galaxy-commits April 2014

galaxy-commits@lists.galaxyproject.org

1 participants
261 discussions

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b423b847f58e/ Changeset: b423b847f58e Branch: next-stable User: carlfeberhard Date: 2014-04-11 22:46:50 Summary: Pack data.js from 86f93a1 Affected #: 1 file diff -r 86f93a18715e8fe22710a8ef788e54db08cdfe6c -r b423b847f58e1d8b1c29bcd9cf3089806bf0ac68 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file +define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/2e7a93837c14/ Changeset: 2e7a93837c14 User: carlfeberhard Date: 2014-04-11 22:48:28 Summary: merge next-stable Affected #: 1 file diff -r 0b98c12b720e4a3276c03cc92d3e358173f7d97f -r 2e7a93837c146a588c8d8fa00e226a6694d0f377 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); +define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/86f93a18715e/ Changeset: 86f93a18715e Branch: next-stable User: carlfeberhard Date: 2014-04-11 22:22:11 Summary: PR #366 from Jian-Long Huang: to next-stable Affected #: 1 file diff -r dcfd828a229e5d43d1610cc510d71088620a1112 -r 86f93a18715e8fe22710a8ef788e54db08cdfe6c static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -21,7 +21,7 @@ initialize: function() { this._set_metadata(); - + // Update metadata on change. this.on('change', this._set_metadata, this); }, @@ -30,7 +30,7 @@ var metadata = new DatasetMetadata(); // Move metadata from dataset attributes to metadata object. - _.each(_.keys(this.attributes), function(k) { + _.each(_.keys(this.attributes), function(k) { if (k.indexOf('metadata_') === 0) { // Found metadata. var new_key = k.split('metadata_')[1]; @@ -108,8 +108,8 @@ }); /** - * Provides a base for table-based, dynamic view of a tabular dataset. - * Do not instantiate directly; use either TopLevelTabularDatasetChunkedView + * Provides a base for table-based, dynamic view of a tabular dataset. + * Do not instantiate directly; use either TopLevelTabularDatasetChunkedView * or EmbeddedTabularDatasetChunkedView. */ var TabularDatasetChunkedView = Backbone.View.extend({ @@ -193,7 +193,7 @@ $cell.attr('colspan', colspan).addClass('stringalign'); } else if (column_types) { if (index < column_types.length) { - if (column_types[index] === 'str' || column_types === 'list') { + if (column_types[index] === 'str' || column_types[index] === 'list') { /* Left align all str columns, right align the rest */ $cell.addClass('stringalign'); } @@ -329,22 +329,22 @@ initialize: function (options) { // check if environment is available var Galaxy = parent.Galaxy; - + // link galaxy modal or create one if (Galaxy && Galaxy.modal) { this.modal = Galaxy.modal; } - + // link galaxy frames if (Galaxy && Galaxy.frame) { this.frame = Galaxy.frame; } - + // check if (!this.modal || !this.frame) { return; } - + // model/metadata var model = options.model; var metadata = model.get('metadata'); @@ -353,10 +353,10 @@ if (!model.get('data_type')) { return; } - + // get data type this.data_type = model.get('data_type'); - + // check for bed-file format if (this.data_type == 'bed') { @@ -394,7 +394,7 @@ return; } } - + // check if(this.col.chrom === undefined) { return; @@ -407,7 +407,7 @@ console.log('TabularButtonTrackster : Dataset identification is missing.'); return; } - + // get url if (model.get('url_viz')) { this.url_viz = model.get('url_viz'); @@ -429,10 +429,10 @@ id : 'btn_viz' }) }); - + // set element this.setElement(options.$el); - + // add to element this.$el.append(btn_viz.render().$el); @@ -446,14 +446,14 @@ 'mouseover tr' : 'show', 'mouseleave' : 'hide' }, - + // show button show: function (e) { // is numeric function is_numeric(n) { return !isNaN(parseFloat(n)) && isFinite(n); }; - + // check if(this.col.chrom === null) return; @@ -470,7 +470,7 @@ // double check location if (!chrom.match("^#") && chrom !== "" && is_numeric(start)) { - + // get target gene region var btn_viz_pars = { dataset_id : this.dataset_id, @@ -494,17 +494,17 @@ $('#btn_viz').hide(); } }, - + // hide button hide: function () { this.$el.find('#btn_viz').hide(); }, - + // create action create_trackster_action : function (vis_url, dataset_params, dbkey) { // link this var self = this; - + // create function return function() { var listTracksParams = {}; @@ -546,13 +546,13 @@ 'Add to visualization': function(){ // hide self.modal.hide(); - + // search selected fields self.modal.$el.find('input[name=id]:checked').each(function(){ // get visualization id var vis_id = $(this).val(); dataset_params.id = vis_id; - + // add widget self.frame.add({ title : 'Trackster', @@ -567,7 +567,7 @@ 'View in new visualization': function(){ // hide self.modal.hide(); - + // add widget self.frame.add({ title : 'Trackster', @@ -619,7 +619,7 @@ delete options.embedded; delete options.parent_elt; delete options.dataset_config; - + // Create and set up view. var view = (embedded ? new EmbeddedTabularDatasetChunkedView(options) : new TopLevelTabularDatasetChunkedView(options)); https://bitbucket.org/galaxy/galaxy-central/commits/adad115b69ee/ Changeset: adad115b69ee User: carlfeberhard Date: 2014-04-11 22:40:12 Summary: merge next-stable Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/0b98c12b720e/ Changeset: 0b98c12b720e User: carlfeberhard Date: 2014-04-11 22:41:45 Summary: pack scripts Affected #: 2 files diff -r adad115b69eeab8447cff22f23a5925282c3afa8 -r 0b98c12b720e4a3276c03cc92d3e358173f7d97f static/scripts/packed/utils/metrics-logger.js --- a/static/scripts/packed/utils/metrics-logger.js +++ b/static/scripts/packed/utils/metrics-logger.js @@ -1,1 +1,1 @@ -define([],function(){function h(z){z=z||{};var y=this;y.consoleLogger=z.consoleLogger||null;y._init(z);return y}h.ALL=0;h.DEBUG=10;h.INFO=20;h.WARN=30;h.ERROR=40;h.METRIC=50;h.NONE=100;h.defaultOptions={logLevel:h.INFO,consoleLevel:h.NONE,defaultNamespace:"Galaxy",clientPrefix:"client.",maxCacheSize:3000,postSize:1000,addTime:true,postUrl:"/api/metrics",postOnUnload:true,getPingData:undefined,onServerResponse:undefined};h.prototype._init=function i(A){var z=this;z.options={};for(var y in h.defaultOptions){if(h.defaultOptions.hasOwnProperty(y)){z.options[y]=(A.hasOwnProperty(y))?(A[y]):(h.defaultOptions[y])}}z.options.logLevel=z._parseLevel(z.options.logLevel);z.options.consoleLevel=z._parseLevel(z.options.consoleLevel);z._sending=false;z._postSize=z.options.postSize;z._initCache();if(z.options.postOnUnload){z.onpageunload=function B(C){C.preventDefault();z._postCache({count:z.cache.length()})};window.addEventListener("unload",z.onpageunload)}return z};h.prototype._initCache=function a(){this.cache=new w({maxSize:this.options.maxCacheSize})};h.prototype._parseLevel=function j(A){var z=typeof A;if(z==="number"){return A}var y=A.toUpperCase();if(z==="string"&&h.hasOwnProperty(y)){return h[y]}throw new Error("Unknown log level: "+A)};h.prototype.emit=function m(B,A,z){var y=this;A=A||y.options.defaultNamespace;if(!B||!z){return y}B=y._parseLevel(B);if(B>=y.options.logLevel){y._addToCache(B,A,z)}if(y.consoleLogger&&B>=y.options.consoleLevel){y._emitToConsole(B,A,z)}return y};h.prototype._addToCache=function b(D,A,z){this._emitToConsole("debug","MetricsLogger",["_addToCache:",arguments,this.options.addTime,this.cache.length()]);var y=this;try{var C=y.cache.add(y._buildEntry(D,A,z));if(C>=y._postSize){y._postCache()}}catch(B){if(y.options.consoleLevel<=h.WARN){console.warn("Metrics logger could not stringify logArguments:",A,z);console.error(B)}}return y};h.prototype._buildEntry=function r(B,z,y){this._emitToConsole("debug","MetricsLogger",["_buildEntry:",arguments]);var A={level:B,namespace:this.options.clientPrefix+z,args:y};if(this.options.addTime){A.time=new Date().toISOString()}return A};h.prototype._postCache=function s(B){B=B||{};this._emitToConsole("info","MetricsLogger",["_postCache",B,this._postSize]);if(!this.options.postUrl||this._sending){return jQuery.when({})}var A=this,D=B.count||A._postSize,y=A.cache.get(D),C=y.length,z=(typeof A.options.getPingData==="function")?(A.options.getPingData()):({});z.metrics=A._preprocessCache(y);A._sending=true;return jQuery.post(A.options.postUrl,z).always(function(){A._sending=false}).fail(function(){A._postSize=A.options.maxCacheSize}).done(function(E){if(typeof A.options.onServerResponse==="function"){A.options.onServerResponse(E)}A.cache.remove(C);console.debug("removed entries:",C,"size now:",A.cache.length());A._postSize=A.options.postSize})};h.prototype._preprocessCache=function f(y){return["[",(y.join(",\n")),"]"].join("\n")};h.prototype._emitToConsole=function c(C,B,A){var y=this;if(!y.consoleLogger){return y}var z=Array.prototype.slice.call(A,0);z.unshift(B);if(C>=h.METRIC&&typeof(y.consoleLogger.info)==="function"){return y.consoleLogger.info.apply(y.consoleLogger,z)}else{if(C>=h.ERROR&&typeof(y.consoleLogger.error)==="function"){return y.consoleLogger.error.apply(y.consoleLogger,z)}else{if(C>=h.WARN&&typeof(y.consoleLogger.warn)==="function"){y.consoleLogger.warn.apply(y.consoleLogger,z)}else{if(C>=h.INFO&&typeof(y.consoleLogger.info)==="function"){y.consoleLogger.info.apply(y.consoleLogger,z)}else{if(C>=h.DEBUG&&typeof(y.consoleLogger.debug)==="function"){y.consoleLogger.debug.apply(y.consoleLogger,z)}else{if(typeof(y.consoleLogger.log)==="function"){y.consoleLogger.log.apply(y.consoleLogger,z)}}}}}}return y};h.prototype.debug=function l(){this.emit(h.DEBUG,this.options.defaultNamespace,arguments)};h.prototype.log=function g(){this.emit(1,this.options.defaultNamespace,arguments)};h.prototype.info=function u(){this.emit(h.INFO,this.options.defaultNamespace,arguments)};h.prototype.warn=function t(){this.emit(h.WARN,this.options.defaultNamespace,arguments)};h.prototype.error=function p(){this.emit(h.ERROR,this.options.defaultNamespace,arguments)};h.prototype.metric=function n(){this.emit(h.METRIC,this.options.defaultNamespace,arguments)};function w(z){var y=this;y._cache=[];return y._init(z||{})}w.defaultOptions={maxSize:5000};w.prototype._init=function i(y){this.maxSize=y.maxSize||w.defaultOptions.maxSize;return this};w.prototype.add=function k(A){var z=this,y=(z.length()+1)-z.maxSize;if(y>0){z.remove(y)}z._cache.push(z._preprocessEntry(A));return z.length()};w.prototype._preprocessEntry=function q(y){return JSON.stringify(y)};w.prototype.length=function e(){return this._cache.length};w.prototype.get=function v(y){return this._cache.slice(0,y)};w.prototype.remove=function x(y){return this._cache.splice(0,y)};w.prototype.stringify=function o(y){return["[",(this.get(y).join(",\n")),"]"].join("\n")};w.prototype.print=function d(){this._cache.forEach(function(y){console.log(y)})};return{MetricsLogger:h}}); \ No newline at end of file +define([],function(){function h(z){z=z||{};var y=this;y.consoleLogger=z.consoleLogger||null;y._init(z);return y}h.ALL=0;h.DEBUG=10;h.INFO=20;h.WARN=30;h.ERROR=40;h.METRIC=50;h.NONE=100;h.defaultOptions={logLevel:h.INFO,consoleLevel:h.NONE,defaultNamespace:"Galaxy",clientPrefix:"client.",maxCacheSize:3000,postSize:1000,addTime:true,postUrl:"/api/metrics",postOnUnload:true,getPingData:undefined,onServerResponse:undefined};h.prototype._init=function i(A){var z=this;z.options={};for(var y in h.defaultOptions){if(h.defaultOptions.hasOwnProperty(y)){z.options[y]=(A.hasOwnProperty(y))?(A[y]):(h.defaultOptions[y])}}z.options.logLevel=z._parseLevel(z.options.logLevel);z.options.consoleLevel=z._parseLevel(z.options.consoleLevel);z._sending=false;z._postSize=z.options.postSize;z._initCache();if(z.options.postOnUnload){z.onpageunload=function B(C){C.preventDefault();z._postCache({count:z.cache.length()})};window.addEventListener("unload",z.onpageunload)}return z};h.prototype._initCache=function a(){this.cache=new w({maxSize:this.options.maxCacheSize})};h.prototype._parseLevel=function j(A){var z=typeof A;if(z==="number"){return A}if(z==="string"){var y=A.toUpperCase();if(h.hasOwnProperty(y)){return h[y]}}throw new Error("Unknown log level: "+A)};h.prototype.emit=function m(B,A,z){var y=this;A=A||y.options.defaultNamespace;if(!B||!z){return y}B=y._parseLevel(B);if(B>=y.options.logLevel){y._addToCache(B,A,z)}if(y.consoleLogger&&B>=y.options.consoleLevel){y._emitToConsole(B,A,z)}return y};h.prototype._addToCache=function b(D,A,z){this._emitToConsole("debug","MetricsLogger",["_addToCache:",arguments,this.options.addTime,this.cache.length()]);var y=this;try{var C=y.cache.add(y._buildEntry(D,A,z));if(C>=y._postSize){y._postCache()}}catch(B){if(y.options.consoleLevel<=h.WARN){console.warn("Metrics logger could not stringify logArguments:",A,z);console.error(B)}}return y};h.prototype._buildEntry=function r(B,z,y){this._emitToConsole("debug","MetricsLogger",["_buildEntry:",arguments]);var A={level:B,namespace:this.options.clientPrefix+z,args:y};if(this.options.addTime){A.time=new Date().toISOString()}return A};h.prototype._postCache=function s(B){B=B||{};this._emitToConsole("info","MetricsLogger",["_postCache",B,this._postSize]);if(!this.options.postUrl||this._sending){return jQuery.when({})}var A=this,D=B.count||A._postSize,y=A.cache.get(D),C=y.length,z=(typeof A.options.getPingData==="function")?(A.options.getPingData()):({});z.metrics=A._preprocessCache(y);A._sending=true;return jQuery.post(A.options.postUrl,z).always(function(){A._sending=false}).fail(function(){A._postSize=A.options.maxCacheSize}).done(function(E){if(typeof A.options.onServerResponse==="function"){A.options.onServerResponse(E)}A.cache.remove(C);console.debug("removed entries:",C,"size now:",A.cache.length());A._postSize=A.options.postSize})};h.prototype._preprocessCache=function f(y){return["[",(y.join(",\n")),"]"].join("\n")};h.prototype._emitToConsole=function c(C,B,A){var y=this;if(!y.consoleLogger){return y}var z=Array.prototype.slice.call(A,0);z.unshift(B);if(C>=h.METRIC&&typeof(y.consoleLogger.info)==="function"){return y.consoleLogger.info.apply(y.consoleLogger,z)}else{if(C>=h.ERROR&&typeof(y.consoleLogger.error)==="function"){return y.consoleLogger.error.apply(y.consoleLogger,z)}else{if(C>=h.WARN&&typeof(y.consoleLogger.warn)==="function"){y.consoleLogger.warn.apply(y.consoleLogger,z)}else{if(C>=h.INFO&&typeof(y.consoleLogger.info)==="function"){y.consoleLogger.info.apply(y.consoleLogger,z)}else{if(C>=h.DEBUG&&typeof(y.consoleLogger.debug)==="function"){y.consoleLogger.debug.apply(y.consoleLogger,z)}else{if(typeof(y.consoleLogger.log)==="function"){y.consoleLogger.log.apply(y.consoleLogger,z)}}}}}}return y};h.prototype.debug=function l(){this.emit(h.DEBUG,this.options.defaultNamespace,arguments)};h.prototype.log=function g(){this.emit(1,this.options.defaultNamespace,arguments)};h.prototype.info=function u(){this.emit(h.INFO,this.options.defaultNamespace,arguments)};h.prototype.warn=function t(){this.emit(h.WARN,this.options.defaultNamespace,arguments)};h.prototype.error=function p(){this.emit(h.ERROR,this.options.defaultNamespace,arguments)};h.prototype.metric=function n(){this.emit(h.METRIC,this.options.defaultNamespace,arguments)};function w(z){var y=this;y._cache=[];return y._init(z||{})}w.defaultOptions={maxSize:5000};w.prototype._init=function i(y){this.maxSize=y.maxSize||w.defaultOptions.maxSize;return this};w.prototype.add=function k(A){var z=this,y=(z.length()+1)-z.maxSize;if(y>0){z.remove(y)}z._cache.push(z._preprocessEntry(A));return z.length()};w.prototype._preprocessEntry=function q(y){return JSON.stringify(y)};w.prototype.length=function e(){return this._cache.length};w.prototype.get=function v(y){return this._cache.slice(0,y)};w.prototype.remove=function x(y){return this._cache.splice(0,y)};w.prototype.stringify=function o(y){return["[",(this.get(y).join(",\n")),"]"].join("\n")};w.prototype.print=function d(){this._cache.forEach(function(y){console.log(y)})};return{MetricsLogger:h,LoggingCache:w}}); \ No newline at end of file diff -r adad115b69eeab8447cff22f23a5925282c3afa8 -r 0b98c12b720e4a3276c03cc92d3e358173f7d97f static/scripts/packed/viz/phyloviz.js --- a/static/scripts/packed/viz/phyloviz.js +++ b/static/scripts/packed/viz/phyloviz.js @@ -1,1 +1,1 @@ -define(["libs/d3","viz/visualization","mvc/data"],function(m,f,g){var l=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(q,o,n){var r=q.val(),s=q.attr("displayLabel")||q.attr("id").replace("phyloViz","");function p(t){return !isNaN(parseFloat(t))&&isFinite(t)}if(!p(r)){alert(s+" is not a number!");return false}if(r>n){alert(s+" is too large.");return false}else{if(r<o){alert(s+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(n){if(n.