"){var h=r.source+"_folder";this.chainCallImportingFolders({paths:q,preserve_dirs:m,link_data:o,source:h,file_type:j,dbkey:p})}else{if(k==="file"){var h=r.source+"_file";this.chainCallImportingUserdirFiles({paths:q,file_type:j,dbkey:p,source:h})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(g)})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets were deleted.")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted. Please make sure you have sufficient permissions.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted. Please make sure you have sufficient permissions.")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},showPageSizePrompt:function(){var g=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));if((g!=null)&&(g==parseInt(g))){Galaxy.libraries.preferences.set({folder_page_size:parseInt(g)});Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1})}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="folder_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" id="page_size_prompt"><%- items_shown %></a> of <%- total_items_count %> items');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},});return{FolderToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(Galaxy.config.user_library_import_dir!==null||Galaxy.config.allow_library_path_paste!==false||Galaxy.config.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},renderPaginator:function(h){this.options=_.extend(this.options,h);var g=this.templatePaginator();this.$el.find("#folder_paginator").html(g({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)}});e.get({url:galaxy_config.root+"api/genomes",success:function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})}})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"library-genome-select",data:g.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"});this.select_extension=new a.View({css:"library-extension-select",data:g.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(g){var i=this;var h=this.templateBrowserModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Please select folders or files",body:h({}),buttons:{Import:function(){i.importFromJstreePath(i,g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+i.id,{trigger:true})}});this.renderSelectBoxes();g.disabled_jstree_element="folders";this.renderJstree(g);$("input[type=radio]").change(function(j){if(j.target.value==="jstree-disable-folders"){g.disabled_jstree_element="folders";i.renderJstree(g);$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(j.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.disabled_jstree_element="files";i.renderJstree(g)}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var j=g.source||"userdir";var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target="+j+"&format=jstree&disable="+h;this.jstree.fetch({success:function(l,k){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(m){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:l},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error(k.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromJstreePath:function(n,r){var g=$("#jstree_browser").jstree().get_selected(true);var m=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var j=this.select_extension.value();var p=this.select_genome.value();var k=g[0].type;var q=[];if(g.length<1){f.info("Please select some items first.")}else{this.modal.disableButton("Import");for(var l=g.length-1;l>=0;l--){if(g[l].li_attr.full_path!==undefined){q.push(g[l].li_attr.full_path)}}this.initChainCallControl({length:q.length,action:"adding_datasets"});if(k==="folder"){var h=r.source+"_folder";this.chainCallImportingFolders({paths:q,preserve_dirs:m,link_data:o,source:h,file_type:j,dbkey:p})}else{if(k==="file"){var h=r.source+"_file";this.chainCallImportingUserdirFiles({paths:q,file_type:j,dbkey:p,source:h})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(g)})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets were deleted.")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted. Please make sure you have sufficient permissions.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted. Please make sure you have sufficient permissions.")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},showPageSizePrompt:function(){var g=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));if((g!=null)&&(g==parseInt(g))){Galaxy.libraries.preferences.set({folder_page_size:parseInt(g)});Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1})}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <a data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></a>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="folder_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" id="page_size_prompt"><%- items_shown %></a> of <%- total_items_count %> items');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},});return{FolderToolbarView:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Rename the egg env vars back to GALAXY_* now that they are not config file options anymore.
