February 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: carlfeberhard: Fix to trackster/util.js exports; Fix to docstring in history_contents; Fix alert text in hda-model
by Bitbucket 12 Feb '13

12 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba8c49884f7d/ changeset: ba8c49884f7d user: carlfeberhard date: 2013-02-12 20:26:30 summary: Fix to trackster/util.js exports; Fix to docstring in history_contents; Fix alert text in hda-model affected #: 5 files diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 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 @@ -113,11 +113,6 @@ """ Returns a dictionary for an HDA that raised an exception when it's dictionary was being built. - { - 'id' : < the encoded dataset id >, - 'type' : < name of the dataset >, - 'url' : < api url to retrieve this datasets full data >, - } """ return { 'id' : hda_id, diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -191,7 +191,7 @@ // if not interruption by iframe reload //TODO: remove when iframes are removed if( !( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ) ){ - alert( _l( 'Error getting history updates from the server.' ) + '\n' + error ); + alert( _l( 'Error getting history updates from the server:' ) + '\n' + error ); history.log( 'stateUpdater error:', error, 'responseText:', xhr.responseText ); } }); diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server:")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 static/scripts/packed/viz/trackster/util.js --- a/static/scripts/packed/viz/trackster/util.js +++ b/static/scripts/packed/viz/trackster/util.js @@ -1,1 +1,1 @@ -define(function(){exports={};exports.ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});exports.get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};return exports}); \ No newline at end of file +define(function(){var b=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(c){return true}},go:function(){var f=$.Deferred(),e=this,h=e.get("ajax_settings"),g=e.get("success_fn"),d=e.get("interval"),c=function(){$.ajax(h).success(function(i){if(g(i)){f.resolve(i)}else{setTimeout(c,d)}})};c();return f}});var a=function(c){if(!c){c="#ffffff"}if(typeof(c)==="string"){c=[c]}for(var l=0;l<c.length;l++){c[l]=parseInt(c[l].slice(1),16)}var p=function(v,u,i){return((v*299)+(u*587)+(i*114))/1000};var g=function(x,w,y,u,i,v){return(Math.max(x,u)-Math.min(x,u))+(Math.max(w,i)-Math.min(w,i))+(Math.max(y,v)-Math.min(y,v))};var j,q,h,m,s,k,t,e,f,d,r,o=false,n=0;do{j=Math.round(Math.random()*16777215);q=(j&16711680)>>16;h=(j&65280)>>8;m=j&255;f=p(q,h,m);o=true;for(l=0;l<c.length;l++){s=c[l];k=(s&16711680)>>16;t=(s&65280)>>8;e=s&255;d=p(k,t,e);r=g(q,h,m,k,t,e);if((Math.abs(f-d)<40)||(r<200)){o=false;break}}n++}while(!o&&n<=10);return"#"+(16777216+j).toString(16).substr(1,6)};return{ServerStateDeferred:b,get_random_color:a}}); \ No newline at end of file diff -r d2e30720ba78cbee8b6a6a63daa91702778040bc -r ba8c49884f7daab5df8b62bd631157058c7ee910 static/scripts/viz/trackster/util.js --- a/static/scripts/viz/trackster/util.js +++ b/static/scripts/viz/trackster/util.js @@ -1,12 +1,10 @@ define(function(){ -exports = {}; - /** * Implementation of a server-state based deferred. Server is repeatedly polled, and when * condition is met, deferred is resolved. */ -exports.ServerStateDeferred = Backbone.Model.extend({ +var ServerStateDeferred = Backbone.Model.extend({ defaults: { ajax_settings: {}, interval: 1000, @@ -44,7 +42,7 @@ * or set of colors. * @param colors a color or list of colors in the format '#RRGGBB' */ -exports.get_random_color = function(colors) { +var get_random_color = function(colors) { // Default for colors is white. if (!colors) { colors = "#ffffff"; } @@ -110,6 +108,9 @@ return '#' + ( 0x1000000 + new_color ).toString(16).substr(1,6); }; -return exports; +return { + ServerStateDeferred : ServerStateDeferred, + get_random_color : get_random_color +}; -}) \ 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: jgoecks: Pack scripts.