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). ");return true}return false}});function h(){var w=this,r=m.layout.hierarchy().sort(null).value(null),v=360,q="Linear",u=18,s=200,t=0,p=0.5,n=50;w.leafHeight=function(x){if(typeof x==="undefined"){return u}else{u=x;return w}};w.layoutMode=function(x){if(typeof x==="undefined"){return q}else{q=x;return w}};w.layoutAngle=function(x){if(typeof x==="undefined"){return v}if(isNaN(x)||x<0||x>360){return w}else{v=x;return w}};w.separation=function(x){if(typeof x==="undefined"){return s}else{s=x;return w}};w.links=function(x){return m.layout.tree().links(x)};w.nodes=function(A,y){if(toString.call(A)==="[object Array]"){A=A[0]}var z=r.call(w,A,y),x=[],C=0,B=0;window._d=A;window._nodes=z;z.forEach(function(D){C=D.depth>C?D.depth:C;x.push(D)});x.forEach(function(D){if(!D.children){B+=1;D.depth=C}});u=q==="Circular"?v/B:u;t=0;o(x[0],C,u,null);return x};function o(B,D,A,z){var y=B.children,x=0;var C=B.dist||p;C=C>1?1:C;B.dist=C;if(z!==null){B.y0=z.y0+C*s}else{B.y0=n}if(!y){B.x0=t*A;t+=1}else{y.forEach(function(E){E.parent=B;x+=o(E,D,A,B)});B.x0=x/y.length}B.x=B.x0;B.y=B.y0;return B.x0}return w}var b=f.Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},initialize:function(n){this.set("dataset",new g.Dataset({id:n.dataset_id}))},root:{},toggle:function(n){if(typeof n==="undefined"){return}if(n.children){n._children=n.children;n.children=null}else{n.children=n._children;n._children=null}},toggleAll:function(n){if(n.children&&n.children.length!==0){n.children.forEach(this.toggleAll);toggle(n)}},getData:function(){return this.root},save:function(){var n=this.root;o(n);function o(q){delete q.parent;if(q._selected){delete q._selected}if(q.children){q.children.forEach(o)}if(q._children){q._children.forEach(o)}}var p=jQuery.extend(true,{},this.attributes);p.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url,type:"POST",dataType:"json",data:{vis_json:JSON.stringify(p)},success:function(q){var r=q.url.split("id=")[1].split("&")[0],s="/visualization?id="+r;window.history.pushState({},"",s+window.location.hash);hide_modal()}})}});var d=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(o){var n=this;n.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",n.updateAndRender,n);n.vis=o.vis;n.i=0;n.maxDepth=-1;n.width=o.width;n.height=o.height},updateAndRender:function(p){var o=m.select(".vis"),n=this;p=p||n.model.root;n.renderNodes(p);n.renderLinks(p);n.addTooltips()},renderLinks:function(n){var w=this;var o=w.diagonal;var p=w.duration;var r=w.layoutMode;var t=w.vis.selectAll("g.completeLink").data(w.tree.links(w.nodes),function(x){return x.target.id});var v=function(x){x.pos0=x.source.y0+" "+x.source.x0;x.pos1=x.source.y0+" "+x.target.x0;x.pos2=x.target.y0+" "+x.target.x0};var u=t.enter().insert("svg:g","g.node").attr("class","completeLink");u.append("svg:path").attr("class","link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1});var s=t.transition().duration(500);s.select("path.link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1+" L "+x.pos2});var q=t.exit().remove()},selectNode:function(o){var n=this;m.selectAll("g.node").classed("selectedHighlight",function(p){if(o.id===p.id){if(o._selected){delete o._selected;return false}else{o._selected=true;return true}}return false});n.model.set("selectedNode",o);$("#phyloVizSelectedNodeName").val(o.name);$("#phyloVizSelectedNodeDist").val(o.dist);$("#phyloVizSelectedNodeAnnotation").val(o.annotation||"")},addTooltips:function(){$(".tooltip").remove();$(".node").attr("data-original-title",function(){var o=this.__data__,n=o.annotation||"None";return o?(o.name?o.name+"<br/>":"")+"Dist: "+o.dist+" <br/>Annotation: "+n:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(o){var n=this;n.margins=o.margins;n.layoutMode="Linear";n.stdInit(o);n.layout();n.updateAndRender(n.model.root)},layout:function(){var n=this;n.tree=new h().layoutMode("Linear");n.diagonal=m.svg.diagonal().projection(function(o){return[o.y,o.x]})},renderNodes:function(n){var u=this,v=u.model.get("fontSize")+"px";u.tree.separation(u.model.get("separation")).leafHeight(u.model.get("leafHeight"));var q=500,o=u.tree.separation(u.model.get("separation")).nodes(u.model.root);var p=u.vis.selectAll("g.node").data(o,function(w){return w.name+w.id||(w.id=++u.i)});u.nodes=o;u.duration=q;var r=p.enter().append("svg:g").attr("class","node").on("dblclick",function(){m.event.stopPropagation()}).on("click",function(w){if(m.event.altKey){u.selectNode(w)}else{if(w.children&&w.children.length===0){return}u.model.toggle(w);u.updateAndRender(w)}});if(toString.call(n)==="[object Array]"){n=n[0]}r.attr("transform",function(w){return"translate("+n.y0+","+n.x0+")"});r.append("svg:circle").attr("r",0.000001).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});r.append("svg:text").attr("class","nodeLabel").attr("x",function(w){return w.children||w._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(w){return w.children||w._children?"end":"start"}).style("fill-opacity",0.000001);var s=p.transition().duration(q);s.attr("transform",function(w){return"translate("+w.y+","+w.x+")"});s.select("circle").attr("r",u.defaults.nodeRadius).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});s.select("text").style("fill-opacity",1).style("font-size",v).text(function(w){return w.name});var t=p.exit().transition().duration(q).remove();t.select("circle").attr("r",0.000001);t.select("text").style("fill-opacity",0.000001);o.forEach(function(w){w.x0=w.x;w.y0=w.y})}});var j=Backbone.View.extend({className:"phyloviz",initialize:function(o){var n=this;n.MIN_SCALE=0.05;n.MAX_SCALE=5;n.MAX_DISPLACEMENT=500;n.margins=[10,60,10,80];n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.radius=n.width;n.data=o.data;$(window).resize(function(){n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.render()});n.phyloTree=new b(o.config);n.phyloTree.root=n.data;n.zoomFunc=m.behavior.zoom().scaleExtent([n.MIN_SCALE,n.MAX_SCALE]);n.zoomFunc.translate(n.phyloTree.get("translate"));n.zoomFunc.scale(n.phyloTree.get("scaleFactor"));n.navMenu=new c(n);n.settingsMenu=new i({phyloTree:n.phyloTree});n.nodeSelectionView=new e({phyloTree:n.phyloTree});n.search=new k();setTimeout(function(){n.zoomAndPan()},1000)},render:function(){var o=this;$("#PhyloViz").empty();o.mainSVG=m.select("#PhyloViz").append("svg:svg").attr("width",o.width).attr("height",o.height).attr("pointer-events","all").call(o.zoomFunc.on("zoom",function(){o.zoomAndPan()}));o.boundingRect=o.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",o.width).attr("height",o.height).attr("stroke","black").attr("fill","white");o.vis=o.mainSVG.append("svg:g").attr("class","vis");o.layoutOptions={model:o.phyloTree,width:o.width,height:o.height,vis:o.vis,margins:o.margins};$("#title").text("Phylogenetic Tree from "+o.phyloTree.get("title")+":");var n=new a(o.layoutOptions)},zoomAndPan:function(n){var t,p;if(typeof n!=="undefined"){t=n.zoom;p=n.translate}var w=this,r=w.zoomFunc.scale(),v=w.zoomFunc.translate(),s="",u="";switch(t){case"reset":r=1;v=[0,0];break;case"+":r*=1.1;break;case"-":r*=0.9;break;default:if(typeof t==="number"){r=t}else{if(m.event!==null){r=m.event.scale}}}if(r<w.MIN_SCALE||r>w.MAX_SCALE){return}w.zoomFunc.scale(r);s="translate("+w.margins[3]+","+w.margins[0]+") scale("+r+")";if(m.event!==null){u="translate("+m.event.translate+")"}else{if(typeof p!=="undefined"){var q=p.split(",")[0];var o=p.split(",")[1];if(!isNaN(q)&&!isNaN(o)){v=[v[0]+parseFloat(q),v[1]+parseFloat(o)]}}w.zoomFunc.translate(v);u="translate("+v+")"}w.phyloTree.set("scaleFactor",r);w.phyloTree.set("translate",v);w.vis.attr("transform",u+s)},reloadViz:function(){var n=this,o=$("#phylovizNexSelector :selected").val();$.getJSON(n.phyloTree.get("dataset").url(),{tree_index:o,data_type:"raw_data"},function(p){n.data=p.data;n.config=p;n.render()})}});var c=Backbone.View.extend({initialize:function(o){var n=this;n.phylovizView=o;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();n.initNavBtns();n.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){n.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var n=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();n.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var o=$("#phylovizNexSelector option:selected").text();if(o){n.phylovizView.phyloTree.set("title",o)}n.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz Help",on_click:function(){window.open("http://wiki.g2.bx.psu.edu/Learn/Visualization/PhylogeneticTree")}}],{tooltip_config:{placement:"bottom"}});$("#panelHeaderRightBtns").append(rightMenu.$el)},initNavBtns:function(){var n=this,o=create_icon_buttons_menu([{icon_class:"zoom-in",title:"Zoom in",on_click:function(){n.phylovizView.zoomAndPan({zoom:"+"})}},{icon_class:"zoom-out",title:"Zoom out",on_click:function(){n.phylovizView.zoomAndPan({zoom:"-"})}},{icon_class:"arrow-circle",title:"Reset Zoom/Pan",on_click:function(){n.phylovizView.zoomAndPan({zoom:"reset"})}}],{tooltip_config:{placement:"bottom"}});$("#phyloVizNavBtns").append(o.$el)}});var i=l.extend({className:"Settings",initialize:function(o){var n=this;n.phyloTree=o.phyloTree;n.el=$("#SettingsMenu");n.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){n.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){n.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){n.apply()})},apply:function(){var n=this;if(!n.isAcceptableValue(n.inputs.separation,50,2500)||!n.isAcceptableValue(n.inputs.leafHeight,5,30)||!n.isAcceptableValue(n.inputs.fontSize,5,20)){return}$.each(n.inputs,function(o,p){n.phyloTree.set(o,p.val())})},updateUI:function(){var n=this;$.each(n.inputs,function(o,p){p.val(n.phyloTree.get(o))})},resetToDefaults:function(){$(".tooltip").remove();var n=this;$.each(n.phyloTree.defaults,function(o,p){n.phyloTree.set(o,p)});n.updateUI()},render:function(){}});var e=l.extend({className:"Settings",initialize:function(o){var n=this;n.el=$("#nodeSelectionView");n.phyloTree=o.phyloTree;n.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};n.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){n.el.hide()});n.UI.saveChanges.off().on("click",function(){n.updateNodes()});n.UI.cancelChanges.off().on("click",function(){n.cancelChanges()});(function(p){p.fn.enable=function(q){return p(this).each(function(){if(q){p(this).removeAttr("disabled")}else{p(this).attr("disabled","disabled")}})}})(jQuery);n.UI.enableEdit.off().on("click",function(){n.toggleUI()})},toggleUI:function(){var n=this,o=n.UI.enableEdit.is(":checked");if(!o){n.cancelChanges()}$.each(n.valuesOfConcern,function(p,q){n.UI[p].enable(o)});if(o){n.UI.saveChanges.show();n.UI.cancelChanges.show()}else{n.UI.saveChanges.hide();n.UI.cancelChanges.hide()}},cancelChanges:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){$.each(n.valuesOfConcern,function(p,q){n.UI[p].val(o[p])})}},updateNodes:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){if(!n.isAcceptableValue(n.UI.dist,0,1)||n.hasIllegalJsonCharacters(n.UI.name)||n.hasIllegalJsonCharacters(n.UI.annotation)){return}$.each(n.valuesOfConcern,function(p,q){(o[p])=n.UI[p].val()});n.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var k=l.extend({initialize:function(){var n=this;$("#phyloVizSearchBtn").on("click",function(){var p=$("#phyloVizSearchTerm"),q=$("#phyloVizSearchCondition").val().split("-"),o=q[0],r=q[1];n.hasIllegalJsonCharacters(p);if(o==="dist"){n.isAcceptableValue(p,0,1)}n.searchTree(o,r,p.val())})},searchTree:function(n,p,o){m.selectAll("g.node").classed("searchHighlight",function(r){var q=r[n];if(typeof q!=="undefined"&&q!==null){if(n==="dist"){switch(p){case"greaterEqual":return q>=+o;case"lesserEqual":return q<=+o;default:return}}else{if(n==="name"||n==="annotation"){return q.toLowerCase().indexOf(o.toLowerCase())!==-1}}}})}});return{PhylovizView:j}}); \ No newline at end of file +define(["libs/d3","viz/visualization","mvc/data"],function(m,f,g){var l=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(q,o,n){var r=q.val(),s=q.attr("displayLabel")||q.attr("id").replace("phyloViz","");function p(t){return !isNaN(parseFloat(t))&&isFinite(t)}if(!p(r)){alert(s+" is not a number!");return false}if(r>n){alert(s+" is too large.");return false}else{if(r<o){alert(s+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(n){if(n.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). ");return true}return false}});function h(){var w=this,r=m.layout.hierarchy().sort(null).value(null),v=360,q="Linear",u=18,s=200,t=0,p=0.5,n=50;w.leafHeight=function(x){if(typeof x==="undefined"){return u}else{u=x;return w}};w.layoutMode=function(x){if(typeof x==="undefined"){return q}else{q=x;return w}};w.layoutAngle=function(x){if(typeof x==="undefined"){return v}if(isNaN(x)||x<0||x>360){return w}else{v=x;return w}};w.separation=function(x){if(typeof x==="undefined"){return s}else{s=x;return w}};w.links=function(x){return m.layout.tree().links(x)};w.nodes=function(A,y){if(toString.call(A)==="[object Array]"){A=A[0]}var z=r.call(w,A,y),x=[],C=0,B=0;window._d=A;window._nodes=z;z.forEach(function(D){C=D.depth>C?D.depth:C;x.push(D)});x.forEach(function(D){if(!D.children){B+=1;D.depth=C}});u=q==="Circular"?v/B:u;t=0;o(x[0],C,u,null);return x};function o(B,D,A,z){var y=B.children,x=0;var C=B.dist||p;C=C>1?1:C;B.dist=C;if(z!==null){B.y0=z.y0+C*s}else{B.y0=n}if(!y){B.x0=t*A;t+=1}else{y.forEach(function(E){E.parent=B;x+=o(E,D,A,B)});B.x0=x/y.length}B.x=B.x0;B.y=B.y0;return B.x0}return w}var b=f.Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},initialize:function(n){this.set("dataset",new g.Dataset({id:n.dataset_id}))},root:{},toggle:function(n){if(typeof n==="undefined"){return}if(n.children){n._children=n.children;n.children=null}else{n.children=n._children;n._children=null}},toggleAll:function(n){if(n.children&&n.children.length!==0){n.children.forEach(this.toggleAll);toggle(n)}},getData:function(){return this.root},save:function(){var n=this.root;o(n);function o(q){delete q.parent;if(q._selected){delete q._selected}if(q.children){q.children.forEach(o)}if(q._children){q._children.forEach(o)}}var p=jQuery.extend(true,{},this.attributes);p.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url,type:"POST",dataType:"json",data:{vis_json:JSON.stringify(p)},success:function(q){var r=q.url.split("id=")[1].split("&")[0],s="/visualization?id="+r;window.history.pushState({},"",s+window.location.hash);hide_modal()}})}});var d=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(o){var n=this;n.