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/916aee1b2e3d/ Changeset: 916aee1b2e3d User: natefoo Date: 2015-02-12 20:42:50+00:00 Summary: Rename the egg env vars back to GALAXY_* now that they are not config file options anymore. Affected #: 3 files diff -r 6730c4cb28dead6bbf57a3e1f599136ab71dd34d -r 916aee1b2e3d74015a727133cd7f4a2ef9c1a447 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -293,9 +293,9 @@ self.py_platform = None if platform is not None: self.py_platform = platform.split( '-' )[0] - self.enable_egg_fetch = string_as_bool(os.environ.get('GALAXY_CONFIG_ENABLE_EGG_FETCH', True)) - self.enable_eggs = string_as_bool(os.environ.get('GALAXY_CONFIG_ENABLE_EGGS', True)) - self.try_dependencies_from_env = string_as_bool(os.environ.get('GALAXY_CONFIG_TRY_DEPENDENCIES_FROM_ENV', False)) + self.enable_egg_fetch = string_as_bool(os.environ.get('GALAXY_ENABLE_EGG_FETCH', True)) + self.enable_eggs = string_as_bool(os.environ.get('GALAXY_ENABLE_EGGS', True)) + self.try_dependencies_from_env = string_as_bool(os.environ.get('GALAXY_TRY_DEPENDENCIES_FROM_ENV', False)) self.galaxy_config = GalaxyConfig( galaxy_config_file ) self.parse() diff -r 6730c4cb28dead6bbf57a3e1f599136ab71dd34d -r 916aee1b2e3d74015a727133cd7f4a2ef9c1a447 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -274,7 +274,7 @@ env = [] crate = galaxy.eggs.Crate() for opt in ('enable_egg_fetch', 'enable_eggs', 'try_dependencies_from_env'): - env.append('GALAXY_CONFIG_%s="%s"; export GALAXY_CONFIG_%s' % (opt.upper(), getattr(crate, opt), opt.upper())) + env.append('GALAXY_%s="%s"; export GALAXY_%s' % (opt.upper(), getattr(crate, opt), opt.upper())) return env def get_job_file(self, job_wrapper, **kwds): diff -r 6730c4cb28dead6bbf57a3e1f599136ab71dd34d -r 916aee1b2e3d74015a727133cd7f4a2ef9c1a447 requirements.txt --- a/requirements.txt +++ b/requirements.txt @@ -12,7 +12,7 @@ # However, you may want to manage these dependencies on your own. If so, this # file can be used with pip to install all of the bare minimum dependencies for # starting a Galaxy server. Use this in conjunction with the -# `GALAXY_CONFIG_ENABLE_EGGS=False` environment variable. +# `GALAXY_ENABLE_EGGS=False` environment variable. # # Note that except in the case of SQLAlchemy, all dependencies will be # installed at their newest versions. Galaxy has not been tested with these and Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a8d9371efef9/ Changeset: a8d9371efef9 User: carlfeberhard Date: 2015-02-12 20:35:24+00:00 Summary: Core: move handlebars load before require (stackoverflow.com/questions/15371918) minor clean up Affected #: 4 files diff -r d540227165d54950208d3948e2bdecd4babc70ca -r a8d9371efef9f10e6c4fce18a6da8ed7916f10ba client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -219,7 +219,7 @@ render : function render( speed ){ speed = ( speed !== undefined )?( speed ):( 'fast' ); //this.log( this + '.render', this.$el, this.el ); -//TODO: not needed + //TODO: not needed var modelData = this.model? this.model.toJSON(): {}; this.$el.html( this.template( modelData ) ); this.renderPanel( speed ); @@ -240,68 +240,21 @@ /** column body template with inner div for panel based on data (model json) */ template : function template( data ){ - data = data || {}; - var html = [ - '<div class="panel-controls clear flex-row">', - this.controlsLeftTemplate( data ), - //'<button class="btn btn-default">Herp</button>', - this.controlsRightTemplate( data ), - '</div>', - '<div class="inner flex-row flex-column-container">', - '<div id="history-', data.id, '" class="history-column history-panel flex-column"></div>', - '</div>' - ].join( '' ); - return $( html ); + data = _.extend( data || {}, { + isCurrentHistory : this.currentHistory + }); + return $([ + '<div class="panel-controls clear flex-row">', + this.controlsLeftTemplate( data ), + //'<button class="btn btn-default">Herp</button>', + this.controlsRightTemplate( data ), + '</div>', + '<div class="inner flex-row flex-column-container">', + '<div id="history-', data.id, '" class="history-column history-panel flex-column"></div>', + '</div>' + ].join( '' )); }, - /** controls template displaying controls above the panel based on this.currentHistory */ - controlsLeftTemplate : function( data ){ - return ( this.currentHistory )? - [ - '<div class="pull-left">', - '<strong class="current-label">', _l( 'Current History' ), '</strong>', - '</div>' - ].join( '' ) - :[ - '<div class="pull-left">', - '<button class="switch-to btn btn-default">', _l( 'Switch to' ), '</button>', - '</div>' - ].join( '' ); - }, - - /** controls template displaying controls above the panel based on this.currentHistory */ - controlsRightTemplate : _.template([ - '<div class="pull-right">', - '<% if( !history.purged ){ %>', - '<div class="panel-menu order btn-group">', - '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', - '<span class="caret"></span>', - '</button>', - '<ul class="dropdown-menu pull-right" role="menu">', - '<% if( !history.deleted ){ %>', - '<li><a href="javascript:void(0);" class="copy-history">', - _l( 'Copy' ), - '</a></li>', - //'<li><a href="javascript:void(0);" class="publish-history">', - // _l( 'Publish' ), - //'</a></li>', - '<li><a href="javascript:void(0);" class="delete-history">', - _l( 'Delete' ), - '</a></li>', - '<% } else /* if is deleted */ { %>', - '<li><a href="javascript:void(0);" class="undelete-history">', - _l( 'Undelete' ), - '</a></li>', - '<% } %>', - //'<li><a href="javascript:void(0);" class="purge-history">', - // _l( 'Purge' ), - //'</a></li>', - '</ul>', - '<% } %>', - '</div>', - '</div>' - ].join( '' ), { variable: 'history' }), - /** render the panel contained in the column using speed for fx speed */ renderPanel : function renderPanel( speed ){ speed = ( speed !== undefined )?