by Bitbucket 12 Feb '13

12 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2e30720ba78/ changeset: d2e30720ba78 user: jgoecks date: 2013-02-12 18:01:37 summary: Pack scripts. affected #: 2 files diff -r a6fe104c109feea61995567336a1aaf515acf0d5 -r d2e30720ba78cbee8b6a6a63daa91702778040bc 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(["libs/backbone/backbone-relational"],function(){var b=Backbone.RelationalModel.extend({});var c=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){var f=new b();_.each(_.keys(this.attributes),function(g){if(g.indexOf("metadata_")===0){var h=g.split("metadata_")[1];f.set(h,this.attributes[g]);delete this.attributes[g]}},this);this.set("metadata",f)},get_metadata:function(f){return this.attributes.metadata.get(f)},urlRoot:galaxy_paths.get("datasets_url")});var a=c.extend({defaults:_.extend({},c.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(f){c.prototype.initialize.call(this);chunk_index=(this.attributes.first_data_chunk?1:0)},set_first_chunk:function(f){this.attributes.first_data_chunk=f;this.attributes.chunk_index=1},get_next_chunk:function(){if(this.attributes.at_eof){return null}var f=this,g=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:f.attributes.chunk_index++}).success(function(h){var i;if(h.ck_data!==""){i=h}else{f.attributes.at_eof=true;i=null}g.resolve(i)});return g}});var e=Backbone.Collection.extend({model:c});var d=Backbone.View.extend({initialize:function(f){},render:function(){this.$el.append($("<div/>").attr("id","loading_indicator"));var i=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(i);var f=this.model.get_metadata("column_names");if(f){i.append("<tr><th>"+f.join("</th><th>")+"</th></tr>")}var h=this.model.get("first_data_chunk");if(h){this._renderChunk(h)}var g=this;$(window).scroll(function(){if($(window).scrollTop()===$(document).height()-$(window).height()){$.when(g.model.get_next_chunk()).then(function(j){if(j){g._renderChunk(j)}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(h,f,i){var g=this.model.get_metadata("column_types");if(i!==undefined){return $("<td>").attr("colspan",i).addClass("stringalign").text(h)}else{if(g[f]==="str"||g==="list"){return $("<td>").addClass("stringalign").text(h)}else{return $("<td>").text(h)}}},_renderRow:function(f){var g=f.split("\t"),i=$("<tr>"),h=this.model.get_metadata("columns");if(g.length===h){_.each(g,function(k,j){i.append(this._renderCell(k,j))},this)}else{if(g.length>h){_.each(g.slice(0,h-1),function(k,j){i.append(this._renderCell(k,j))},this);i.append(this._renderCell(g.slice(h-1).join("\t"),h-1))}else{if(h>5&&g.length===h-1){_.each(g,function(k,j){i.append(this._renderCell(k,j))},this);i.append($("<td>"))}else{i.append(this._renderCell(f,0,h))}}}return i},_renderChunk:function(f){var g=this.$el.find("table");_.each(f.ck_data.split("\n"),function(h,i){g.append(this._renderRow(h))},this)}});return{Dataset:c,TabularDataset:a,DatasetCollection:e,TabularDatasetChunkedView:d}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var c=Backbone.RelationalModel.extend({});var d=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){var h=new c();_.each(_.keys(this.attributes),function(i){if(i.indexOf("metadata_")===0){var j=i.split("metadata_")[1];h.set(j,this.attributes[i]);delete this.attributes[i]}},this);this.set("metadata",h)},get_metadata:function(h){return this.attributes.metadata.get(h)},urlRoot:galaxy_paths.get("datasets_url")});var b=d.extend({defaults:_.extend({},d.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(h){d.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 h=this,i=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:h.attributes.chunk_index++}).success(function(j){var k;if(j.ck_data!==""){k=j}else{h.attributes.at_eof=true;k=null}i.resolve(k)});return i}});var f=Backbone.Collection.extend({model:d});var e=Backbone.View.extend({initialize:function(h){},render:function(){this.