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",n.updateAndRender,n);n.vis=o.vis;n.i=0;n.maxDepth=-1;n.width=o.width;n.height=o.height},updateAndRender:function(p){var o=m.select(".vis"),n=this;p=p||n.model.root;n.renderNodes(p);n.renderLinks(p);n.addTooltips()},renderLinks:function(n){var w=this;var o=w.diagonal;var p=w.duration;var r=w.layoutMode;var t=w.vis.selectAll("g.completeLink").data(w.tree.links(w.nodes),function(x){return x.target.id});var v=function(x){x.pos0=x.source.y0+" "+x.source.x0;x.pos1=x.source.y0+" "+x.target.x0;x.pos2=x.target.y0+" "+x.target.x0};var u=t.enter().insert("svg:g","g.node").attr("class","completeLink");u.append("svg:path").attr("class","link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1});var s=t.transition().duration(500);s.select("path.link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1+" L "+x.pos2});var q=t.exit().remove()},selectNode:function(o){var n=this;m.selectAll("g.node").classed("selectedHighlight",function(p){if(o.id===p.id){if(o._selected){delete o._selected;return false}else{o._selected=true;return true}}return false});n.model.set("selectedNode",o);$("#phyloVizSelectedNodeName").val(o.name);$("#phyloVizSelectedNodeDist").val(o.dist);$("#phyloVizSelectedNodeAnnotation").val(o.annotation||"")},addTooltips:function(){$(".tooltip").remove();$(".node").attr("data-original-title",function(){var o=this.__data__,n=o.annotation||"None";return o?(o.name?o.name+"<br/>":"")+"Dist: "+o.dist+" <br/>Annotation: "+n:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(o){var n=this;n.margins=o.margins;n.layoutMode="Linear";n.stdInit(o);n.layout();n.updateAndRender(n.model.root)},layout:function(){var n=this;n.tree=new h().layoutMode("Linear");n.diagonal=m.svg.diagonal().projection(function(o){return[o.y,o.x]})},renderNodes:function(n){var u=this,v=u.model.get("fontSize")+"px";u.tree.separation(u.model.get("separation")).leafHeight(u.model.get("leafHeight"));var q=500,o=u.tree.separation(u.model.get("separation")).nodes(u.model.root);var p=u.vis.selectAll("g.node").data(o,function(w){return w.name+w.id||(w.id=++u.i)});u.nodes=o;u.duration=q;var r=p.enter().append("svg:g").attr("class","node").on("dblclick",function(){m.event.stopPropagation()}).on("click",function(w){if(m.event.altKey){u.selectNode(w)}else{if(w.children&&w.children.length===0){return}u.model.toggle(w);u.updateAndRender(w)}});if(toString.call(n)==="[object Array]"){n=n[0]}r.attr("transform",function(w){return"translate("+n.y0+","+n.x0+")"});r.append("svg:circle").attr("r",0.000001).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});r.append("svg:text").attr("class","nodeLabel").attr("x",function(w){return w.children||w._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(w){return w.children||w._children?"end":"start"}).style("fill-opacity",0.000001);var s=p.transition().duration(q);s.attr("transform",function(w){return"translate("+w.y+","+w.x+")"});s.select("circle").attr("r",u.defaults.nodeRadius).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});s.select("text").style("fill-opacity",1).style("font-size",v).text(function(w){return w.name});var t=p.exit().transition().duration(q).remove();t.select("circle").attr("r",0.000001);t.select("text").style("fill-opacity",0.000001);o.forEach(function(w){w.x0=w.x;w.y0=w.y})}});var j=Backbone.View.extend({className:"phyloviz",initialize:function(o){var n=this;n.MIN_SCALE=0.05;n.MAX_SCALE=5;n.MAX_DISPLACEMENT=500;n.margins=[10,60,10,80];n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.radius=n.width;n.data=o.data;$(window).resize(function(){n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.render()});n.phyloTree=new b(o.config);n.phyloTree.root=n.data;n.zoomFunc=m.behavior.zoom().scaleExtent([n.MIN_SCALE,n.MAX_SCALE]);n.zoomFunc.translate(n.phyloTree.get("translate"));n.zoomFunc.scale(n.phyloTree.get("scaleFactor"));n.navMenu=new c(n);n.settingsMenu=new i({phyloTree:n.phyloTree});n.nodeSelectionView=new e({phyloTree:n.phyloTree});n.search=new k();setTimeout(function(){n.zoomAndPan()},1000)},render:function(){var o=this;$("#PhyloViz").empty();o.mainSVG=m.select("#PhyloViz").append("svg:svg").attr("width",o.width).attr("height",o.height).attr("pointer-events","all").call(o.zoomFunc.on("zoom",function(){o.zoomAndPan()}));o.boundingRect=o.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",o.width).attr("height",o.height).attr("stroke","black").attr("fill","white");o.vis=o.mainSVG.append("svg:g").attr("class","vis");o.layoutOptions={model:o.phyloTree,width:o.width,height:o.height,vis:o.vis,margins:o.margins};$("#title").text("Phylogenetic Tree from "+o.phyloTree.get("title")+":");var n=new a(o.layoutOptions)},zoomAndPan:function(n){var t,p;if(typeof n!=="undefined"){t=n.zoom;p=n.translate}var w=this,r=w.zoomFunc.scale(),v=w.zoomFunc.translate(),s="",u="";switch(t){case"reset":r=1;v=[0,0];break;case"+":r*=1.1;break;case"-":r*=0.9;break;default:if(typeof t==="number"){r=t}else{if(m.event!==null){r=m.event.scale}}}if(r<w.MIN_SCALE||r>w.MAX_SCALE){return}w.zoomFunc.scale(r);s="translate("+w.margins[3]+","+w.margins[0]+") scale("+r+")";if(m.event!==null){u="translate("+m.event.translate+")"}else{if(typeof p!=="undefined"){var q=p.split(",")[0];var o=p.split(",")[1];if(!isNaN(q)&&!isNaN(o)){v=[v[0]+parseFloat(q),v[1]+parseFloat(o)]}}w.zoomFunc.translate(v);u="translate("+v+")"}w.phyloTree.set("scaleFactor",r);w.phyloTree.set("translate",v);w.vis.attr("transform",u+s)},reloadViz:function(){var n=this,o=$("#phylovizNexSelector :selected").val();$.getJSON(n.phyloTree.get("dataset").url(),{tree_index:o,data_type:"raw_data"},function(p){n.data=p.data;n.config=p;n.render()})}});var c=Backbone.View.extend({initialize:function(o){var n=this;n.phylovizView=o;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();n.initNavBtns();n.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){n.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var n=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();n.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var o=$("#phylovizNexSelector option:selected").text();if(o){n.phylovizView.phyloTree.set("title",o)}n.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz Help",on_click:function(){window.open("https://wiki.galaxyproject.org/Learn/Visualization/PhylogeneticTree")}}],{tooltip_config:{placement:"bottom"}});$("#panelHeaderRightBtns").append(rightMenu.$el)},initNavBtns:function(){var n=this,o=create_icon_buttons_menu([{icon_class:"zoom-in",title:"Zoom in",on_click:function(){n.phylovizView.zoomAndPan({zoom:"+"})}},{icon_class:"zoom-out",title:"Zoom out",on_click:function(){n.phylovizView.zoomAndPan({zoom:"-"})}},{icon_class:"arrow-circle",title:"Reset Zoom/Pan",on_click:function(){n.phylovizView.zoomAndPan({zoom:"reset"})}}],{tooltip_config:{placement:"bottom"}});$("#phyloVizNavBtns").append(o.$el)}});var i=l.extend({className:"Settings",initialize:function(o){var n=this;n.phyloTree=o.phyloTree;n.el=$("#SettingsMenu");n.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){n.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){n.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){n.apply()})},apply:function(){var n=this;if(!n.isAcceptableValue(n.inputs.separation,50,2500)||!n.isAcceptableValue(n.inputs.leafHeight,5,30)||!n.isAcceptableValue(n.inputs.fontSize,5,20)){return}$.each(n.inputs,function(o,p){n.phyloTree.set(o,p.val())})},updateUI:function(){var n=this;$.each(n.inputs,function(o,p){p.val(n.phyloTree.get(o))})},resetToDefaults:function(){$(".tooltip").remove();var n=this;$.each(n.phyloTree.defaults,function(o,p){n.phyloTree.set(o,p)});n.updateUI()},render:function(){}});var e=l.extend({className:"Settings",initialize:function(o){var n=this;n.el=$("#nodeSelectionView");n.phyloTree=o.phyloTree;n.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};n.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){n.el.hide()});n.UI.saveChanges.off().on("click",function(){n.updateNodes()});n.UI.cancelChanges.off().on("click",function(){n.cancelChanges()});(function(p){p.fn.enable=function(q){return p(this).each(function(){if(q){p(this).removeAttr("disabled")}else{p(this).attr("disabled","disabled")}})}})(jQuery);n.UI.enableEdit.off().on("click",function(){n.toggleUI()})},toggleUI:function(){var n=this,o=n.UI.enableEdit.is(":checked");if(!o){n.cancelChanges()}$.each(n.valuesOfConcern,function(p,q){n.UI[p].enable(o)});if(o){n.UI.saveChanges.show();n.UI.cancelChanges.show()}else{n.UI.saveChanges.hide();n.UI.cancelChanges.hide()}},cancelChanges:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){$.each(n.valuesOfConcern,function(p,q){n.UI[p].val(o[p])})}},updateNodes:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){if(!n.isAcceptableValue(n.UI.dist,0,1)||n.hasIllegalJsonCharacters(n.UI.name)||n.hasIllegalJsonCharacters(n.UI.annotation)){return}$.each(n.valuesOfConcern,function(p,q){(o[p])=n.UI[p].val()});n.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var k=l.extend({initialize:function(){var n=this;$("#phyloVizSearchBtn").on("click",function(){var p=$("#phyloVizSearchTerm"),q=$("#phyloVizSearchCondition").val().split("-"),o=q[0],r=q[1];n.hasIllegalJsonCharacters(p);if(o==="dist"){n.isAcceptableValue(p,0,1)}n.searchTree(o,r,p.val())})},searchTree:function(n,p,o){m.selectAll("g.node").classed("searchHighlight",function(r){var q=r[n];if(typeof q!=="undefined"&&q!==null){if(n==="dist"){switch(p){case"greaterEqual":return q>=+o;case"lesserEqual":return q<=+o;default:return}}else{if(n==="name"||n==="annotation"){return q.toLowerCase().indexOf(o.toLowerCase())!==-1}}}})}});return{PhylovizView:j}}); \ 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: jlhg: Fix the column alignment in the tabular format data
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/14df6b188d7e/ Changeset: 14df6b188d7e User: jlhg Date: 2014-04-11 21:29:53 Summary: Fix the column alignment in the tabular format data Affected #: 2 files diff -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 -r 14df6b188d7e09046e1e42c2c5c9113322a191f9 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -21,7 +21,7 @@ initialize: function() { this._set_metadata(); - + // Update metadata on change. this.on('change', this._set_metadata, this); }, @@ -30,7 +30,7 @@ var metadata = new DatasetMetadata(); // Move metadata from dataset attributes to metadata object. - _.each(_.keys(this.attributes), function(k) { + _.each(_.keys(this.attributes), function(k) { if (k.indexOf('metadata_') === 0) { // Found metadata. var new_key = k.split('metadata_')[1]; @@ -108,8 +108,8 @@ }); /** - * Provides a base for table-based, dynamic view of a tabular dataset. - * Do not instantiate directly; use either TopLevelTabularDatasetChunkedView + * Provides a base for table-based, dynamic view of a tabular dataset. + * Do not instantiate directly; use either TopLevelTabularDatasetChunkedView * or EmbeddedTabularDatasetChunkedView. */ var TabularDatasetChunkedView = Backbone.View.extend({ @@ -193,7 +193,7 @@ $cell.attr('colspan', colspan).addClass('stringalign'); } else if (column_types) { if (index < column_types.length) { - if (column_types[index] === 'str' || column_types === 'list') { + if (column_types[index] === 'str' || column_types[index] === 'list') { /* Left align all str columns, right align the rest */ $cell.addClass('stringalign'); } @@ -329,22 +329,22 @@ initialize: function (options) { // check if environment is available var Galaxy = parent.Galaxy; - + // link galaxy modal or create one if (Galaxy && Galaxy.modal) { this.modal = Galaxy.modal; } - + // link galaxy frames if (Galaxy && Galaxy.frame) { this.frame = Galaxy.frame; } - + // check if (!this.modal || !this.frame) { return; } - + // model/metadata var model = options.model; var metadata = model.get('metadata'); @@ -353,10 +353,10 @@ if (!model.get('data_type')) { return; } - + // get data type this.data_type = model.get('data_type'); - + // check for bed-file format if (this.data_type == 'bed') { @@ -394,7 +394,7 @@ return; } } - + // check if(this.col.chrom === undefined) { return; @@ -407,7 +407,7 @@ console.log('TabularButtonTrackster : Dataset identification is missing.'); return; } - + // get url if (model.get('url_viz')) { this.url_viz = model.get('url_viz'); @@ -429,10 +429,10 @@ id : 'btn_viz' }) }); - + // set element this.setElement(options.$el); - + // add to element this.$el.append(btn_viz.render().$el); @@ -446,14 +446,14 @@ 'mouseover tr' : 'show', 'mouseleave' : 'hide' }, - + // show button show: function (e) { // is numeric function is_numeric(n) { return !isNaN(parseFloat(n)) && isFinite(n); }; - + // check if(this.col.chrom === null) return; @@ -470,7 +470,7 @@ // double check location if (!chrom.match("^#") && chrom !== "" && is_numeric(start)) { - + // get target gene region var btn_viz_pars = { dataset_id : this.dataset_id, @@ -494,17 +494,17 @@ $('#btn_viz').hide(); } }, - + // hide button hide: function () { this.$el.find('#btn_viz').hide(); }, - + // create action create_trackster_action : function (vis_url, dataset_params, dbkey) { // link this var self = this; - + // create function return function() { var listTracksParams = {}; @@ -546,13 +546,13 @@ 'Add to visualization': function(){ // hide self.modal.hide(); - + // search selected fields self.modal.$el.find('input[name=id]:checked').each(function(){ // get visualization id var vis_id = $(this).val(); dataset_params.id = vis_id; - + // add widget self.frame.add({ title : 'Trackster', @@ -567,7 +567,7 @@ 'View in new visualization': function(){ // hide self.modal.hide(); - + // add widget self.frame.add({ title : 'Trackster', @@ -619,7 +619,7 @@ delete options.embedded; delete options.parent_elt; delete options.dataset_config; - + // Create and set up view. var view = (embedded ? new EmbeddedTabularDatasetChunkedView(options) : new TopLevelTabularDatasetChunkedView(options)); diff -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 -r 14df6b188d7e09046e1e42c2c5c9113322a191f9 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file +define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); 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: 3 new changesets