( speed ):( 'fast' ); @@ -360,6 +313,51 @@ historyCopyDialog( this.model ); }, + // ------------------------------------------------------------------------ templates + /** controls template displaying controls above the panel based on this.currentHistory */ + controlsLeftTemplate : _.template([ + '<div class="pull-left">', + '<% if( history.isCurrentHistory ){ %>', + '<strong class="current-label">', _l( 'Current History' ), '</strong>', + '<% } else { %>', + '<button class="switch-to btn btn-default">', _l( 'Switch to' ), '</button>', + '<% } %>', + '</div>' + ].join( '' ), { variable : 'history' }), + + /** controls template displaying controls above the panel based on this.currentHistory */ + controlsRightTemplate : _.template([ + '<div class="pull-right">', + '<% if( !history.purged ){ %>', + '<div class="panel-menu order btn-group">', + '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', + '<span class="caret"></span>', + '</button>', + '<ul class="dropdown-menu pull-right" role="menu">', + '<% if( !history.deleted ){ %>', + '<li><a href="javascript:void(0);" class="copy-history">', + _l( 'Copy' ), + '</a></li>', + //'<li><a href="javascript:void(0);" class="publish-history">', + // _l( 'Publish' ), + //'</a></li>', + '<li><a href="javascript:void(0);" class="delete-history">', + _l( 'Delete' ), + '</a></li>', + '<% } else /* if is deleted */ { %>', + '<li><a href="javascript:void(0);" class="undelete-history">', + _l( 'Undelete' ), + '</a></li>', + '<% } %>', + //'<li><a href="javascript:void(0);" class="purge-history">', + // _l( 'Purge' ), + //'</a></li>', + '</ul>', + '<% } %>', + '</div>', + '</div>' + ].join( '' ), { variable: 'history' }), + // ------------------------------------------------------------------------ misc /** String rep */ toString : function(){ @@ -388,7 +386,7 @@ } this.currentHistoryId = options.currentHistoryId; -//TODO: move these to some defaults + //TODO: move these to some defaults this.options = { columnWidth : 312, borderWidth : 1, @@ -632,7 +630,7 @@ multipanel._recalcFirstColumnHeight(); } -//TODO: to freeColumn (where Columns have freePanel) + //TODO: to freeColumn (where Columns have freePanel) multipanel.stopListening( column.panel ); multipanel.stopListening( column ); delete multipanel.columnMap[ column.model.id ]; diff -r d540227165d54950208d3948e2bdecd4babc70ca -r a8d9371efef9f10e6c4fce18a6da8ed7916f10ba static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -219,7 +219,7 @@ render : function render( speed ){ speed = ( speed !== undefined )?( speed ):( 'fast' ); //this.log( this + '.render', this.$el, this.el ); -//TODO: not needed + //TODO: not needed var modelData = this.model? this.model.toJSON(): {}; this.$el.html( this.template( modelData ) ); this.renderPanel( speed ); @@ -240,68 +240,21 @@ /** column body template with inner div for panel based on data (model json) */ template : function template( data ){ - data = data || {}; - var html = [ - '<div class="panel-controls clear flex-row">', - this.controlsLeftTemplate( data ), - //'<button class="btn btn-default">Herp</button>', - this.controlsRightTemplate( data ), - '</div>', - '<div class="inner flex-row flex-column-container">', - '<div id="history-', data.id, '" class="history-column history-panel flex-column"></div>', - '</div>' - ].join( '' ); - return $( html ); + data = _.extend( data || {}, { + isCurrentHistory : this.currentHistory + }); + return $([ + '<div class="panel-controls clear flex-row">', + this.controlsLeftTemplate( data ), + //'<button class="btn btn-default">Herp</button>', + this.controlsRightTemplate( data ), + '</div>', + '<div class="inner flex-row flex-column-container">', + '<div id="history-', data.id, '" class="history-column history-panel flex-column"></div>', + '</div>' + ].join( '' )); }, - /** controls template displaying controls above the panel based on this.currentHistory */ - controlsLeftTemplate : function( data ){ - return ( this.currentHistory )? - [ - '<div class="pull-left">', - '<strong class="current-label">', _l( 'Current History' ), '</strong>', - '</div>' - ].join( '' ) - :[ - '<div class="pull-left">', - '<button class="switch-to btn btn-default">', _l( 'Switch to' ), '</button>', - '</div>' - ].join( '' ); - }, - - /** controls template displaying controls above the panel based on this.currentHistory */ - controlsRightTemplate : _.template([ - '<div class="pull-right">', - '<% if( !history.purged ){ %>', - '<div class="panel-menu order btn-group">', - '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', - '<span class="caret"></span>', - '</button>', - '<ul class="dropdown-menu pull-right" role="menu">', - '<% if( !history.deleted ){ %>', - '<li><a href="javascript:void(0);" class="copy-history">', - _l( 'Copy' ), - '</a></li>', - //'<li><a href="javascript:void(0);" class="publish-history">', - // _l( 'Publish' ), - //'</a></li>', - '<li><a href="javascript:void(0);" class="delete-history">', - _l( 'Delete' ), - '</a></li>', - '<% } else /* if is deleted */ { %>', - '<li><a href="javascript:void(0);" class="undelete-history">', - _l( 'Undelete' ), - '</a></li>', - '<% } %>', - //'<li><a href="javascript:void(0);" class="purge-history">', - // _l( 'Purge' ), - //'</a></li>', - '</ul>', - '<% } %>', - '</div>', - '</div>' - ].join( '' ), { variable: 'history' }), - /** render the panel contained in the column using speed for fx speed */ renderPanel : function renderPanel( speed ){ speed = ( speed !== undefined )?