$el.append($("<div/>").attr("id","loading_indicator"));var l=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(l);var h=this.model.get_metadata("column_names");if(h){l.append("<tr><th>"+h.join("</th><th>")+"</th></tr>")}var j=this.model.get("first_data_chunk");if(j){this._renderChunk(j)}var i=this,m=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"}),k=false;if(!m){m=window}m=$(m);m.scroll(function(){if(!k&&(i.$el.height()-m.scrollTop()-m.height()<=0)){k=true;$.when(i.model.get_next_chunk()).then(function(n){if(n){i._renderChunk(n);k=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(j,h,k){var i=this.model.get_metadata("column_types");if(k!==undefined){return $("<td>").attr("colspan",k).addClass("stringalign").text(j)}else{if(i[h]==="str"||i==="list"){return $("<td>").addClass("stringalign").text(j)}else{return $("<td>").text(j)}}},_renderRow:function(h){var i=h.split("\t"),k=$("<tr>"),j=this.model.get_metadata("columns");if(i.length===j){_.each(i,function(m,l){k.append(this._renderCell(m,l))},this)}else{if(i.length>j){_.each(i.slice(0,j-1),function(m,l){k.append(this._renderCell(m,l))},this);k.append(this._renderCell(i.slice(j-1).join("\t"),j-1))}else{if(j>5&&i.length===j-1){_.each(i,function(m,l){k.append(this._renderCell(m,l))},this);k.append($("<td>"))}else{k.append(this._renderCell(h,0,j))}}}return k},_renderChunk:function(h){var i=this.$el.find("table");_.each(h.ck_data.split("\n"),function(j,k){i.append(this._renderRow(j))},this)}});var a=function(k,i,l,h){var j=new i({model:new k(l)});j.render();if(h){h.append(j.$el)}return j};var g=function(j,h){var i=$("<div/>").appendTo(h);return new e({el:i,model:new b(j)}).render()};return{Dataset:d,TabularDataset:b,DatasetCollection:f,TabularDatasetChunkedView:e,createTabularDatasetChunkedView:g}}); \ No newline at end of file diff -r a6fe104c109feea61995567336a1aaf515acf0d5 -r d2e30720ba78cbee8b6a6a63daa91702778040bc static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,errorJSON);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 12 Feb '13

12 Feb '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1f1072317efd/ changeset: 1f1072317efd branch: stable user: natefoo date: 2013-02-12 14:46:28 summary: Allow the CLI runner to handle command stdout >65K. affected #: 2 files diff -r 961ae35ba61230ac1f5991b7629e5da0559cd0b5 -r 1f1072317efd5cf82cb791d75ba968c4bacffaf4 lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -316,6 +316,7 @@ if which_try == self.app.config.retry_job_output_collection: stdout = '' stderr = 'Job output not returned from cluster' + exit_code = 0 log.debug( stderr ) else: time.sleep(1) diff -r 961ae35ba61230ac1f5991b7629e5da0559cd0b5 -r 1f1072317efd5cf82cb791d75ba968c4bacffaf4 lib/galaxy/jobs/runners/cli_shell/rsh.py --- a/lib/galaxy/jobs/runners/cli_shell/rsh.py +++ b/lib/galaxy/jobs/runners/cli_shell/rsh.py @@ -4,6 +4,7 @@ import time import logging +import tempfile import subprocess from galaxy.util.bunch import Bunch @@ -28,7 +29,9 @@ fullcmd = '%s %s %s' % (self.rsh, self.hostname, cmd) else: fullcmd = '%s -l %s %s %s' % (self.rsh, self.username, self.hostname, cmd) - p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + # Read stdout to a tempfile in case it's large (>65K) + outf = tempfile.TemporaryFile() + p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=outf, stderr=subprocess.PIPE) # poll until timeout for i in range(timeout/3): r = p.poll() @@ -44,7 +47,8 @@ except: log.warning('Killing pid %s (cmd: "%s") with signal %s failed' % (p.pid, fullcmd, sig)) return Bunch(stdout='', stderr='Execution timed out', returncode=-1) - return Bunch(stdout=p.stdout.read(), stderr=p.stderr.read(), returncode=p.returncode) + outf.seek(0) + return Bunch(stdout=outf.read(), stderr=p.stderr.read(), returncode=p.returncode) class