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e02cccf0fb8a/ Changeset: e02cccf0fb8a User: dcnorris Date: 2014-04-10 15:48:59 Summary: Added IGB display support for bed graph files Affected #: 6 files diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -26,6 +26,7 @@ </datatype><datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"><converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/bedgraph.xml" /></datatype><datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /><datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 display_applications/igb/bam.xml --- a/display_applications/igb/bam.xml +++ b/display_applications/igb/bam.xml @@ -1,4 +1,4 @@ -<display id="igb_bam" version="0.0.0" name="display in IGB"> +<display id="igb_bam" version="0.0.0" name="Display in IGB"><link id="View" name="View"><url>http://bioviz.org/igb/galaxy.html?version=${bam_file.dbkey}&feature_url…</url><param type="data" name="bam_file_for_name" viewable="False"/> diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 display_applications/igb/bb.xml --- a/display_applications/igb/bb.xml +++ b/display_applications/igb/bb.xml @@ -1,4 +1,4 @@ -<display id="igb_bb" version="1.0.0" name="display in IGB"> +<display id="igb_bb" version="1.0.0" name="Display in IGB"><link id="View" name="View"><url>http://bioviz.org/igb/galaxy.html?version=${bigbed_file.dbkey}&loadresi…</url> diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 display_applications/igb/bed.xml --- a/display_applications/igb/bed.xml +++ b/display_applications/igb/bed.xml @@ -1,4 +1,4 @@ -<display id="igb_bed" version="1.0.0" name="display in IGB"> +<display id="igb_bed" version="1.0.0" name="Display in IGB"><link id="View" name="View"><url>$bioviz</url> diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 display_applications/igb/bedgraph.xml --- /dev/null +++ b/display_applications/igb/bedgraph.xml @@ -0,0 +1,17 @@ +<display id="igb_bedgraph" version="1.0.0" name="Display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="bedgraph_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bedgraph_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bedgraph_file" url="${niceName}.bed.bedgraph" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${bedgraph_file.dbkey}&loadre… + </param> + </link> +</display> \ No newline at end of file diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 display_applications/igb/wig.xml --- a/display_applications/igb/wig.xml +++ b/display_applications/igb/wig.xml @@ -1,4 +1,4 @@ -<display id="igb_wig" version="1.0.0" name="display in IGB"> +<display id="igb_wig" version="1.0.0" name="Display in IGB"><link id="View" name="View"><url>http://bioviz.org/igb/galaxy.html?version=${wig_file.dbkey}&${position}…</url> https://bitbucket.org/galaxy/galaxy-central/commits/c8866f186e4d/ Changeset: c8866f186e4d User: dcnorris Date: 2014-04-11 19:41:07 Summary: Reverted capitalization Affected #: 6 files diff -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a display_applications/igb/bam.xml --- a/display_applications/igb/bam.xml +++ b/display_applications/igb/bam.xml @@ -1,4 +1,4 @@ -<display id="igb_bam" version="0.0.0" name="Display in IGB"> +<display id="igb_bam" version="0.0.0" name="display in IGB"><link id="View" name="View"><url>http://bioviz.org/igb/galaxy.html?version=${bam_file.dbkey}&feature_url…</url><param type="data" name="bam_file_for_name" viewable="False"/> diff -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a display_applications/igb/bb.xml --- a/display_applications/igb/bb.xml +++ b/display_applications/igb/bb.xml @@ -1,4 +1,4 @@ -<display id="igb_bb" version="1.0.0" name="Display in IGB"> +<display id="igb_bb" version="1.0.0" name="display in IGB"><link id="View" name="View"><url>http://bioviz.org/igb/galaxy.html?version=${bigbed_file.dbkey}&loadresi…</url> diff -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a display_applications/igb/bed.xml --- a/display_applications/igb/bed.xml +++ b/display_applications/igb/bed.xml @@ -1,4 +1,4 @@ -<display id="igb_bed" version="1.0.0" name="Display in IGB"> +<display id="igb_bed" version="1.0.0" name="display in IGB"><link id="View" name="View"><url>$bioviz</url> diff -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a display_applications/igb/bedgraph.xml --- a/display_applications/igb/bedgraph.xml +++ b/display_applications/igb/bedgraph.xml @@ -1,4 +1,4 @@ -<display id="igb_bedgraph" version="1.0.0" name="Display in IGB"> +<display id="igb_bedgraph" version="1.0.0" name="display in IGB"><link id="View" name="View"><url>$bioviz</url> @@ -14,4 +14,4 @@ http://bioviz.org/igb/galaxy.html?version=${bedgraph_file.dbkey}&loadre… </param></link> -</display> \ No newline at end of file +</display> diff -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a display_applications/igb/bigwig.xml --- a/display_applications/igb/bigwig.xml +++ b/display_applications/igb/bigwig.xml @@ -1,4 +1,4 @@ -<display id="igb_bigwig" version="1.0.0" name="Display in IGB"> +<display id="igb_bigwig" version="1.0.0" name="display in IGB"><link id="View" name="View"><url>http://bioviz.org/igb/galaxy.html?version=${bigwig_file.dbkey}&loadresi…</url> diff -r e02cccf0fb8a6385ec2e8ee3b57b4327169fcb55 -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a display_applications/igb/wig.xml --- a/display_applications/igb/wig.xml +++ b/display_applications/igb/wig.xml @@ -1,4 +1,4 @@ -<display id="igb_wig" version="1.0.0" name="Display in IGB"> +<display id="igb_wig" version="1.0.0" name="display in IGB"><link id="View" name="View"><url>http://bioviz.org/igb/galaxy.html?version=${wig_file.dbkey}&${position}…</url> https://bitbucket.org/galaxy/galaxy-central/commits/18ac7049d256/ Changeset: 18ac7049d256 User: hillrunner2008 Date: 2014-04-11 19:41:31 Summary: Merged galaxy/galaxy-central into default Affected #: 114 files diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -51,7 +51,6 @@ // append views this.$el.append(this.viewer_view.$el); this.$el.append(this.editor_view.$el); - this.$el.css('height', 'inherit'); // pick start screen if (!this.storage.load()) { diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 config/plugins/visualizations/charts/static/charts/nvd3/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/config.js @@ -1,15 +1,15 @@ define([], function() { return { - title : '', - library : 'nvd3.js', - element : 'svg', + title : '', + library : 'nvd3.js', + element : 'svg', columns : { y : { title : 'Values for y-axis' } }, - settings : { + settings : { separator_label : { title : 'X axis', type : 'separator' diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js @@ -1,7 +1,18 @@ -define(['plugin/charts/nvd3/config'], function(nvd3_config) { +define([], function() { -return $.extend(true, {}, nvd3_config, { - title : 'Pie chart', -}); +return { + title : 'Pie chart', + library : 'nvd3.js', + element : 'svg', + columns : { + label : { + title : 'Labels', + any_type : true + }, + y : { + title : 'Values' + } + } +}; }); \ No newline at end of file diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js @@ -27,29 +27,29 @@ for (var key in group.values) { var value = group.values[key]; pie_data.push ({ - key : value.x, - y : value.y + y : value.y, + x : value.label }); } + } + + // add graph to screen + nv.addGraph(function() { + self.chart_3d = nv.models.pieChart() + .donut(true) + .showLegend(false); - // add graph to screen - nv.addGraph(function() { - self.chart_3d = nv.models.pieChart() - .donut(true) - .showLegend(false); - - self.options.canvas.datum(pie_data) - .call(self.chart_3d); + self.options.canvas.datum(pie_data) + .call(self.chart_3d); - nv.utils.windowResize(self.chart_3d.update); - - // set chart state - chart.state('ok', 'Pie chart drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); - } + nv.utils.windowResize(self.chart_3d.update); + + // set chart state + chart.state('ok', 'Chart has been drawn.'); + + // unregister process + chart.deferred.done(process_id); + }); }); } }); diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 config/plugins/visualizations/charts/static/library/deferred.js --- a/config/plugins/visualizations/charts/static/library/deferred.js +++ b/config/plugins/visualizations/charts/static/library/deferred.js @@ -59,17 +59,19 @@ // unregister process done: function(id) { - // delete tag - delete this.process[id]; - - // decrease process counter - this.counter--; - - // log - console.debug('Deferred:done() - Unregistering ' + id); - - // trigger change - this.trigger('refresh'); + if (this.process[id]) { + // delete tag + delete this.process[id]; + + // decrease process counter + this.counter--; + + // log + console.debug('Deferred:done() - Unregistering ' + id); + + // trigger change + this.trigger('refresh'); + } }, // ready diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -5,9 +5,6 @@ // widget return Backbone.View.extend( { - // columns - columns: [], - // initialize initialize: function(app, options) { // link app @@ -121,24 +118,29 @@ // get dataset this.app.datasets.request({id : dataset_id}, function(dataset) { - // configure columns - self.columns = []; - var meta = dataset.metadata_column_types; - for (var key in meta) { - // check type - if(meta[key] == 'int' || meta[key] == 'float') { - // add to selection - self.columns.push({ - 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', - 'value' : key - }); + // update select fields + for (var id in list) { + + // is a numeric number required + var any_type = chart_settings.columns[id].any_type; + + // configure columns + var columns = []; + var meta = dataset.metadata_column_types; + for (var key in meta) { + // check type + if (meta[key] == 'int' || meta[key] == 'float' || any_type) { + // add to selection + columns.push({ + 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'value' : key + }); + } } - } - // update select fields - for (var key in list) { - list[key].update(self.columns); - list[key].show(); + // list + list[id].update(columns); + list[id].show(); } // loading diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 doc/source/lib/galaxy.webapps.galaxy.api.rst~ --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst~ +++ /dev/null @@ -1,179 +0,0 @@ -api Package -=========== - -:mod:`datasets` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.api.datasets - :members: - :undoc-members: - :show-inheritance: - -:mod:`folder_contents` Module ------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.folder_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`folders` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.folders - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`genomes` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.genomes - :members: - :undoc-members: - :show-inheritance: - -:mod:`group_roles` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`group_users` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_users - :members: - :undoc-members: - :show-inheritance: - -:mod:`groups` Module --------------------- - -.. automodule:: galaxy.webapps.galaxy.api.groups - :members: - :undoc-members: - :show-inheritance: - -:mod:`histories` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.histories - :members: - :undoc-members: - :show-inheritance: - -:mod:`history_contents` Module ------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.history_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`libraries` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.libraries - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_contents` Module ------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.library_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`permissions` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.permissions - :members: - :undoc-members: - :show-inheritance: - -:mod:`quotas` Module --------------------- - -.. automodule:: galaxy.webapps.galaxy.api.quotas - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_types` Module ---------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.request_types - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.api.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`roles` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`samples` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.samples - :members: - :undoc-members: - :show-inheritance: - -:mod:`tools` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tools - :members: - :undoc-members: - :show-inheritance: - -:mod:`users` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.users - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualizations` Module ----------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.visualizations - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflows` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.workflows - :members: - :undoc-members: - :show-inheritance: - diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -3,7 +3,7 @@ ; ; This file is version controlled and should not be edited by hand! ; For more information, see: -; http://wiki.g2.bx.psu.edu/Admin/Config/Eggs +; https://wiki.galaxyproject.org/Admin/Config/Eggs ; [general] diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -110,7 +110,7 @@ <!-- Traditionally, the LWR client sends request to LWR server to populate various system properties. This extra step can be disabled and these calculated here - on client by uncommenting job_directory and + on client by uncommenting jobs_directory and specifying any additional remote_property_ of interest. When using message queues this is nessecary not optional. diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -217,7 +217,7 @@ self.message_box_visible = kwargs.get( 'message_box_visible', False ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) - self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) + self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -60,6 +60,10 @@ status_code = 400 err_code = error_codes.MALFORMED_ID +class UnknownContentsType( MessageException ): + status_code = 400 + err_code = error_codes.UNKNOWN_CONTENTS_TYPE + class RequestParameterMissingException( MessageException ): status_code = 400 err_code = error_codes.USER_REQUEST_MISSING_PARAMETER diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/exceptions/error_codes.json --- a/lib/galaxy/exceptions/error_codes.json +++ b/lib/galaxy/exceptions/error_codes.json @@ -50,6 +50,11 @@ "message": "The id of the resource is malformed." }, { + "name": "UNKNOWN_CONTENTS_TYPE", + "code": 400010, + "message": "The request contains unknown type of contents." + }, + { "name": "USER_NO_API_KEY", "code": 403001, "message": "API authentication required for this request" diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -72,9 +72,9 @@ 'Variable_List' : '-v', } -# From pbs' job.h +# From pbs' pbs_job.h JOB_EXIT_STATUS = { - 0: "job exec successful", + 0: "job exec successful", -1: "job exec failed, before files, no retry", -2: "job exec failed, after files, no retry", -3: "job execution failed, do retry", @@ -83,7 +83,10 @@ -6: "job aborted on MOM init, chkpt, ok migrate", -7: "job restart failed", -8: "exec() of user command failed", - -11: "job maximum walltime exceeded", # Added by John, not from job.h. + -9: "could not create/open stdout stderr files", + -10: "job exceeded a memory limit", + -11: "job exceeded a walltime limit", + -12: "job exceeded a cpu time limit", } diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -4,6 +4,7 @@ from galaxy.util.bunch import Bunch from galaxy.util import asbool from tool_shed.util import common_util +from urlparse import urljoin log = logging.getLogger( __name__ ) @@ -73,6 +74,12 @@ def can_reinstall_or_activate( self ): return self.deleted + def get_sharable_url( self, app ): + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, self.tool_shed ) + if tool_shed_url: + return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) + return tool_shed_url + def get_shed_config_filename( self ): shed_config_filename = None if self.metadata: diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -28,7 +28,9 @@ ----------------------------------------------------------------------------- job id: ${job_id} tool id: ${job_tool_id} +tool version: ${tool_version} job pid or drm id: ${job_runner_external_id} +job tool version: ${job_tool_version} ----------------------------------------------------------------------------- job command line: ${job_command_line} @@ -86,7 +88,9 @@ history_item_name=hda.get_display_name(), history_view_link=history_view_link, job_id=job.id, + tool_version=job.tool_version, job_tool_id=job.tool_id, + job_tool_version=hda.tool_version, job_runner_external_id=job.job_runner_external_id, job_command_line=job.command_line, job_stderr=util.unicodify( job.stderr ), diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -979,7 +979,7 @@ if option[2]: # Found selected option. value = option[1] - d[ 'value' ] = options + d[ 'value' ] = value return d diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/util/biostar.py --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -86,7 +86,14 @@ def populate_tool_payload( payload=None, tool=None ): payload = populate_tag_payload( payload=payload, tool=tool ) payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name ) - payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ) + tool_url = None + if tool.tool_shed_repository: + tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) + if tool_url: + tool_url = '</br>ToolShed URL: <a href="%s">%s</a>' % ( tool_url, tool_url ) + if not tool_url: + tool_url = '' + payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s%s</p></br>' % ( tool.name, tool.version, tool.id, tool_url ) return payload def determine_cookie_domain( galaxy_hostname, biostar_hostname ): diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ b/lib/galaxy/webapps/demo_sequencer/config.py @@ -50,7 +50,7 @@ self.smtp_server = kwargs.get( 'smtp_server', None ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) - self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) + self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,13 +1,15 @@ """ -API operations on the contents of a folder. +API operations on the contents of a library folder. """ -import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage -from galaxy import util, datatypes, jobs, web, util -from galaxy.web.base.controller import * -from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * +from galaxy import web +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from sqlalchemy.orm.exc import MultipleResultsFound +from sqlalchemy.orm.exc import NoResultFound +from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems +import logging log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): @@ -15,7 +17,111 @@ Class controls retrieval, creation and updating of folder contents. """ - def load_folder_contents( self, trans, folder ): + @expose_api_anonymous + def index( self, trans, folder_id, **kwd ): + """ + GET /api/folders/{encoded_folder_id}/contents + Displays a collection (list) of a folder's contents (files and folders). + Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. + Full path is provided in response as a separate object providing data for breadcrumb path building. + """ + + if ( len( folder_id ) == 17 and folder_id.startswith( 'F' ) ): + try: + decoded_folder_id = trans.security.decode_id( folder_id[ 1: ] ) + except TypeError: + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) ) + else: + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) ) + + try: + folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_folder_id ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple folders with same id found.' ) + except NoResultFound: + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + except Exception: + raise exceptions.InternalServerError( 'Error loading from the database.' ) + + current_user_roles = trans.get_current_user_roles() + can_add_library_item = trans.user_is_admin() or trans.app.security_agent.can_add_library_item( current_user_roles, folder ) + + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + if folder.parent_id == None: + try: + library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.root_folder_id == decoded_folder_id ).one() + except Exception: + raise exceptions.InternalServerError( 'Error loading from the database.' ) + if trans.app.security_agent.library_is_public( library, contents=False ): + pass + else: + if trans.user: + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) + else: + log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + else: + if trans.user: + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) + else: + log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + + def build_path( folder ): + """ + Search the path upwards recursively and load the whole route of names and ids for breadcrumb building purposes. + """ + path_to_root = [] + # We are almost in root + if folder.parent_id is None: + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + else: + # We add the current folder and traverse up one folder. + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( build_path( upper_folder ) ) + return path_to_root + + # Return the reversed path so it starts with the library node. + full_path = build_path( folder )[::-1] + + folder_contents = [] + time_updated = '' + time_created = '' + # Go through every accessible item in the folder and include its meta-data. + for content_item in self._load_folder_contents( trans, folder ): + if trans.app.security_agent.can_access_library_item( current_user_roles, content_item, trans.user ): + return_item = {} + encoded_id = trans.security.encode_id( content_item.id ) + time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) + + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_id = 'F' + encoded_id + return_item.update ( dict ( item_count = content_item.item_count ) ) + + if content_item.api_type == 'file': + library_dataset_dict = content_item.to_dict() + library_dataset_dict['data_type'] + library_dataset_dict['file_size'] + library_dataset_dict['date_uploaded'] + return_item.update ( dict ( data_type = library_dataset_dict['data_type'], + file_size = library_dataset_dict['file_size'], + date_uploaded = library_dataset_dict['date_uploaded'] ) ) + + # For every item return also the default meta-data + return_item.update( dict( id = encoded_id, + type = content_item.api_type, + name = content_item.name, + time_updated = time_updated, + time_created = time_created + ) ) + folder_contents.append( return_item ) + + return { 'metadata' : { 'full_path' : full_path, 'can_add_library_item': can_add_library_item }, 'folder_contents' : folder_contents } + + def _load_folder_contents( self, trans, folder ): """ Loads all contents of the folder (folders and data sets) but only in the first level. """ @@ -37,101 +143,11 @@ return content_items @web.expose_api - def index( self, trans, folder_id, **kwd ): - """ - GET /api/folders/{encoded_folder_id}/contents - Displays a collection (list) of a folder's contents (files and folders). - Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. - Full path is provided as a separate object in response providing data for breadcrumb path building. - """ - folder_container = [] - current_user_roles = trans.get_current_user_roles() - - if ( folder_id.startswith( 'F' ) ): - try: - decoded_folder_id = trans.security.decode_id( folder_id[1:] ) - except TypeError: - trans.response.status = 400 - return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) - - try: - folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) - except: - folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) - - # We didn't find the folder or user does not have an access to it. - if not folder: - trans.response.status = 400 - return "Invalid folder id ( %s ) specified." % str( folder_id ) - - if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): - log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) - trans.response.status = 400 - return "Invalid folder id ( %s ) specified." % str( folder_id ) - - path_to_root = [] - def build_path ( folder ): - """ - Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. - """ - path_to_root = [] - # We are almost in root - if folder.parent_id is None: - path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) - else: - # We add the current folder and traverse up one folder. - path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) - upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) - path_to_root.extend( build_path( upper_folder ) ) - return path_to_root - - # Return the reversed path so it starts with the library node. - full_path = build_path( folder )[::-1] - folder_container.append( dict( full_path = full_path ) ) - - folder_contents = [] - time_updated = '' - time_created = '' - # Go through every item in the folder and include its meta-data. - for content_item in self.load_folder_contents( trans, folder ): - return_item = {} - encoded_id = trans.security.encode_id( content_item.id ) - time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) - time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) - - # For folder return also hierarchy values - if content_item.api_type == 'folder': - encoded_id = 'F' + encoded_id - return_item.update ( dict ( item_count = content_item.item_count ) ) - - if content_item.api_type == 'file': - library_dataset_dict = content_item.to_dict() - library_dataset_dict['data_type'] - library_dataset_dict['file_size'] - library_dataset_dict['date_uploaded'] - return_item.update ( dict ( data_type = library_dataset_dict['data_type'], - file_size = library_dataset_dict['file_size'], - date_uploaded = library_dataset_dict['date_uploaded'] ) ) - - # For every item return also the default meta-data - return_item.update( dict( id = encoded_id, - type = content_item.api_type, - name = content_item.name, - time_updated = time_updated, - time_created = time_created - ) ) - folder_contents.append( return_item ) - # Put the data in the container - folder_container.append( dict( folder_contents = folder_contents ) ) - return folder_container - - @web.expose_api def show( self, trans, id, library_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/ """ - pass + raise exceptions.NotImplemented( 'Showing the library folder content is not implemented.' ) @web.expose_api def create( self, trans, library_id, payload, **kwd ): @@ -140,20 +156,11 @@ Creates a new folder. This should be superseded by the LibraryController. """ - pass + raise exceptions.NotImplemented( 'Creating the library folder content is not implemented.' ) @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ PUT /api/folders/{encoded_folder_id}/contents """ - pass - - # TODO: Move to library_common. - def __decode_library_content_id( self, trans, content_id ): - if ( len( content_id ) % 16 == 0 ): - return 'LibraryDataset', content_id - elif ( content_id.startswith( 'F' ) ): - return 'LibraryFolder', content_id[1:] - else: - raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) ) + raise exceptions.NotImplemented( 'Updating the library folder content is not implemented.' ) diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/folders.py --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -1,14 +1,17 @@ """ -API operations on folders +API operations on library folders """ -import logging, os, string, shutil, urllib, re, socket, traceback +import os, string, shutil, urllib, re, socket, traceback from galaxy import datatypes, jobs, web, security +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web.base.controller import BaseAPIController,UsesLibraryMixin,UsesLibraryMixinItems from galaxy.util.sanitize_html import sanitize_html from cgi import escape, FieldStorage from paste.httpexceptions import HTTPBadRequest +import logging log = logging.getLogger( __name__ ) class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): @@ -18,9 +21,9 @@ """ GET /api/folders/ This would normally display a list of folders. However, that would - be across multiple libraries, so it's not implemented yet. + be across multiple libraries, so it's not implemented. """ - pass + raise exceptions.NotImplemented( 'Listing all accessible library folders is not implemented.' ) @web.expose_api def show( self, trans, id, **kwd ): diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -1,7 +1,7 @@ -from galaxy import config, tools, web, util -from galaxy.web.base.controller import BaseController, BaseAPIController -from galaxy.util.bunch import Bunch +from galaxy import web, util +from galaxy.web.base.controller import BaseAPIController from galaxy.web.framework.helpers import is_true +from galaxy.webapps.galaxy.controllers.data_admin import build_param_dict as massage def get_id( base, format ): if format: @@ -76,7 +76,6 @@ # 'download' Download and index # 'index' Index only params = util.Params( payload ) - from galaxy.web.controllers.data_admin import build_param_dict as massage paramdict = massage( params, trans ) func = params.get( 'func', 'download' ) if func == 'download': diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/group_users.py --- a/lib/galaxy/webapps/galaxy/api/group_users.py +++ b/lib/galaxy/webapps/galaxy/api/group_users.py @@ -58,7 +58,7 @@ email = user.email, url = url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This if not item: - item = "user %s not in group %s" % (user.email,group.name) + item = "user %s not in group %s" % (user.email, group.name) except Exception, e: item = "Error in group_user API group %s user %s" % (group.name, user.email) log.error(item + ": %s" % str(e)) @@ -92,7 +92,7 @@ email = user.email, url = url_for( 'group_user', group_id=group_id, id=user_id) ) except Exception, e: - item = "Error in group_user API Adding user %s to group %s" % (user.email,group.name) + item = "Error in group_user API Adding user %s to group %s" % (user.email, group.name) log.error(item + ": %s" % str(e)) return item @@ -117,8 +117,8 @@ email = user.email, url = url_for( 'group_user', group_id=group_id, id=user_id) ) if not item: - item = "user %s not in group %s" % (user.email,group.name) + item = "user %s not in group %s" % (user.email, group.name) except Exception, e: - item = "Error in group_user API Removing user %s from group %s" % (user.email,group.name) + item = "Error in group_user API Removing user %s from group %s" % (user.email, group.name) log.error(item + ": %s" % str(e)) return item diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -8,7 +8,6 @@ pkg_resources.require( "Paste" ) from galaxy import exceptions -from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web import _future_expose_api_raw as expose_api_raw diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -4,7 +4,6 @@ from galaxy import exceptions from galaxy import util -from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous @@ -18,7 +17,6 @@ from galaxy.web.base.controller import UsesTagsMixin from galaxy.web.base.controller import url_for -from galaxy.util.sanitize_html import sanitize_html from galaxy.webapps.galaxy.api import histories @@ -190,8 +188,7 @@ hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) return hda_dict - #TODO: allow anon users to copy hdas, ldas - @expose_api + @expose_api_anonymous def create( self, trans, history_id, payload, **kwd ): """ create( self, trans, history_id, payload, **kwd ) @@ -436,10 +433,7 @@ return validated_payload def __handle_unknown_contents_type( self, trans, contents_type ): - # TODO: raise a message exception instead of setting status and returning dict. - trans.response.status = 400 - return { 'error': 'Unknown contents type %s' % type } - + raise exceptions.UnknownContentsType('Unknown contents type: %s' % type) class HDAManager( object ): diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -12,9 +12,13 @@ import urllib import urllib2 import zipfile -from paste.httpexceptions import HTTPBadRequest -from galaxy import util, web -from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +# from paste.httpexceptions import HTTPBadRequest +from galaxy import util +from galaxy import web +# from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound from galaxy.security import Action from galaxy.util.streamball import StreamBall from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin @@ -24,7 +28,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): - @web.expose_api + @expose_api_anonymous def show( self, trans, id, **kwd ): """ show( self, trans, id, **kwd ) @@ -41,19 +45,20 @@ try: dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True ) except Exception, e: - trans.response.status = 500 - return str( e ) - try: - rval = dataset.to_dict() - except Exception, e: - rval = "Error in dataset API at listing contents: " + str( e ) - log.error( rval + ": %s" % str(e), exc_info=True ) - trans.response.status = 500 - return "Error in dataset API at listing contents: " + str( e ) + raise exceptions.ObjectNotFound( 'Requested dataset was not found.' ) + # trans.response.status = 500 + # return str( e ) + # try: + rval = dataset.to_dict() + # except Exception, e: + # rval = "Error in dataset API at listing contents: " + str( e ) + # log.error( rval + ": %s" % str(e), exc_info=True ) + # trans.response.status = 500 + # return "Error in dataset API at listing contents: " + str( e ) rval['id'] = trans.security.encode_id(rval['id']); rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); - rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) + rval['folder_id'] = 