( speed ):( 'fast' ); @@ -360,6 +313,51 @@ historyCopyDialog( this.model ); }, + // ------------------------------------------------------------------------ templates + /** controls template displaying controls above the panel based on this.currentHistory */ + controlsLeftTemplate : _.template([ + '<div class="pull-left">', + '<% if( history.isCurrentHistory ){ %>', + '<strong class="current-label">', _l( 'Current History' ), '</strong>', + '<% } else { %>', + '<button class="switch-to btn btn-default">', _l( 'Switch to' ), '</button>', + '<% } %>', + '</div>' + ].join( '' ), { variable : 'history' }), + + /** controls template displaying controls above the panel based on this.currentHistory */ + controlsRightTemplate : _.template([ + '<div class="pull-right">', + '<% if( !history.purged ){ %>', + '<div class="panel-menu order btn-group">', + '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', + '<span class="caret"></span>', + '</button>', + '<ul class="dropdown-menu pull-right" role="menu">', + '<% if( !history.deleted ){ %>', + '<li><a href="javascript:void(0);" class="copy-history">', + _l( 'Copy' ), + '</a></li>', + //'<li><a href="javascript:void(0);" class="publish-history">', + // _l( 'Publish' ), + //'</a></li>', + '<li><a href="javascript:void(0);" class="delete-history">', + _l( 'Delete' ), + '</a></li>', + '<% } else /* if is deleted */ { %>', + '<li><a href="javascript:void(0);" class="undelete-history">', + _l( 'Undelete' ), + '</a></li>', + '<% } %>', + //'<li><a href="javascript:void(0);" class="purge-history">', + // _l( 'Purge' ), + //'</a></li>', + '</ul>', + '<% } %>', + '</div>', + '</div>' + ].join( '' ), { variable: 'history' }), + // ------------------------------------------------------------------------ misc /** String rep */ toString : function(){ @@ -388,7 +386,7 @@ } this.currentHistoryId = options.currentHistoryId; -//TODO: move these to some defaults + //TODO: move these to some defaults this.options = { columnWidth : 312, borderWidth : 1, @@ -632,7 +630,7 @@ multipanel._recalcFirstColumnHeight(); } -//TODO: to freeColumn (where Columns have freePanel) + //TODO: to freeColumn (where Columns have freePanel) multipanel.stopListening( column.panel ); multipanel.stopListening( column ); delete multipanel.columnMap[ column.model.id ]; diff -r d540227165d54950208d3948e2bdecd4babc70ca -r a8d9371efef9f10e6c4fce18a6da8ed7916f10ba static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(D){D=D||{};var C=['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(D),this.controlsRightTemplate(D),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',D.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join("");return $(C)},controlsLeftTemplate:function(C){return(this.currentHistory)?['<div class="pull-left">','<strong class="current-label">',_l("Current History"),"</strong>","</div>"].join(""):['<div class="pull-left">','<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","</div>"].join("")},controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !history.purged ){ %>",'<div class="panel-menu order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"history"}),renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-history-columns",initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.trigger("order:change",C,this);this.$(".current-order").text(C);this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")},"click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<button class="open-more-options btn btn-default">','<span class="fa fa-ellipsis-h" title="More options"></span>',"</button>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>",'<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.order %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(C){C=_.extend(C||{},{isCurrentHistory:this.currentHistory});return $(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(C),this.controlsRightTemplate(C),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',C.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);if(this.currentHistory){this.panel.$list().before(this.panel._renderDropTargetHelp())}return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var C=this;this.model._delete().fail(function(F,D,E){alert(_l("Could not delete the history")+":\n"+E)}).done(function(D){C.render()})},"click .undelete-history":function(){var C=this;this.model.undelete().fail(function(F,D,E){alert(_l("Could not undelete the history")+":\n"+E)}).done(function(D){C.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var C=this;this.model.purge().fail(function(F,D,E){alert(_l("Could not purge the history")+":\n"+E)}).done(function(D){C.render()})}},"click .copy-history":"copy"},copy:function s(){g(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"history"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !history.purged ){ %>",'<div class="panel-menu order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","</ul>","<% } %>","</div>","</div>"].join(""),{variable:"history"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({className:"multi-history-columns",initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.trigger("order:change",C,this);this.$(".current-order").text(C);this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.mainTemplate(C));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")},"click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},_clickToggleDeletedHistories:function(C){return this.toggleDeletedHistories($(C.currentTarget).is(":checked"))},toggleDeletedHistories:function(C){if(C){window.location=Galaxy.options.root+"history/view_multiple?include_deleted_histories=True"}else{window.location=Galaxy.options.root+"history/view_multiple"}},_clickToggleDeletedDatasets:function(C){return this.toggleDeletedDatasets($(C.currentTarget).is(":checked"))},toggleDeletedDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowDeleted(C,false)},E*200)})},_clickToggleHiddenDatasets:function(C){return this.toggleHiddenDatasets($(C.currentTarget).is(":checked"))},toggleHiddenDatasets:function(C){C=C!