SecureShell(RemoteShell): https://bitbucket.org/galaxy/galaxy-central/commits/056ff69b05c4/ changeset: 056ff69b05c4 user: natefoo date: 2013-02-12 14:46:28 summary: Allow the CLI runner to handle command stdout >65K. affected #: 2 files diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r 056ff69b05c435f26650c5e7f65cffd764a40a08 lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -316,6 +316,7 @@ if which_try == self.app.config.retry_job_output_collection: stdout = '' stderr = 'Job output not returned from cluster' + exit_code = 0 log.debug( stderr ) else: time.sleep(1) diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r 056ff69b05c435f26650c5e7f65cffd764a40a08 lib/galaxy/jobs/runners/cli_shell/rsh.py --- a/lib/galaxy/jobs/runners/cli_shell/rsh.py +++ b/lib/galaxy/jobs/runners/cli_shell/rsh.py @@ -4,6 +4,7 @@ import time import logging +import tempfile import subprocess from galaxy.util.bunch import Bunch @@ -28,7 +29,9 @@ fullcmd = '%s %s %s' % (self.rsh, self.hostname, cmd) else: fullcmd = '%s -l %s %s %s' % (self.rsh, self.username, self.hostname, cmd) - p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + # Read stdout to a tempfile in case it's large (>65K) + outf = tempfile.TemporaryFile() + p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=outf, stderr=subprocess.PIPE) # poll until timeout for i in range(timeout/3): r = p.poll() @@ -44,7 +47,8 @@ except: log.warning('Killing pid %s (cmd: "%s") with signal %s failed' % (p.pid, fullcmd, sig)) return Bunch(stdout='', stderr='Execution timed out', returncode=-1) - return Bunch(stdout=p.stdout.read(), stderr=p.stderr.read(), returncode=p.returncode) + outf.seek(0) + return Bunch(stdout=outf.read(), stderr=p.stderr.read(), returncode=p.returncode) class SecureShell(RemoteShell): https://bitbucket.org/galaxy/galaxy-central/commits/a6fe104c109f/ changeset: a6fe104c109f user: natefoo date: 2013-02-12 15:04:17 summary: Merged heads. affected #: 2 files diff -r 056ff69b05c435f26650c5e7f65cffd764a40a08 -r a6fe104c109feea61995567336a1aaf515acf0d5 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -22,7 +22,7 @@ parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) parser.add_option( '', '--read-mismatches', dest='read_mismatches' ) parser.add_option( '', '--bowtie-n', action="store_true", dest='bowtie_n' ) - parser.add_option( '', '--report-discordant-pair-alignments', action="store_true", dest='report_discordant_pairs' ) + parser.add_option( '', '--no-discordant', action="store_true", dest='report_concordant_pairs_only' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) @@ -141,8 +141,8 @@ opts = '-p %s %s' % ( options.num_threads, space ) if options.single_paired == 'paired': opts += ' -r %s' % options.mate_inner_dist - if options.report_discordant_pairs: - opts += ' --report-discordant-pair-alignments' + if options.report_concordant_pairs_only: + opts += ' --no-discordant' # Read group options. if options.rgid: if not options.rglb or not options.rgpl or not options.rgsm: diff -r 056ff69b05c435f26650c5e7f65cffd764a40a08 -r a6fe104c109feea61995567336a1aaf515acf0d5 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -37,8 +37,8 @@ -r $singlePaired.mate_inner_distance --mate-std-dev=$singlePaired.mate_std_dev - #if str($singlePaired.report_discordant_pairs) == "Yes": - --report-discordant-pair-alignments + #if str($singlePaired.report_discordant_pairs) == "No": + --no-discordant #end if #end if @@ -138,8 +138,8 @@ <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/><param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?"> - <option selected="true" value="No">No</option> - <option value="Yes">Yes</option> + <option value="No">No</option> + <option selected="True" value="Yes">Yes</option></param></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: joachimjacob: Fixed --no-discordant parameter in tophat2_wrapper.xml and .py.