'F' + trans.security.encode_id(rval['folder_id']) return rval @web.expose diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -7,7 +7,7 @@ from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.model.orm import and_, not_, or_ -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.web.base.controller import BaseAPIController import logging log = logging.getLogger( __name__ ) @@ -61,7 +61,6 @@ if trans.app.security_agent.library_is_public( library, contents=False ): item[ 'public' ] = True current_user_roles = trans.get_current_user_roles() - # can_user_add = trans.app.security_agent.can_add_library_item( current_user_roles, library.root_folder ) if not trans.user_is_admin(): item['can_user_add'] = trans.app.security_agent.can_add_library_item( current_user_roles, library ) item['can_user_modify'] = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) @@ -98,7 +97,7 @@ deleted = util.string_as_bool( deleted ) try: decoded_library_id = trans.security.decode_id( library_id ) - except Exception: + except TypeError: raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % id ) try: library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id ) @@ -144,7 +143,14 @@ library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() - return library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) + + item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) + item['can_user_add'] = True + item['can_user_modify'] = True + item['can_user_manage'] = True + if trans.app.security_agent.library_is_public( library, contents=False ): + item[ 'public' ] = True + return item @expose_api def update( self, trans, id, **kwd ): diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -17,8 +17,7 @@ log = logging.getLogger( __name__ ) -class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, - UsesHistoryDatasetAssociationMixin ): +class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ): @expose_api def index( self, trans, library_id, **kwd ): diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/metrics.py --- a/lib/galaxy/webapps/galaxy/api/metrics.py +++ b/lib/galaxy/webapps/galaxy/api/metrics.py @@ -7,7 +7,6 @@ import datetime from galaxy import exceptions -from galaxy import web from galaxy.web import require_admin from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -152,48 +152,6 @@ # -- Helper methods -- # - def _run_tool( self, trans, tool_id, target_dataset_id, **kwargs ): - """ - Run a tool. This method serves as a general purpose way to run tools asynchronously. - """ - - # - # Set target history (the history that tool will use for outputs) using - # target dataset. If user owns dataset, put new data in original - # dataset's history; if user does not own dataset (and hence is accessing - # dataset via sharing), put new data in user's current history. - # - target_dataset = self.get_dataset( trans, target_dataset_id, check_ownership=False, check_accessible=True ) - if target_dataset.history.user == trans.user: - target_history = target_dataset.history - else: - target_history = trans.get_history( create=True ) - - # HACK: tools require unencoded parameters but kwargs are typically - # encoded, so try decoding all parameter values. - for key, value in kwargs.items(): - try: - value = trans.security.decode_id( value ) - kwargs[ key ] = value - except: - pass - - # - # Execute tool. - # - tool = trans.app.toolbox.get_tool( tool_id ) - if not tool: - return trans.app.model.Dataset.conversion_messages.NO_TOOL - - # HACK: add run button so that tool.handle_input will run tool. - kwargs['runtool_btn'] = 'Execute' - params = util.Params( kwargs, sanitize=False ) - template, vars = tool.handle_input( trans, params.__dict__, history=target_history ) - - # TODO: check for errors and ensure that output dataset is available. - output_datasets = vars[ 'out_data' ].values() - return self.add_track_async( trans, output_datasets[0].id ) - def _rerun_tool( self, trans, payload, **kwargs ): """ Rerun a tool to produce a new output dataset that corresponds to a @@ -318,7 +276,7 @@ else: # Recursive search. return_val = False - for name, value in param_dict.items(): + for value in param_dict.values(): if isinstance( value, dict ): return_val = set_value( value, group_name, group_index, param_name, param_value) if return_val: diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -284,7 +284,7 @@ # ==================== # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + webapp.add_route( '/admin_toolshed/static/images/:repository_id/{image_file:.+?}', controller='admin_toolshed', action='display_image_in_repository', repository_id=None, diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -16,6 +16,7 @@ from tool_shed.util import data_manager_util from tool_shed.util import datatype_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import readme_util from tool_shed.util import repository_dependency_util @@ -941,7 +942,7 @@ message += 'attribute value which is a directory relative to the Galaxy installation directory in order ' message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> ' message += 'whose <b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' - message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation ' + message += '<a href="https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy" target="_blank">Installation ' message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool ' message += 'Shed wiki for all of the details.' return trans.show_error_message( message ) @@ -1851,7 +1852,7 @@ repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, name ) ) else: repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) ) - repo = hg.repository( suc.get_configured_ui(), path=repo_files_dir ) + repo = hg.repository( hg_util.get_configured_ui(), path=repo_files_dir ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) repository_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) suc.update_repository( repo, latest_ctx_rev ) diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -39,7 +39,7 @@ self.message_box_visible = kwargs.get( 'message_box_visible', False ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) - self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) + self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -13,6 +13,7 @@ import tool_shed.util.shed_util_common as suc from tool_shed.galaxy_install import repository_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util @@ -49,7 +50,7 @@ log.debug( error_message ) return [] repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) return ordered_installable_revisions else: @@ -133,7 +134,7 @@ # The changeset_revision column in the repository_metadata table has been updated with a new # value value, so find the changeset_revision to which we need to update. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, @@ -276,7 +277,7 @@ @web.expose_api def repository_ids_for_setting_metadata( self, trans, my_writable=False, **kwd ): """ - GET /api/get_repository_ids_for_setting_metadata + GET /api/repository_ids_for_setting_metadata Displays a collection (list) of repository ids ordered for setting metadata. diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -6,6 +6,7 @@ from galaxy.model.orm import and_, not_, select from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest from tool_shed.util import export_util +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc from galaxy import eggs @@ -26,7 +27,7 @@ Creates and saves a gzip compressed tar archive of a repository and optionally all of it's repository dependencies. The following parameters are included in the payload. - :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed + :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository is to be exported :param name (required): the name of the Repository :param owner (required): the owner of the Repository :param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository @@ -168,7 +169,7 @@ # The changeset_revision column in the repository_metadata table has been updated with a new # value value, so find the changeset_revision to which we need to update. repo_dir = repository_dependency.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository_dependency, repo, changeset_revision ) diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -96,8 +96,8 @@ self.message_box_visible = kwargs.get( 'message_box_visible', False ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) - self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) - self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) + self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' ) + self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.biostar_url = kwargs.get( 'biostar_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -19,6 +19,7 @@ from tool_shed.util import container_util from tool_shed.util import encoding_util from tool_shed.util import export_util +from tool_shed.util import hg_util from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import readme_util @@ -719,7 +720,7 @@ status = kwd.get( 'status', 'done' ) commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) # Update repository files for browsing. suc.update_repository( repo ) changeset_revision = repository.tip( trans.app ) @@ -891,9 +892,9 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Default to the current changeset revision. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) latest_changeset_revision = changeset_revision from_update_manager = kwd.get( 'from_update_manager', False ) if from_update_manager: @@ -937,10 +938,10 @@ update_to_changeset_hash = None for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) - ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: if changeset_hash == repository.tip( trans.app ): - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash break else: @@ -949,7 +950,7 @@ changeset_hash ) if repository_metadata: # We found a RepositoryMetadata record. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash break else: @@ -1213,7 +1214,7 @@ else: containers_dict = None export_repository_dependencies_check_box = None - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) return trans.fill_template( "/webapps/tool_shed/repository/export_repository.mako", changeset_revision=changeset_revision, containers_dict=containers_dict, @@ -1466,9 +1467,9 @@ has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] includes_workflows = has_galaxy_utilities_dict[ 'includes_workflows' ] repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Default to the received changeset revision and ctx_rev. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) ctx_rev = str( update_to_ctx.rev() ) latest_changeset_revision = changeset_revision update_dict = dict( changeset_revision=changeset_revision, @@ -1497,7 +1498,7 @@ has_repository_dependencies = False has_repository_dependencies_only_if_compiling_contained_td = False changeset_hash = str( repo.changectx( changeset ) ) - ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: update_to_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), @@ -1515,10 +1516,10 @@ # We found a RepositoryMetadata record. if changeset_hash == repository.tip( trans.app ): # The current ctx is the repository tip, so use it. - update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash else: - update_to_ctx = suc.get_changectx_for_changeset( repo, update_to_changeset_hash ) + update_to_ctx = hg_util.get_changectx_for_changeset( repo, update_to_changeset_hash ) latest_changeset_revision = update_to_changeset_hash break elif not update_to_changeset_hash and changeset_hash == changeset_revision: @@ -1544,8 +1545,8 @@ changeset_revision = kwd[ 'changeset_revision' ] repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) if ctx: return str( ctx.rev() ) return '' @@ -1560,8 +1561,8 @@ def get_file_from_changeset_revision( self, repo_files_dir, changeset_revision, file_name, dir ): """Return file_name from the received changeset_revision of the repository manifest.""" stripped_file_name = suc.strip_path( file_name ) - repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) named_tmp_file = suc.get_named_tmpfile_from_ctx( ctx, file_name, dir ) return named_tmp_file @@ -1604,7 +1605,7 @@ trans.model.Repository.table.c.user_id == user.id ) ): repository = repository_metadata.repository repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) latest_downloadable_changeset_revsion = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) if repository_metadata.changeset_revision == latest_downloadable_changeset_revsion: # We'll display only the test run for the latest installable revision in the rss feed. @@ -1672,7 +1673,7 @@ if repository_name is not None and repository_owner is not None: repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) if repository: - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) return suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) return suc.INITIAL_CHANGELOG_HASH @@ -1855,7 +1856,7 @@ changeset_revision = kwd[ 'changeset_revision' ] repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) tool_version_dicts = [] for changeset in repo.changelog: current_changeset_revision = str( repo.changectx( changeset ) ) @@ -1880,7 +1881,7 @@ repository_id = trans.security.encode_id( repository.id ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if not repository_metadata: # The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository @@ -1889,7 +1890,7 @@ repo, after_changeset_revision=changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = repository_util.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=changeset_revision, @@ -2165,7 +2166,7 @@ repository = suc.get_repository_in_tool_shed( trans, id ) repository_type = kwd.get( 'repository_type', str( repository.type ) ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repo_name = kwd.get( 'repo_name', repository.name ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) description = kwd.get( 'description', repository.description ) @@ -2317,7 +2318,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - revision_label = suc.get_revision_label( trans, repository, repository.tip( trans.app ), include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, repository.tip( trans.app ), include_date=False ) repository_metadata = None metadata = None is_malicious = False @@ -2326,7 +2327,7 @@ if changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious else: @@ -2337,7 +2338,7 @@ if previous_changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, previous_changeset_revision ) if repository_metadata: - revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, previous_changeset_revision, include_date=False ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious changeset_revision = previous_changeset_revision @@ -2443,7 +2444,7 @@ # There is no repository_metadata defined for the changeset_revision, so see if it was defined # in a previous changeset in the changelog. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) previous_changeset_revision = \ suc.get_previous_metadata_changeset_revision( repository, repo, @@ -2520,7 +2521,7 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Get the next installable changeset_revision beyond the received changeset_revision. changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) if changeset_revision: @@ -2540,7 +2541,7 @@ status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: @@ -2570,17 +2571,14 @@ invalid = True break if invalid: - message += 'The repository dependency definitions for this repository are invalid and will be ignored. ' - message += 'The complete dependency hierarchy could not be determined. The cause of repository dependency ' - message += 'definition errors like this can usually be seen when viewing the repository directly from the ' - message += 'Tool Shed. The exact cause cannot be determined when visiting the Tool Shed from Galaxy to ' - message += 'install the repository.' + message = repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata, + error_from_tuple=False ) status = 'error' else: repository_metadata_id = None metadata = None repository_dependencies = None - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, @@ -2610,7 +2608,7 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) # Get the lower bound changeset revision. lower_bound_changeset_revision = suc.get_previous_metadata_changeset_revision( repository, repo, changeset_revision, downloadable=True ) # Build the list of changeset revision hashes. @@ -2636,7 +2634,7 @@ status='error' ) ) repository = suc.get_repository_in_tool_shed( trans, id ) changeset_revision = repository.tip( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) if repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -2654,7 +2652,7 @@ changeset_revision, metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, @@ -2705,7 +2703,7 @@ commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) selected_files_to_delete = kwd.get( 'selected_files_to_delete', '' ) if kwd.get( 'select_files_to_delete_button', False ): if selected_files_to_delete: @@ -2745,7 +2743,7 @@ # Update the repository files for browsing. suc.update_repository( repo ) # Get the new repository tip. - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) if tip == repository.tip( trans.app ): message += 'No changes to repository. ' kwd[ 'message' ] = message @@ -2934,7 +2932,7 @@ if not repository_metadata: # Get updates to the received changeset_revision if any exist. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) upper_bound_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) if upper_bound_changeset_revision: changeset_revision = upper_bound_changeset_revision @@ -2974,7 +2972,7 @@ trans.security.encode_id( repository.id ), changeset_revision ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) tool_shed_status_dict = {} # Handle repository deprecation. tool_shed_status_dict[ 'repository_deprecated' ] = str( repository.deprecated ) @@ -3066,7 +3064,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) changesets = [] for changeset in repo.changelog: ctx = repo.changectx( changeset ) @@ -3077,7 +3075,7 @@ change_dict = { 'ctx' : ctx, 'rev' : str( ctx.rev() ), 'date' : date, - 'display_date' : suc.get_readable_ctx_date( ctx ), + 'display_date' : hg_util.get_readable_ctx_date( ctx ), 'description' : ctx.description(), 'files' : ctx.files(), 'user' : ctx.user(), @@ -3101,8 +3099,8 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, ctx_str ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = hg_util.get_changectx_for_changeset( repo, ctx_str ) if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' @@ -3132,7 +3130,7 @@ metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) # For rendering the prev button. if ctx_parent: - ctx_parent_date = suc.get_readable_ctx_date( ctx_parent ) + ctx_parent_date = hg_util.get_readable_ctx_date( ctx_parent ) ctx_parent_rev = ctx_parent.rev() if ctx_parent_rev < 0: prev = None @@ -3141,7 +3139,7 @@ else: prev = None if ctx_child: - ctx_child_date = suc.get_readable_ctx_date( ctx_child ) + ctx_child_date = hg_util.get_readable_ctx_date( ctx_child ) ctx_child_rev = ctx_child.rev() next = "<b>%s:%s</b><i>(%s)</i>" % ( ctx_child_rev, ctx_child, ctx_child_date ) else: @@ -3190,7 +3188,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) display_reviews = kwd.get( 'display_reviews', False ) @@ -3224,7 +3222,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata @@ -3280,13 +3278,13 @@ render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_files_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_files_dir ) tool_metadata_dict = {} tool_lineage = [] tool = None guid = None original_tool_data_path = trans.app.config.tool_data_path - revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=False ) + revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=False ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ) diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -7,6 +7,7 @@ from galaxy.webapps.tool_shed.util import ratings_util from tool_shed.util.container_util import STRSEP import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import review_util from galaxy.util.odict import odict import tool_shed.grids.repository_review_grids as repository_review_grids @@ -72,8 +73,8 @@ status = kwd.get( 'status', 'done' ) review = review_util.get_review( trans, kwd[ 'id' ] ) repository = review.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/browse_review.mako', repository=repository, changeset_revision_label=changeset_revision_label, @@ -232,7 +233,7 @@ for component in review_util.get_components( trans ): components_dict[ component.name ] = dict( component=component, component_review=None ) repository = review.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) for component_review in review.component_reviews: if component_review and component_review.component: component_name = component_review.component.name @@ -337,7 +338,7 @@ name='revision_approved', selected_value=selected_value, for_component=False ) - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/edit_review.mako', repository=repository, review=review, @@ -470,7 +471,7 @@ if repository_id: repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] reviews_dict = odict() @@ -478,7 +479,7 @@ ctx = repo.changectx( changeset ) changeset_revision = str( ctx ) if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes: - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) if changeset_revision in reviewed_revision_hashes: # Find the review for this changeset_revision repository_reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) @@ -517,9 +518,9 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako', repository=repository, @@ -582,9 +583,9 @@ status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] ) changeset_revision = kwd.get( 'changeset_revision', None ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) previous_reviews_dict = review_util.get_previous_repository_reviews( trans, repository, changeset_revision ) - rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako', repository=repository, changeset_revision=changeset_revision, diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -11,6 +11,7 @@ import tool_shed.repository_types.util as rt_util import tool_shed.util.shed_util_common as suc from tool_shed.util import commit_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import repository_dependency_util from tool_shed.util import tool_dependency_util @@ -39,7 +40,7 @@ repository_id = kwd.get( 'repository_id', '' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) ) remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) ) uploaded_file = None @@ -63,7 +64,7 @@ repo_url = 'http%s' % url[ len( 'hg' ): ] repo_url = repo_url.encode( 'ascii', 'replace' ) try: - commands.clone( suc.get_configured_ui(), repo_url, uploaded_directory ) + commands.clone( hg_util.get_configured_ui(), repo_url, uploaded_directory ) except Exception, e: message = 'Error uploading via mercurial clone: %s' % suc.to_html_string( str( e ) ) status = 'error' @@ -288,7 +289,8 @@ status = 'error' # Handle messaging for invalid repository dependencies. invalid_repository_dependencies_message = \ - repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict ) + repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict, + error_from_tuple=True ) if invalid_repository_dependencies_message: message += invalid_repository_dependencies_message status = 'error' @@ -322,7 +324,7 @@ def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 if upload_point is not None: @@ -386,7 +388,7 @@ def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): # Upload a tar archive of files. repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 ok, message = commit_util.check_archive( repository, tar ) diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -15,6 +15,7 @@ from tool_shed.util import data_manager_util from tool_shed.util import datatype_util from tool_shed.util import encoding_util +from tool_shed.util import hg_util from tool_shed.util import repository_dependency_util from tool_shed.util import metadata_util from tool_shed.util import tool_dependency_util @@ -186,7 +187,7 @@ def get_repo_info_dict( trans, repository_id, changeset_revision ): repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, @@ -225,7 +226,7 @@ has_repository_dependencies_only_if_compiling_contained_td = False includes_tool_dependencies = False includes_tools_for_display_in_tool_panel = False - ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=changeset_revision, @@ -574,7 +575,7 @@ current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) if current_ctx_rev != ctx_rev: - repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) + repo = hg.repository( hg_util.get_configured_ui(), path=os.path.abspath( install_dir ) ) pull_repository( repo, repository_clone_url, current_changeset_revision ) suc.update_repository( repo, ctx_rev=current_ctx_rev ) handle_repository_contents( trans, @@ -804,7 +805,7 @@ def pull_repository( repo, repository_clone_url, ctx_rev ): """Pull changes from a remote repository to a local one.""" - commands.pull( suc.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] ) + commands.pull( hg_util.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] ) def repair_tool_shed_repository( trans, repository, repo_info_dict ): diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -5,6 +5,7 @@ from galaxy.webapps.tool_shed import model from galaxy.model.orm import and_ import tool_shed.util.shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.grids.repository_grids import CategoryGrid from tool_shed.grids.repository_grids import RepositoryGrid @@ -425,9 +426,11 @@ def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - return suc.get_revision_label( trans, repository, repository_metadata.changeset_revision, include_date=True ) + return hg_util.get_revision_label( trans, + repository, + repository_metadata.changeset_revision, + include_date=True, + include_hash=True ) class ToolsColumn( grids.TextColumn ): diff -r c8866f186e4d33a76aa7c4c6cbc975cd0c4e654a -r 18ac7049d256b9fbe24e6b6c0eb1fef79b941549 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -6,6 +6,7 @@ from galaxy.model.orm import or_ from galaxy.util import json from galaxy.util import listify +from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc import tool_shed.grids.util as grids_util import tool_shed.repository_types.util as rt_util @@ -116,7 +117,7 @@ def get_value( self, trans, grid, repository ): """Display the current repository heads.""" repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) heads = suc.get_repository_heads( repo ) multiple_heads = len( heads ) > 1 if multiple_heads: @@ -124,7 +125,7 @@ else: heads_str = '' for ctx in heads: - heads_str += '%s<br/>' % suc.get_revision_label_from_ctx( ctx, include_date=True ) + heads_str += '%s<br/>' % hg_util.get_revision_label_from_ctx( ctx, include_date=True ) heads_str.rstrip( '<br/>' ) if multiple_heads: heads_str += '</font>' @@ -1338,7 +1339,7 @@ def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository changeset_revision = repository_metadata.changeset_revision - changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision, include_date=True ) + changeset_revision_label = hg_util.get_revision_label( trans, repository, changeset_revision, include_date=True ) return changeset_revision_label @@ -1482,7 +1483,7 @@ changeset_revision ) if not required_repository_metadata: repo_dir = required_repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) updated_changeset_revision = suc.get_next_downloadable_changeset_revision( required_repository, repo, changeset_revision ) required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, required_repository_id, @@ -2029,7 +2030,7 @@ tool_dependency_definition. """ encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) repository_metadata = None try: @@ -2077,7 +2078,7 @@ tool_dependency_definition. """ encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) try: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, tip_ctx ) This diff is so big that we needed to truncate the remainder. 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: carlfeberhard: QA: allow grunt watch on qunit tests, add stubs for metrics-logger and hda-base
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/144c0473003e/ Changeset: 144c0473003e User: carlfeberhard Date: 2014-04-11 19:34:06 Summary: QA: allow grunt watch on qunit tests, add stubs for metrics-logger and hda-base Affected #: 9 files diff -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 -r 144c0473003e87d747087b2f04814a7fb6282264 static/scripts/utils/metrics-logger.js --- a/static/scripts/utils/metrics-logger.js +++ b/static/scripts/utils/metrics-logger.js @@ -125,9 +125,11 @@ MetricsLogger.prototype._parseLevel = function _parseLevel( level ){ var type = typeof level; if( type === 'number' ){ return level; } - var upper = level.toUpperCase(); - if( type === 'string' && MetricsLogger.hasOwnProperty( upper ) ){ - return MetricsLogger[ upper ]; + if( type === 'string' ){ + var upper = level.toUpperCase(); + if( MetricsLogger.hasOwnProperty( upper ) ){ + return MetricsLogger[ upper ]; + } } throw new Error( 'Unknown log level: ' + level ); }; @@ -381,6 +383,7 @@ //============================================================================= return { - MetricsLogger : MetricsLogger + MetricsLogger : MetricsLogger, + LoggingCache : LoggingCache }; }); diff -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 -r 144c0473003e87d747087b2f04814a7fb6282264 test/qunit/Gruntfile.js --- a/test/qunit/Gruntfile.js +++ b/test/qunit/Gruntfile.js @@ -1,17 +1,33 @@ -module.exports = function(grunt) { - grunt.initConfig({ - pkg: grunt.file.readJSON('package.json'), - - qunit: { - all: ['tests/**/*.html'], - options: { - } - }, +module.exports = function( grunt ){ + grunt.initConfig({ + pkg: grunt.file.readJSON( 'package.json' ), - }); + qunit: { + all: [ 'tests/**/*.html' ], + options: { + } + }, - grunt.loadNpmTasks('grunt-contrib-qunit'); - // register one or more task lists (you should ALWAYS have a "default" task list) - grunt.registerTask('default', ['qunit']); + watch: { + // watch for changes in the src dir + files: [ 'tests/**.js', '../../static/scripts/**/**.js' ], + tasks: [ 'default' ] + } + }); + + // use 'grunt --test=my-tests.html' or 'grunt watch --test=my-tests.html' + // to only run the tests in tests/my-tests.html + if( grunt.option( 'test' ) ){ + grunt.config.set( 'qunit.all', 'tests/' + grunt.option( 'test' ) ); + grunt.log.writeln( '(only testing ' + grunt.config.get( 'qunit.all' ) + ')' ); + } + + grunt.loadNpmTasks( 'grunt-contrib-qunit' ); + + // use 'grunt watch' to have the qunit tests run when scripts or tests are changed + grunt.loadNpmTasks( 'grunt-contrib-watch' ); + + // register one or more task lists (you should ALWAYS have a "default" task list) + grunt.registerTask( 'default', [ 'qunit' ] ); }; diff -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 -r 144c0473003e87d747087b2f04814a7fb6282264 test/qunit/README.txt --- a/test/qunit/README.txt +++ b/test/qunit/README.txt @@ -6,6 +6,19 @@ % npm install % grunt +To watch for changes to