==undefined?C:false;var D=this;D.sortedFilteredColumns().forEach(function(F,E){_.delay(function(){F.panel.toggleShowHidden(C,false)},E*200)})},setUpBehaviors:function(){var D=this;D._moreOptionsPopover();D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:true,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTarget=false;C.panel.$(".history-drop-target").remove()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<button class="open-more-options btn btn-default">','<span class="fa fa-ellipsis-h" title="More options"></span>',"</button>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>",'<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.order %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:m}}); \ No newline at end of file diff -r d540227165d54950208d3948e2bdecd4babc70ca -r a8d9371efef9f10e6c4fce18a6da8ed7916f10ba templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -35,11 +35,11 @@ 'libs/bootstrap', 'libs/underscore', 'libs/backbone/backbone', + 'libs/handlebars.runtime', 'libs/require', 'libs/d3', 'galaxy.base', - 'galaxy.panels', - 'libs/handlebars.runtime' + 'galaxy.panels' )} ## send errors to Sntry server if configured https://bitbucket.org/galaxy/galaxy-central/commits/6730c4cb28de/ Changeset: 6730c4cb28de User: carlfeberhard Date: 2015-02-12 20:35:47+00:00 Summary: Merge Affected #: 2 files diff -r a8d9371efef9f10e6c4fce18a6da8ed7916f10ba -r 6730c4cb28dead6bbf57a3e1f599136ab71dd34d lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -61,15 +61,13 @@ self.distribution = None self.dir = None self.removed_location = None - self.enable_fetch = crate.galaxy_config.enable_egg_fetch + self.enable_fetch = crate.enable_egg_fetch if self.name is not None and self.version is not None: self.set_distribution() def set_dir( self ): global eggs_dir self.dir = eggs_dir - if not os.path.exists( self.dir ): - os.makedirs( self.dir ) def set_distribution( self ): """ @@ -131,6 +129,8 @@ def _fetch(): if self.url is None: return False + if not os.path.exists( self.dir ): + os.makedirs( self.dir ) alternative = None try: url = self.url + '/' + self.distribution.egg_name() + '.egg' @@ -284,7 +284,7 @@ """ config_file = os.path.join( galaxy_dir, 'eggs.ini' ) - def __init__( self, galaxy_config_file, platform=None ): + def __init__( self, galaxy_config_file=None, platform=None ): self.eggs = {} self.config = CaseSensitiveConfigParser() self.repo = None @@ -293,6 +293,9 @@ self.py_platform = None if platform is not None: self.py_platform = platform.split( '-' )[0] + self.enable_egg_fetch = string_as_bool(os.environ.get('GALAXY_CONFIG_ENABLE_EGG_FETCH', True)) + self.enable_eggs = string_as_bool(os.environ.get('GALAXY_CONFIG_ENABLE_EGGS', True)) + self.try_dependencies_from_env = string_as_bool(os.environ.get('GALAXY_CONFIG_TRY_DEPENDENCIES_FROM_ENV', False)) self.galaxy_config = GalaxyConfig( galaxy_config_file ) self.parse() @@ -381,7 +384,7 @@ """ Try to resolve (e.g. fetch) all eggs in the crate. """ - if self.galaxy_config.enable_eggs and not self.galaxy_config.try_dependencies_from_env: + if self.enable_eggs and not self.try_dependencies_from_env: if all: eggs = self.all_eggs else: @@ -403,19 +406,12 @@ always_conditional = ( 'pysam', 'ctypes', 'python_daemon' ) def __init__( self, config_file ): - self.enable_egg_fetch = True - self.enable_eggs = True - self.try_dependencies_from_env = False if config_file is None: self.config = None else: self.config = ConfigParser.ConfigParser() if self.config.read( config_file ) == []: raise Exception( "error: unable to read Galaxy config from %s" % config_file ) - for opt in ('enable_egg_fetch', 'enable_eggs', 'try_dependencies_from_env'): - var = 'GALAXY_CONFIG_' + opt.upper() - if var in os.environ: - setattr(self, opt, string_as_bool(os.environ[var])) def check_conditional( self, egg_name ): def check_pysam(): @@ -470,11 +466,11 @@ def require( req_str ): c = Crate( None ) req = pkg_resources.Requirement.parse( req_str ) - if c.galaxy_config.try_dependencies_from_env or not c.galaxy_config.enable_eggs: + if c.try_dependencies_from_env or not c.enable_eggs: try: return pkg_resources.working_set.require( req_str ) except Exception as exc: - if not c.galaxy_config.enable_eggs: + if not c.enable_eggs: raise log.info("%s not found in local environment, will try Galaxy egg: %s", (req_str, exc)) # TODO: This breaks egg version requirements. Not currently a problem, but diff -r a8d9371efef9f10e6c4fce18a6da8ed7916f10ba -r 6730c4cb28dead6bbf57a3e1f599136ab71dd34d lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -12,6 +12,7 @@ from Queue import Queue, Empty +import galaxy.eggs import galaxy.jobs from galaxy.jobs.command_factory import build_command from galaxy import model @@ -269,12 +270,20 @@ external_metadata_proc.wait() log.debug( 'execution of external set_meta for job %d finished' % job_wrapper.job_id ) + def _get_egg_env_opts(self): + env = [] + crate = galaxy.eggs.Crate() + for opt in ('enable_egg_fetch', 'enable_eggs', 'try_dependencies_from_env'): + env.append('GALAXY_CONFIG_%s="%s"; export GALAXY_CONFIG_%s' % (opt.upper(), getattr(crate, opt), opt.upper())) + return env + def get_job_file(self, job_wrapper, **kwds): job_metrics = job_wrapper.app.job_metrics job_instrumenter = job_metrics.job_instrumenters[ job_wrapper.job_destination.id ] env_setup_commands = kwds.get( 'env_setup_commands', [] ) env_setup_commands.append( job_wrapper.get_env_setup_clause() or '' ) + env_setup_commands.extend( self._get_egg_env_opts() or [] ) destination = job_wrapper.job_destination or {} envs = destination.get( "env", [] ) for env in envs: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Pass the egg env variables onto jobs.