by Bitbucket 12 Feb '13

12 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b1d3a6a907d1/ changeset: b1d3a6a907d1 user: joachimjacob date: 2013-02-12 09:55:44 summary: Fixed --no-discordant parameter in tophat2_wrapper.xml and .py. affected #: 2 files diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r b1d3a6a907d1ee4847fbcea61a162067b3be0f49 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -22,7 +22,7 @@ parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) parser.add_option( '', '--read-mismatches', dest='read_mismatches' ) parser.add_option( '', '--bowtie-n', action="store_true", dest='bowtie_n' ) - parser.add_option( '', '--report-discordant-pair-alignments', action="store_true", dest='report_discordant_pairs' ) + parser.add_option( '', '--no-discordant', action="store_true", dest='report_concordant_pairs_only' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) @@ -141,8 +141,8 @@ opts = '-p %s %s' % ( options.num_threads, space ) if options.single_paired == 'paired': opts += ' -r %s' % options.mate_inner_dist - if options.report_discordant_pairs: - opts += ' --report-discordant-pair-alignments' + if options.report_concordant_pairs_only: + opts += ' --no-discordant' # Read group options. if options.rgid: if not options.rglb or not options.rgpl or not options.rgsm: diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r b1d3a6a907d1ee4847fbcea61a162067b3be0f49 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -37,8 +37,8 @@ -r $singlePaired.mate_inner_distance --mate-std-dev=$singlePaired.mate_std_dev - #if str($singlePaired.report_discordant_pairs) == "Yes": - --report-discordant-pair-alignments + #if str($singlePaired.report_discordant_pairs) == "No": + --no-discordant #end if #end if @@ -138,8 +138,8 @@ <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/><param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?"> - <option selected="true" value="No">No</option> - <option value="Yes">Yes</option> + <option value="No">No</option> + <option selected="True" value="Yes">Yes</option></param></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Uncomment the previously added sentry_dsn.
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e5dcefc328bb/ changeset: e5dcefc328bb user: inithello date: 2013-02-12 05:17:13 summary: Uncomment the previously added sentry_dsn. affected #: 1 file diff -r 6be149267ed6016351819a0605213fb3d34b25ef -r e5dcefc328bb4fadcd0097787d167c7f43db5627 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -41,7 +41,7 @@ self.log_events = False self.cookie_path = kwargs.get( "cookie_path", "/" ) # Error logging with sentry - # self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) + self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) #Parse global_conf global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Add sentry_dsn to reports webapp configuration.
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6be149267ed6/ changeset: 6be149267ed6 user: inithello date: 2013-02-12 05:15:34 summary: Add sentry_dsn to reports webapp configuration. affected #: 1 file diff -r 42e0e5d9b7a479d884f9556a59aadea7886c131e -r 6be149267ed6016351819a0605213fb3d34b25ef lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -40,6 +40,8 @@ self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False self.cookie_path = kwargs.get( "cookie_path", "/" ) + # Error logging with sentry + # self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) #Parse global_conf global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Return a dict instead of a list if a [galaxy:tool_*] section is missing from the config.
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/42e0e5d9b7a4/ changeset: 42e0e5d9b7a4 user: natefoo date: 2013-02-11 22:50:16 summary: Return a dict instead of a list if a [galaxy:tool_*] section is missing from the config. affected #: 1 file diff -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 -r 42e0e5d9b7a479d884f9556a59aadea7886c131e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -304,7 +304,7 @@ return rval except ConfigParser.NoSectionError: - return [] + return {} def get( self, key, default ): return self.config_dict.get( key, default ) def get_bool( self, key, default ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Use tabular chunked data diplay for shared/published datasets.