scripts and tests and automatically re-run tests: + + % grunt watch + +You can limit the tests run to a single file using the test option (note: +that 'tests/' is prepended to the path): + + % grunt --test=metrics-logger.html + (only testing tests/metrics-logger.html) + + % grunt watch --test=metrics-logger.html + (only testing tests/metrics-logger.html) + From Web Browser (no additional dependencies): Just open test HTML file in Web Browser. diff -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 -r 144c0473003e87d747087b2f04814a7fb6282264 test/qunit/package.json --- a/test/qunit/package.json +++ b/test/qunit/package.json @@ -2,6 +2,7 @@ "name": "galaxy-qunit-tests", "devDependencies": { "grunt": "^0.4.4", - "grunt-contrib-qunit": "^0.4.0" + "grunt-contrib-qunit": "^0.4.0", + "grunt-contrib-watch": "~0.5.3" } } diff -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 -r 144c0473003e87d747087b2f04814a7fb6282264 test/qunit/test-common.js --- a/test/qunit/test-common.js +++ b/test/qunit/test-common.js @@ -13,7 +13,7 @@ // Custom paths for qunit testing dependencies... "QUnit": qunit_absolute_directory + "test-libs/qunit-1.14.0", // .. because baseUrl is scripts to match Galaxy. "sinon": qunit_absolute_directory + "test-libs/sinon-1.9.1", - "sinon-qunit": qunit_absolute_directory + "test-libs/sinon-qunit-1.0.0", + "sinon-qunit": qunit_absolute_directory + "test-libs/sinon-qunit-1.0.0" }, shim: { // Ensure correct Qunit order in light of requirejs loading... @@ -32,12 +32,12 @@ deps: [ 'sinon', "QUnit" ], exports: "sinon" // Odd but seems to work }, - "underscore": { - exports: "_" + "underscore": { + exports: "_" }, "backbone": { deps: [ 'underscore', 'jquery' ], - exports: "Backbone" + exports: "Backbone" } } } ); @@ -48,10 +48,10 @@ root: '/' }; - require( [ "jquery", "QUnit" ], function( $, QUnit ) { // Bootstrap HTML for displaying Qunit results. - $('head').append( $('<link rel="stylesheet" type="text/css" />').attr( "href", qunit_absolute_directory + "test-libs/qunit-1.14.0.css") ); + $('head').append( $('<link rel="stylesheet" type="text/css" />') + .attr( "href", qunit_absolute_directory + "test-libs/qunit-1.14.0.css") ); $('body').append( $('<div id="qunit">') ); $('body').append( $('<div id="qunit-fixture">') ); @@ -60,7 +60,6 @@ // underscore + backbone loaded here because they are assumed globals by // much of the Galaxy client code. require( [ "underscore", "backbone" ], function( _, Backbone ) { - require( [ test_module_path ], function( ) { QUnit.load(); QUnit.start(); diff -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 -r 144c0473003e87d747087b2f04814a7fb6282264 test/qunit/tests/hda-base.html --- /dev/null +++ b/test/qunit/tests/hda-base.html @@ -0,0 +1,10 @@ +<!doctype html> + +<html> + <head> + <script data-main="../test-common" src="../scripts/libs/require.js"></script> + </head> + <body> + </body> +</html> diff -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 -r 144c0473003e87d747087b2f04814a7fb6282264 test/qunit/tests/hda-base.js --- /dev/null +++ b/test/qunit/tests/hda-base.js @@ -0,0 +1,35 @@ +// This file isn't really testing anything useful yet, it is just testing +// (or demonstrating) qunit+backbone interactions. +define([ + "mvc/dataset/hda-model", + "mvc/dataset/hda-base", + "jquery", + "sinon-qunit", + "utils/localization" +], function( + hdaModel, + hdaBase, + $, + sinon +){ + /*globals equal test module expect deepEqual strictEqual */ + "use strict"; + + module( "HDA base backbone view tests" ); + + test( "Base HDA view default construction, initialize", function() { + var hda = new hdaModel.HistoryDatasetAssociation({ + id : '123' + }), + view = new hdaBase.HDABaseView({ model: hda }); + + strictEqual( view.model, hda ); + + equal( view.linkTarget, '_blank' ); + equal( view.selectable, false ); + equal( view.selected, false ); + equal( view.expanded, false ); + equal( view.draggable, false ); + equal( view.id(), 'hda-123' ); + }); +}); diff -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 -r 144c0473003e87d747087b2f04814a7fb6282264 test/qunit/tests/metrics-logger.html --- /dev/null +++ b/test/qunit/tests/metrics-logger.html @@ -0,0 +1,10 @@ +<!doctype html> + +<html> + <head> + <script data-main="../test-common" src="../scripts/libs/require.js"></script> + </head> + <body> + </body> +</html> diff -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 -r 144c0473003e87d747087b2f04814a7fb6282264 test/qunit/tests/metrics-logger.js --- /dev/null +++ b/test/qunit/tests/metrics-logger.js @@ -0,0 +1,56 @@ +// This file isn't really testing anything useful yet, it is just testing +// (or demonstrating) qunit+backbone interactions. +define([ + "utils/metrics-logger", + "jquery", + "sinon-qunit" +], function( + metrics, + $, + sinon +){ + /*globals equal test module expect deepEqual strictEqual throws */ + "use strict"; + + module( "Metrics logger tests" ); + + test( "logger construction/initializiation defaults", function() { + var logger = new metrics.MetricsLogger({}); + equal( logger.consoleLogger, null ); + equal( logger.options.logLevel, metrics.MetricsLogger.INFO ); + equal( logger.options.consoleLevel, metrics.MetricsLogger.NONE ); + equal( logger.options.defaultNamespace, 'Galaxy' ); + equal( logger.options.clientPrefix, 'client.' ); + equal( logger.options.postSize, 1000 ); + equal( logger.options.maxCacheSize, 3000 ); + equal( logger.options.addTime, true ); + + equal( logger._postSize, 1000 ); + equal( logger.cache.constructor, metrics.LoggingCache ); + }); + + test( "_parseLevel", function() { + var logger = new metrics.MetricsLogger({}); + equal( logger._parseLevel( 'all' ), metrics.MetricsLogger.ALL ); + equal( logger._parseLevel( 'debug' ), metrics.MetricsLogger.DEBUG ); + equal( logger._parseLevel( 'info' ), metrics.MetricsLogger.INFO ); + equal( logger._parseLevel( 'warn' ), metrics.MetricsLogger.WARN ); + equal( logger._parseLevel( 'error' ), metrics.MetricsLogger.ERROR ); + equal( logger._parseLevel( 'metric' ), metrics.MetricsLogger.METRIC ); + equal( logger._parseLevel( 'none' ), metrics.MetricsLogger.NONE ); + equal( logger._parseLevel( 15 ), 15 ); + + throws( function(){ + logger._parseLevel( undefined ); + }, /Unknown log level/, 'Unknown log level throws error' ); + throws( function(){ + logger._parseLevel( 'nope' ); + }, /Unknown log level/, 'Unknown log level throws error' ); + }); + + test( "cache construction/initializiation defaults", function() { + var cache = new metrics.LoggingCache(); + equal( cache.maxSize, 5000 ); + equal( $.type( cache._cache ), 'array' ); + }); +}); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Merged in jlhg/galaxy-central (pull request #365)
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b7e3e7d7a62a/ Changeset: b7e3e7d7a62a User: dannon Date: 2014-04-11 17:33:20 Summary: Merged in jlhg/galaxy-central (pull request #365) Update the job exit codes Affected #: 1 file diff -r 5a6b80f9a287c05a4138f5252a7c92d7f6f09f23 -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -72,9 +72,9 @@ 'Variable_List' : '-v', } -# From pbs' job.h +# From pbs' pbs_job.h JOB_EXIT_STATUS = { - 0: "job exec successful", + 0: "job exec successful", -1: "job exec failed, before files, no retry", -2: "job exec failed, after files, no retry", -3: "job execution failed, do retry", @@ -83,7 +83,10 @@ -6: "job aborted on MOM init, chkpt, ok migrate", -7: "job restart failed", -8: "exec() of user command failed", - -11: "job maximum walltime exceeded", # Added by John, not from job.h. + -9: "could not create/open stdout stderr files", + -10: "job exceeded a memory limit", + -11: "job exceeded a walltime limit", + -12: "job exceeded a cpu time limit", } 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 11 Apr '14

11 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8105df30de51/ Changeset: 8105df30de51 User: Jian-Long Huang Date: 2014-04-11 15:41:39 Summary: Update the job exit codes Affected #: 1 file diff -r 5d666f5fae293488bc4f934125778f67627bc1e5 -r 8105df30de51754b5ce2ca3713b3425baf22c8fe lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -72,9 +72,9 @@ 'Variable_List' : '-v', } -# From pbs' job.h +# From pbs' pbs_job.h JOB_EXIT_STATUS = { - 0: "job exec successful", + 0: "job exec successful", -1: "job exec failed, before files, no retry", -2: "job exec failed, after files, no retry", -3: "job execution failed, do retry", @@ -83,7 +83,10 @@ -6: "job aborted on MOM init, chkpt, ok migrate", -7: "job restart failed", -8: "exec() of user command failed", - -11: "job maximum walltime exceeded", # Added by John, not from job.h. + -9: "could not create/open stdout stderr files", + -10: "job exceeded a memory limit", + -11: "job exceeded a walltime limit", + -12: "job exceeded a cpu time limit", } https://bitbucket.org/galaxy/galaxy-central/commits/b7e3e7d7a62a/ Changeset: b7e3e7d7a62a User: dannon Date: 2014-04-11 17:33:20 Summary: Merged in jlhg/galaxy-central (pull request #365) Update the job exit codes Affected #: 1 file diff -r 5a6b80f9a287c05a4138f5252a7c92d7f6f09f23 -r b7e3e7d7a62a724a3ffb0f04a05ceb0459630004 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -72,9 +72,9 @@ 'Variable_List' : '-v', } -# From pbs' job.h +# From pbs' pbs_job.h JOB_EXIT_STATUS = { - 0: "job exec successful", + 0: "job exec successful", -1: "job exec failed, before files, no retry", -2: "job exec failed, after files, no retry", -3: "job execution failed, do retry", @@ -83,7 +83,10 @@ -6: "job aborted on MOM init, chkpt, ok migrate", -7: "job restart failed", -8: "exec() of user command failed", - -11: "job maximum walltime exceeded", # Added by John, not from job.h. + -9: "could not create/open stdout stderr files", + -10: "job exceeded a memory limit", + -11: "job exceeded a walltime limit", + -12: "job exceeded a cpu time limit", } 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: carlfeberhard: QA: update anon API tests due to d46493c
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5a6b80f9a287/ Changeset: 5a6b80f9a287 User: carlfeberhard Date: 2014-04-11 16:20:09 Summary: QA: update anon API tests due to d46493c Affected #: 1 file diff -r ac7fc8911184064056255224711031153f9421db -r 5a6b80f9a287c05a4138f5252a7c92d7f6f09f23 test/casperjs/api-anon-history-permission-tests.js --- a/test/casperjs/api-anon-history-permission-tests.js +++ b/test/casperjs/api-anon-history-permission-tests.js @@ -82,13 +82,11 @@ 'hda show worked' ); this.test.comment( 'Attempting to copy an accessible hda (default is accessible)' - + ' fails from accessible history (currently login is required): ' + history.name ); - this.api.assertRaises( function(){ - this.api.hdas.create( this.api.histories.show( 'current' ).id, { - source : 'hda', - content : hdas[0].id - }); - }, 403, 'API authentication required for this request', 'update authentication required' ); + + ' should work from accessible history: ' + history.name ); + this.api.hdas.create( this.api.histories.show( 'current' ).id, { + source : 'hda', + content : hdas[0].id + }); } function testAnonReadFunctionsOnInaccessible( history, hdas ){ @@ -121,7 +119,7 @@ content : hdas[0].id }); this.debug( this.jsonStr( returned ) ); - }, 403, 'API authentication required for this request', 'hda copy from failed with error' ); + }, 403, 'History is not accessible to the current user', 'hda copy from failed with error' ); } @@ -158,7 +156,7 @@ // should error before it checks the id content : 'bler' }); - }, 403, 'API authentication required for this request', 'hda copy to failed' ); + }, 403, 'Must be logged in to manage Galaxy histories', 'hda copy to failed' ); } function testAnonInaccessible( history, hdas ){ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Close branch remove-stale-ignored
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/65bbbb2d227e/ Changeset: 65bbbb2d227e Branch: remove-stale-ignored User: dannon Date: 2014-04-11 15:04:46 Summary: Close branch remove-stale-ignored Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Merged in trevorw/galaxy-central-t/remove-stale-ignored (pull request #364)
by commits-noreply＠bitbucket.org 11 Apr '14

11 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ac7fc8911184/ Changeset: ac7fc8911184 User: dannon Date: 2014-04-11 15:04:46 Summary: Merged in trevorw/galaxy-central-t/remove-stale-ignored (pull request #364) remove misc files that slipped past hgignore Affected #: 2 files diff -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 -r ac7fc8911184064056255224711031153f9421db doc/source/lib/galaxy.webapps.galaxy.api.rst~ --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst~ +++ /dev/null @@ -1,179 +0,0 @@ -api Package -=========== - -:mod:`datasets` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.api.datasets - :members: - :undoc-members: - :show-inheritance: - -:mod:`folder_contents` Module ------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.folder_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`folders` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.folders - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`genomes` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.genomes - :members: - :undoc-members: - :show-inheritance: - -:mod:`group_roles` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`group_users` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_users - :members: - :undoc-members: - :show-inheritance: - -:mod:`groups` Module --------------------- - -.. automodule:: galaxy.webapps.galaxy.api.groups - :members: - :undoc-members: - :show-inheritance: - -:mod:`histories` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.histories - :members: - :undoc-members: - :show-inheritance: - -:mod:`history_contents` Module ------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.history_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`libraries` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.libraries - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_contents` Module ------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.library_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`permissions` Module -------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.permissions - :members: - :undoc-members: - :show-inheritance: - -:mod:`quotas` Module --------------------- - -.. automodule:: galaxy.webapps.galaxy.api.quotas - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_types` Module ---------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.request_types - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.api.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`roles` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`samples` Module ---------------------- - -.. automodule:: galaxy.webapps.galaxy.api.samples - :members: - :undoc-members: - :show-inheritance: - -:mod:`tools` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tools - :members: - :undoc-members: - :show-inheritance: - -:mod:`users` Module -------------------- - -.. automodule:: galaxy.webapps.galaxy.api.users - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualizations` Module ----------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.visualizations - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflows` Module ------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.workflows - :members: - :undoc-members: - :show-inheritance: - diff -r 2c6c7971d666166eb41ea4bd5838f31f3caabd41 -r ac7fc8911184064056255224711031153f9421db static/jqtouch/.DS_Store Binary file static/jqtouch/.DS_Store has changed 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

← Newer
1
...
16
17
18
19
20
21
22
...
27
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

galaxy-commits April 2014