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/db70af871fd0/ Changeset: db70af871fd0 User: natefoo Date: 2015-02-12 20:35:19+00:00 Summary: Pass the egg env variables onto jobs. Affected #: 2 files diff -r d540227165d54950208d3948e2bdecd4babc70ca -r db70af871fd0f32b67109dcf9a5a8f2ef5846e55 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -61,15 +61,13 @@ self.distribution = None self.dir = None self.removed_location = None - self.enable_fetch = crate.galaxy_config.enable_egg_fetch + self.enable_fetch = crate.enable_egg_fetch if self.name is not None and self.version is not None: self.set_distribution() def set_dir( self ): global eggs_dir self.dir = eggs_dir - if not os.path.exists( self.dir ): - os.makedirs( self.dir ) def set_distribution( self ): """ @@ -131,6 +129,8 @@ def _fetch(): if self.url is None: return False + if not os.path.exists( self.dir ): + os.makedirs( self.dir ) alternative = None try: url = self.url + '/' + self.distribution.egg_name() + '.egg' @@ -284,7 +284,7 @@ """ config_file = os.path.join( galaxy_dir, 'eggs.ini' ) - def __init__( self, galaxy_config_file, platform=None ): + def __init__( self, galaxy_config_file=None, platform=None ): self.eggs = {} self.config = CaseSensitiveConfigParser() self.repo = None @@ -293,6 +293,9 @@ self.py_platform = None if platform is not None: self.py_platform = platform.split( '-' )[0] + self.enable_egg_fetch = string_as_bool(os.environ.get('GALAXY_CONFIG_ENABLE_EGG_FETCH', True)) + self.enable_eggs = string_as_bool(os.environ.get('GALAXY_CONFIG_ENABLE_EGGS', True)) + self.try_dependencies_from_env = string_as_bool(os.environ.get('GALAXY_CONFIG_TRY_DEPENDENCIES_FROM_ENV', False)) self.galaxy_config = GalaxyConfig( galaxy_config_file ) self.parse() @@ -381,7 +384,7 @@ """ Try to resolve (e.g. fetch) all eggs in the crate. """ - if self.galaxy_config.enable_eggs and not self.galaxy_config.try_dependencies_from_env: + if self.enable_eggs and not self.try_dependencies_from_env: if all: eggs = self.all_eggs else: @@ -403,19 +406,12 @@ always_conditional = ( 'pysam', 'ctypes', 'python_daemon' ) def __init__( self, config_file ): - self.enable_egg_fetch = True - self.enable_eggs = True - self.try_dependencies_from_env = False if config_file is None: self.config = None else: self.config = ConfigParser.ConfigParser() if self.config.read( config_file ) == []: raise Exception( "error: unable to read Galaxy config from %s" % config_file ) - for opt in ('enable_egg_fetch', 'enable_eggs', 'try_dependencies_from_env'): - var = 'GALAXY_CONFIG_' + opt.upper() - if var in os.environ: - setattr(self, opt, string_as_bool(os.environ[var])) def check_conditional( self, egg_name ): def check_pysam(): @@ -470,11 +466,11 @@ def require( req_str ): c = Crate( None ) req = pkg_resources.Requirement.parse( req_str ) - if c.galaxy_config.try_dependencies_from_env or not c.galaxy_config.enable_eggs: + if c.try_dependencies_from_env or not c.enable_eggs: try: return pkg_resources.working_set.require( req_str ) except Exception as exc: - if not c.galaxy_config.enable_eggs: + if not c.enable_eggs: raise log.info("%s not found in local environment, will try Galaxy egg: %s", (req_str, exc)) # TODO: This breaks egg version requirements. Not currently a problem, but diff -r d540227165d54950208d3948e2bdecd4babc70ca -r db70af871fd0f32b67109dcf9a5a8f2ef5846e55 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -12,6 +12,7 @@ from Queue import Queue, Empty +import galaxy.eggs import galaxy.jobs from galaxy.jobs.command_factory import build_command from galaxy import model @@ -269,12 +270,20 @@ external_metadata_proc.wait() log.debug( 'execution of external set_meta for job %d finished' % job_wrapper.job_id ) + def _get_egg_env_opts(self): + env = [] + crate = galaxy.eggs.Crate() + for opt in ('enable_egg_fetch', 'enable_eggs', 'try_dependencies_from_env'): + env.append('GALAXY_CONFIG_%s="%s"; export GALAXY_CONFIG_%s' % (opt.upper(), getattr(crate, opt), opt.upper())) + return env + def get_job_file(self, job_wrapper, **kwds): job_metrics = job_wrapper.app.job_metrics job_instrumenter = job_metrics.job_instrumenters[ job_wrapper.job_destination.id ] env_setup_commands = kwds.get( 'env_setup_commands', [] ) env_setup_commands.append( job_wrapper.get_env_setup_clause() or '' ) + env_setup_commands.extend( self._get_egg_env_opts() or [] ) destination = job_wrapper.job_destination or {} envs = destination.get( "env", [] ) for env in envs: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: There's no reliable way to use the Galaxy config file to control egg use/fetching since so many things use galaxy.eggs from outside of Galaxy, so drop the support for the config file options and rely on the environment variables only. Reverse the defaults so that eggs and fetching are enabled by default. I'll make sure that they properly get passed to the tool execution environments in the next commit.
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d540227165d5/ Changeset: d540227165d5 User: natefoo Date: 2015-02-12 20:10:19+00:00 Summary: There's no reliable way to use the Galaxy config file to control egg use/fetching since so many things use galaxy.eggs from outside of Galaxy, so drop the support for the config file options and rely on the environment variables only. Reverse the defaults so that eggs and fetching are enabled by default. I'll make sure that they properly get passed to the tool execution environments in the next commit. Affected #: 4 files diff -r fd753316154e8ad2a92bebffda9441c8614a06f5 -r d540227165d54950208d3948e2bdecd4babc70ca config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -125,34 +125,6 @@ # but prefixed with install_ are also available). #install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE -# -- Galaxy framework dependencies (eggs) - -# Options in this section can also be provided as environment variables in the -# form `GALAXY_CONFIG_<OPTION_NAME>`, e.g. `GALAXY_CONFIG_ENABLE_EGGS=False`, -# etc. Environment variables override the settings in this config. - -# For more details, see the `requirements.txt` file at the root of the Galaxy -# source distribution. - -# Galaxy