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41f4c9c90959/ changeset: 41f4c9c90959 user: jgoecks date: 2013-02-11 21:56:50 summary: Use tabular chunked data diplay for shared/published datasets. affected #: 5 files diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -69,6 +69,9 @@ <class 'galaxy.datatypes.metadata.MetadataParameter'> """ + # Data is not chunkable by default. + CHUNKABLE = False + #: dictionary of metadata fields for this datatype:: metadata_spec = None diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -20,6 +20,9 @@ class Tabular( data.Text ): """Tab delimited data""" + + # All tabular data is chunkable. + CHUNKABLE = True CHUNK_SIZE = 50000 """Add metadata elements""" diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -642,6 +642,11 @@ truncated, dataset_data = self.get_data( dataset, preview ) dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset ) + # If dataset is chunkable, get first chunk. + first_chunk = None + if dataset.datatype.CHUNKABLE: + first_chunk = dataset.datatype.get_chunk(trans, dataset, 0) + # If data is binary or an image, stream without template; otherwise, use display template. # TODO: figure out a way to display images in display template. if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image) or isinstance(dataset.datatype, datatypes.images.Html): @@ -658,8 +663,10 @@ user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, dataset ) - return trans.fill_template_mako( "/dataset/display.mako", item=dataset, item_data=dataset_data, truncated=truncated, - user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) + return trans.fill_template_mako( "/dataset/display.mako", item=dataset, item_data=dataset_data, + truncated=truncated, user_item_rating = user_item_rating, + ave_item_rating=ave_item_rating, num_ratings=num_ratings, + first_chunk=first_chunk ) else: raise web.httpexceptions.HTTPNotFound() diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -102,7 +102,10 @@ }); /** - * Provides table-based, dynamic view of a tabular dataset. + * Provides table-based, dynamic view of a tabular dataset. + * NOTE: view's el must be in DOM already and provided when + * createing the view so that scrolling event can be attached + * to the correct container. */ var TabularDatasetChunkedView = Backbone.View.extend({ @@ -129,13 +132,31 @@ this._renderChunk(first_chunk); } - // Show new chunks during scrolling. - var self = this; - $(window).scroll(function() { - if ($(window).scrollTop() === $(document).height() - $(window).height()) { + // -- Show new chunks during scrolling. -- + + var self = this, + // Element that does the scrolling. + scroll_elt = _.find(this.$el.parents(), function(p) { + return $(p).css('overflow') === 'auto'; + }), + // Flag to ensure that only one chunk is loaded at a time. + loading_chunk = false; + + // If no scrolling element found, use window. + if (!scroll_elt) { scroll_elt = window; } + + // Wrap scrolling element for easy access. + scroll_elt = $(scroll_elt); + + // Set up chunk loading when scrolling using the scrolling element. + scroll_elt.scroll(function() { + // If not already loading a chunk and have scrolled to the bottom of this element, get next chunk. + if ( !loading_chunk && (self.$el.height() - scroll_elt.scrollTop() - scroll_elt.height() <= 0) ) { + loading_chunk = true; $.when(self.model.get_next_chunk()).then(function(result) { if (result) { self._renderChunk(result); + loading_chunk = false; } }); } @@ -218,7 +239,7 @@ if (parent_elt) { parent_elt.append(a_view.$el); } - + return a_view; }; @@ -227,7 +248,14 @@ * and appends to parent_elt. */ var createTabularDatasetChunkedView = function(dataset_config, parent_elt) { - return createModelAndView(TabularDataset, TabularDatasetChunkedView, dataset_config, parent_elt); + // Create view element and add to parent. + var view_div = $('<div/>').appendTo(parent_elt); + + // Create view with model, render, and return. + return new TabularDatasetChunkedView({ + el: view_div, + model: new TabularDataset(dataset_config) + }).render(); }; return { diff -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 -r 41f4c9c9095919b080dc0e32a5d540865fdf0fa7 templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -5,6 +5,35 @@ <%def name="javascripts()"> ${parent.javascripts()} + ## If data is chunkable, use JavaScript for display. + %if item.datatype.CHUNKABLE: + + <script type="text/javascript"> + require.config({ + baseUrl: "${h.url_for('/static/scripts')}", + shim: { + "libs/backbone/backbone": { exports: "Backbone" }, + "libs/backbone/backbone-relational": ["libs/backbone/backbone"] + } + }); + + require(['mvc/data'], function(data) { + data.createTabularDatasetChunkedView( + // Dataset config. TODO: encode id. + _.extend( ${h.to_json_string( item.get_api_value() )}, + { + chunk_url: "${h.url_for( controller='/dataset', action='display', + dataset_id=trans.security.encode_id( item.id ))}", + first_data_chunk: ${first_chunk} + } + ), + // Append view to body. + $('.page-body') + ); + }); + </script> + + %endif </%def><%def name="init()"> @@ -31,14 +60,17 @@ </%def><%def name="render_item( data, data_to_render )"> - %if truncated: - <div class="warningmessagelarge"> - This dataset is large and only the first megabyte is shown below. | - <a href="${h.url_for( controller='dataset', action='display_by_username_and_slug', username=data.history.user.username, slug=trans.security.encode_id( data.id ), preview=False )}">Show all</a> - </div> + ## Chunkable data is rendered in JavaScript above; render unchunkable data below. + %if not data.datatype.CHUNKABLE: + %if truncated: + <div class="warningmessagelarge"> + This dataset is large and only the first megabyte is shown below. | + <a href="${h.url_for( controller='dataset', action='display_by_username_and_slug', username=data.history.user.username, slug=trans.security.encode_id( data.id ), preview=False )}">Show all</a> + </div> + %endif + ## TODO: why is the default font size so small? + <pre style="font-size: 135%">${ data_to_render | h }</pre> %endif - ## TODO: why is the default font size so small? - <pre style="font-size: 135%">${ data_to_render | h }</pre></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Don't attempt to load tool destinations when loading tools unless the application has a job config (i.e. it's Galaxy, not the Tool Shed).
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/422f368eb097/ changeset: 422f368eb097 user: natefoo date: 2013-02-11 21:21:00 summary: Don't attempt to load tool destinations when loading tools unless the application has a job config (i.e. it's Galaxy, not the Tool Shed). affected #: 1 file diff -r fbf37e72e1f430d20ec1da7f14c8eeec146abce6 -r 422f368eb0978b7d8ed5a320f1700603aea22ca1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1022,7 +1022,9 @@ if self.old_id != self.id: # Handle toolshed guids self_ids = [ self.id.lower(), self.id.lower().rsplit('/',1)[0], self.old_id.lower() ] - self.job_tool_configurations = self.app.job_config.get_job_tool_configurations(self_ids) + # In the toolshed context, there is no job config. + if 'job_config' in dir(self.app): + self.job_tool_configurations = self.app.job_config.get_job_tool_configurations(self_ids) # Is this a 'hidden' tool (hidden in tool menu) self.hidden = util.xml_text(root, "hidden") if self.hidden: self.hidden = util.string_as_bool(self.hidden) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the new sharable link to a repository in the tool shed to the email alerts messages for new repositories and updates to existing repositories.
by Bitbucket 11 Feb '13

11 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fbf37e72e1f4/ changeset: fbf37e72e1f4 user: greg date: 2013-02-11 20:53:54 summary: Add the new sharable link to a repository in the tool shed to the email alerts messages for new repositories and updates to existing repositories. affected #: 1 file diff -r 4f562e319784d0a316157f8e8f6eea1202c7023e -r fbf37e72e1f430d20ec1da7f14c8eeec146abce6 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -43,6 +43,7 @@ VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) new_repo_email_alert_template = """ +Sharable link: ${sharable_link} Repository name: ${repository_name} Revision: ${revision} Change description: @@ -63,8 +64,9 @@ """ email_alert_template = """ +Sharable link: ${sharable_link} Repository name: ${repository_name} -Revision: ${revision} +Revision: ${revision} Change description: ${description} @@ -2364,6 +2366,7 @@ # that was included in the change set. repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) + sharable_link = generate_sharable_link_for_repository_in_tool_shed( trans, repository, changeset_revision=None ) smtp_server = trans.app.config.smtp_server if smtp_server and ( new_repo_alert or repository.email_alerts ): # Send email alert to users that want them. @@ -2389,6 +2392,7 @@ else: template = email_alert_template admin_body = string.Template( template ).safe_substitute( host=trans.request.host, + sharable_link=sharable_link, repository_name=repository.name, revision='%s:%s' %( str( ctx.rev() ), ctx ), display_date=display_date, @@ -2396,6 +2400,7 @@ username=username, content_alert_str=content_alert_str ) body = string.Template( template ).safe_substitute( host=trans.request.host, + sharable_link=sharable_link, repository_name=repository.name, revision='%s:%s' %( str( ctx.rev() ), ctx ), display_date=display_date, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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