manages all of its dependent Python modules by downloading Python eggs -# from the Galaxy eggs distribution server at https://eggs.galaxyproject.org. -# You may choose to disable this and attempt to install dependencies by hand -# (e.g. with pip), but beware that this may cause problems due to version -# incompatibilities between Galaxy and its dependencies. Do not do this unless -# you know what you're doing. -#enable_eggs = True - -# You may choose to keep eggs enabled but disable fetching them automatically. -# (hint: To do a one-time fetch, you can disable here and then use -# `GALAXY_CONFIG_ENABLE_EGG_FETCH=True python ./scripts/fetch_eggs.py` from the -# root of the Galaxy source. -#enable_egg_fetch = True - -# If you'd like to prefer any dependencies found in your local environment -# before (fetching and) using Galaxy's egg of that dependency, you can enable -# the following option: -#try_dependencies_from_env = False - # -- Files and directories # Dataset files are stored in this directory. diff -r fd753316154e8ad2a92bebffda9441c8614a06f5 -r d540227165d54950208d3948e2bdecd4babc70ca lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -403,8 +403,8 @@ always_conditional = ( 'pysam', 'ctypes', 'python_daemon' ) def __init__( self, config_file ): - self.enable_egg_fetch = False - self.enable_eggs = False + self.enable_egg_fetch = True + self.enable_eggs = True self.try_dependencies_from_env = False if config_file is None: self.config = None @@ -412,13 +412,6 @@ self.config = ConfigParser.ConfigParser() if self.config.read( config_file ) == []: raise Exception( "error: unable to read Galaxy config from %s" % config_file ) - self.enable_egg_fetch = True - self.enable_eggs = True - for opt in ('enable_egg_fetch', 'enable_eggs', 'try_dependencies_from_env'): - try: - setattr(self, opt, string_as_bool(self.config.get('app:main', opt))) - except: - pass # use default for opt in ('enable_egg_fetch', 'enable_eggs', 'try_dependencies_from_env'): var = 'GALAXY_CONFIG_' + opt.upper() if var in os.environ: diff -r fd753316154e8ad2a92bebffda9441c8614a06f5 -r d540227165d54950208d3948e2bdecd4babc70ca requirements.txt --- a/requirements.txt +++ b/requirements.txt @@ -12,8 +12,7 @@ # However, you may want to manage these dependencies on your own. If so, this # file can be used with pip to install all of the bare minimum dependencies for # starting a Galaxy server. Use this in conjunction with the -# `enable_eggs = False` galaxy.ini option or `GALAXY_CONFIG_ENABLE_EGGS=False` -# environment variable +# `GALAXY_CONFIG_ENABLE_EGGS=False` environment variable. # # Note that except in the case of SQLAlchemy, all dependencies will be # installed at their newest versions. Galaxy has not been tested with these and @@ -62,4 +61,3 @@ Parsley WebError http://svgfig.googlecode.com/files/svgfig-1.1.6.tgz - diff -r fd753316154e8ad2a92bebffda9441c8614a06f5 -r d540227165d54950208d3948e2bdecd4babc70ca scripts/paster.py --- a/scripts/paster.py +++ b/scripts/paster.py @@ -30,36 +30,6 @@ _log_tempfile = TempFile() import tempfile -try: - serve = sys.argv.index('serve') -except: - print >>sys.stderr, "Galaxy does not use the real Paste Script, the only supported command is 'serve'" - sys.exit(1) - -# eggs.require() can be called inside the app without access to the Galaxy -# config, so we need to push the egg options into the environment so they are -# available to Crate instantiated in require() - -# locate the arg containing the path to the config file -config = None -p = configparser.ConfigParser() -for arg in sys.argv: - try: - p.read(arg) - assert 'app:main' in p.sections() - config = arg - break - except (configparser.Error, AssertionError): - pass - -# find any egg options set in the config -crate = eggs.Crate(config) -for opt in ('enable_eggs', 'enable_egg_fetch', 'try_dependencies_from_env'): - env = 'GALAXY_CONFIG_' + opt.upper() - # don't overwrite existing env vars configured by the user - if env not in os.environ: - os.environ[env] = str(getattr(crate.galaxy_config, opt)) - eggs.require( "Paste" ) eggs.require( "PasteDeploy" ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Update original parse_xml function with Carl's fix. It's safe, and I know I saw that same doctype deprecation somewhere else, might as well share it.
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd753316154e/ Changeset: fd753316154e User: dannon Date: 2015-02-12 19:56:33+00:00 Summary: Update original parse_xml function with Carl's fix. It's safe, and I know I saw that same doctype deprecation somewhere else, might as well share it. Affected #: 2 files diff -r 2e13b048a9b707224b1f499dbdaf12a45ffd413c -r fd753316154e8ad2a92bebffda9441c8614a06f5 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -169,11 +169,15 @@ return md5(str( random.getrandbits( KEY_SIZE ) )).hexdigest() -def parse_xml(fname): +def parse_xml( fname ): """Returns a parsed xml tree""" - tree = ElementTree.parse(fname) - root = tree.getroot() - ElementInclude.include(root) + # handle deprecation warning for XMLParsing a file with DOCTYPE + class DoctypeSafeCallbackTarget( ElementTree.TreeBuilder ): + def doctype( *args ): + pass + tree = ElementTree.ElementTree() + root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) + ElementInclude.include( root ) return tree diff -r 2e13b048a9b707224b1f499dbdaf12a45ffd413c -r fd753316154e8ad2a92bebffda9441c8614a06f5 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -7,8 +7,6 @@ import os import shutil import glob -from xml.etree import ElementTree -from xml.etree import ElementInclude from galaxy import util import galaxy.model @@ -85,16 +83,6 @@ return True -def parse_xml( fname ): - # handle deprecation warning for XMLParsing a file with DOCTYPE - class DoctypeSafeCallbackTarget( ElementTree.TreeBuilder ): - def doctype( *args ): - pass - tree = ElementTree.ElementTree() - root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) - ElementInclude.include( root ) - return tree - # ------------------------------------------------------------------- the registry class VisualizationsRegistry( pluginframework.PageServingPluginManager ): @@ -406,7 +394,7 @@ Parse the given XML file for visualizations data. :returns: visualization config dictionary """ - xml_tree = parse_xml( xml_filepath ) + xml_tree = util.parse_xml( xml_filepath ) visualization = self.parse_visualization( xml_tree.getroot() ) return visualization Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Visualizations registry: remove ElementTree doctype deprecation warning
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2e13b048a9b7/ Changeset: 2e13b048a9b7 User: carlfeberhard Date: 2015-02-12 19:47:45+00:00 Summary: Visualizations registry: remove ElementTree doctype deprecation warning Affected #: 1 file diff -r 45072dc79c5c8a5d6f1bbc9883e25bb3cb8b6319 -r 2e13b048a9b707224b1f499dbdaf12a45ffd413c lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -7,6 +7,8 @@ import os import shutil import glob +from xml.etree import ElementTree +from xml.etree import ElementInclude from galaxy import util import galaxy.model @@ -83,6 +85,16 @@ return True +def parse_xml( fname ): + # handle deprecation warning for XMLParsing a file with DOCTYPE + class DoctypeSafeCallbackTarget( ElementTree.TreeBuilder ): + def doctype( *args ): + pass + tree = ElementTree.ElementTree() + root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) + ElementInclude.include( root ) + return tree + # ------------------------------------------------------------------- the registry class VisualizationsRegistry( pluginframework.PageServingPluginManager ): @@ -394,7 +406,7 @@ Parse the given XML file for visualizations data. :returns: visualization config dictionary """ - xml_tree = galaxy.util.parse_xml( xml_filepath ) + xml_tree = parse_xml( xml_filepath ) visualization = self.parse_visualization( xml_tree.getroot() ) return visualization @@ -416,7 +428,7 @@ # allow manually turning off a vis by checking for a disabled property if 'disabled' in xml_tree.attrib: - log.info( '%s, plugin disabled: %s. Skipping...', self, returned[ 'name' ] ) + log.info( 'Visualizations plugin disabled: %s. Skipping...', returned[ 'name' ] ) return None # record the embeddable flag - defaults to false Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Place the new egg config options into the environment at Galaxy startup since
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45072dc79c5c/ Changeset: 45072dc79c5c User: natefoo Date: 2015-02-12 19:27:37+00:00 Summary: Place the new egg config options into the environment at Galaxy startup since eggs.require() has no access to the config file. Affected #: 1 file diff -r c981094a4d50f40e4dae3f0fd49089b46a0e2897 -r 45072dc79c5c8a5d6f1bbc9883e25bb3cb8b6319 scripts/paster.py --- a/scripts/paster.py +++ b/scripts/paster.py @@ -7,6 +7,11 @@ import os, sys +try: + import configparser +except: + import ConfigParser as configparser + # ensure supported version from check_python import check_python try: @@ -19,15 +24,44 @@ sys.path = new_path from galaxy import eggs -import pkg_resources if 'LOG_TEMPFILES' in os.environ: from log_tempfile import TempFile _log_tempfile = TempFile() import tempfile -pkg_resources.require( "Paste" ) -pkg_resources.require( "PasteDeploy" ) +try: + serve = sys.argv.index('serve') +except: + print >>sys.stderr, "Galaxy does not use the real Paste Script, the only supported command is 'serve'" + sys.exit(1) + +# eggs.require() can be called inside the app without access to the Galaxy +# config, so we need to push the egg options into the environment so they are +# available to Crate instantiated in require() + +# locate the arg containing the path to the config file +config = None +p = configparser.ConfigParser() +for arg in sys.argv: + try: + p.read(arg) + assert 'app:main' in p.sections() + config = arg + break + except (configparser.Error, AssertionError): + pass + +# find any egg options set in the config +crate = eggs.Crate(config) +for opt in ('enable_eggs', 'enable_egg_fetch', 'try_dependencies_from_env'): + env = 'GALAXY_CONFIG_' + opt.upper() + # don't overwrite existing env vars configured by the user + if env not in os.environ: + os.environ[env] = str(getattr(crate.galaxy_config, opt)) + +eggs.require( "Paste" ) +eggs.require( "PasteDeploy" ) from galaxy.util.pastescript import serve serve.run() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merge from stable.
by commits-noreply＠bitbucket.org 12 Feb '15

12 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c981094a4d50/ Changeset: c981094a4d50 User: dannon Date: 2015-02-12 18:40:22+00:00 Summary: Merge from stable. Affected #: 13 files diff -r 82644ba2a73d5e2b2f07975b39b6e70aefedff9b -r c981094a4d50f40e4dae3f0fd49089b46a0e2897 .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,18 +8,18 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 -8f9dcac033694e4cabcf5daae5cca1cfefbe967f latest_2014.04.14 +c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 +b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 -19e56e66b0b344c6e2afa4541f6988e4fdb9af29 latest_2013.06.03 -cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 -7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 -0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 +aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 +db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 +52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 +746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 +6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 +782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -4039bfd5584aac053f686197a76ac176253e6f3d latest_2015.01.13 +577b270034b48d90e58ffbea296e700d229545c9 latest_2015.01.13 diff -r 82644ba2a73d5e2b2f07975b39b6e70aefedff9b -r c981094a4d50f40e4dae3f0fd49089b46a0e2897 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2863,7 +2863,7 @@ return True if user: user = user.id - log.debug( "User (%s) attempted to access a data manager tool (%s), but is not an admin.", user, self.id ) + log.debug( "User (%s) attempted to access a data manager tool (%s), but is not an admin.", user, self.id ) return False # Populate tool_type to ToolClass mappings Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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