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September 2014

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commit/galaxy-central: guerler: ToolForm: Add wait modal and error modal
by commits-noreply＠bitbucket.org 26 Sep '14

26 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/10bf4bbcc3fa/ Changeset: 10bf4bbcc3fa User: guerler Date: 2014-09-26 15:39:32+00:00 Summary: ToolForm: Add wait modal and error modal Affected #: 12 files diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -24,6 +24,13 @@ // link this var self = this; + // link galaxy modal or create one + if (parent.Galaxy && parent.Galaxy.modal) { + this.modal = parent.Galaxy.modal; + } else { + this.modal = new Ui.Modal.View(); + } + // link options this.options = options; diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -32,23 +32,41 @@ console.debug('tools-jobs::submit - Submission canceled. Validation failed.'); return; } - console.log(job_def); + + // debug + console.debug(job_def); + + // show progress modal + this.app.modal.show({title: 'Please wait...', body: 'progress'}); // post job Utils.request('POST', galaxy_config.root + 'api/tools', job_def, // success handler function(response) { + self.app.modal.hide(); self.app.message(ToolTemplate.success(response)); self._refreshHdas(); }, // error handler - function(response) { - console.debug(response); + function(response, response_full) { + self.app.modal.hide(); if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { self._foundError(input_id, error_messages[input_id]); } + } else { + // show modal with error message + self.app.modal.show({ + title: response_full.statusText, + body: ToolTemplate.error(job_def), + closing_events: true, + buttons: { + 'Close': function() { + self.app.modal.hide(); + } + } + }); } } ); diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -40,6 +40,17 @@ return tmpl; }, + error: function(job_def) { + return '<div>' + + '<p>' + + 'Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.' + + '</p>' + + '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + + JSON.stringify(job_def, undefined, 4) + + '</textarea>' + + '</div>'; + }, + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 client/galaxy/scripts/utils/utils.js --- a/client/galaxy/scripts/utils/utils.js +++ b/client/galaxy/scripts/utils/utils.js @@ -13,6 +13,12 @@ // generic function to send json to url function request (method, url, data, success, error) { + // configure + var ajaxConfig = { + url : url, + type : method, + 'contentType' : 'application/json' + } // encode data into url if (method == 'GET' || method == 'DELETE') { @@ -22,40 +28,25 @@ url += '&'; } url += $.param(data) + } else { + ajaxConfig['data'] = JSON.stringify(data); + ajaxConfig['dataType'] = 'json'; } - // prepare request - var xhr = new XMLHttpRequest(); - xhr.open(method, url, true); - xhr.setRequestHeader('Accept', 'application/json'); - xhr.setRequestHeader('Cache-Control', 'no-cache'); - xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest'); - xhr.setRequestHeader('Content-Type', 'application/json'); - xhr.onloadend = function() { - // get status - var status = xhr.status; - - // read response + // make request + $.ajax(ajaxConfig) + .done(function(response) { + success && success(response); + }) + .fail(function(response) { + var response_text = null; try { - response = jQuery.parseJSON(xhr.responseText); + response_text = jQuery.parseJSON(response.responseText); } catch (e) { - response = xhr.responseText; + response_text = response.responseText; } - - // parse response - if (status == 200) { - success && success(response); - } else { - error && error(response); - } - }; - - // make request - if (method == 'GET' || method == 'DELETE') { - xhr.send(); - } else { - xhr.send(JSON.stringify(data)); - } + error && error(response_text, response); + }); }; // get css value diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -24,6 +24,13 @@ // link this var self = this; + // link galaxy modal or create one + if (parent.Galaxy && parent.Galaxy.modal) { + this.modal = parent.Galaxy.modal; + } else { + this.modal = new Ui.Modal.View(); + } + // link options this.options = options; diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -32,23 +32,41 @@ console.debug('tools-jobs::submit - Submission canceled. Validation failed.'); return; } - console.log(job_def); + + // debug + console.debug(job_def); + + // show progress modal + this.app.modal.show({title: 'Please wait...', body: 'progress'}); // post job Utils.request('POST', galaxy_config.root + 'api/tools', job_def, // success handler function(response) { + self.app.modal.hide(); self.app.message(ToolTemplate.success(response)); self._refreshHdas(); }, // error handler - function(response) { - console.debug(response); + function(response, response_full) { + self.app.modal.hide(); if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { self._foundError(input_id, error_messages[input_id]); } + } else { + // show modal with error message + self.app.modal.show({ + title: response_full.statusText, + body: ToolTemplate.error(job_def), + closing_events: true, + buttons: { + 'Close': function() { + self.app.modal.hide(); + } + } + }); } } ); diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -40,6 +40,17 @@ return tmpl; }, + error: function(job_def) { + return '<div>' + + '<p>' + + 'Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.' + + '</p>' + + '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + + JSON.stringify(job_def, undefined, 4) + + '</textarea>' + + '</div>'; + }, + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(h,l,j,a,f,d,i,k,c,g){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(n){var m=this;this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:n.id});this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.datasets=new i({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")},_initializeToolForm:function(){var n=this;var o=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var p=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});this.model.fetch({error:function(q){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");n.portlet=new h.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),buttons:{execute:new l.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){n.job_handler.submit()}})},operations:{button_question:o,button_search:p,button_share:m}});if(!n.options.biostar_url){o.$el.hide();p.$el.hide()}n.$el.append(n.portlet.$el);if(n.options.help!=""){n.$el.append(d.help(n.options.help))}if(n.options.citations){n.$el.append(d.citations());var q=new j.ToolCitationCollection();q.tool_id=n.options.id;var r=new a.CitationListView({collection:q});r.render();q.fetch()}n.setElement(n.portlet.content());n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}}); \ No newline at end of file +define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(h,l,j,a,f,d,i,k,c,g){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(n){var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:n.id});this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.datasets=new i({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")},_initializeToolForm:function(){var n=this;var o=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var p=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});this.model.fetch({error:function(q){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");n.portlet=new h.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),buttons:{execute:new l.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){n.job_handler.submit()}})},operations:{button_question:o,button_search:p,button_share:m}});if(!n.options.biostar_url){o.$el.hide();p.$el.hide()}n.$el.append(n.portlet.$el);if(n.options.help!=""){n.$el.append(d.help(n.options.help))}if(n.options.citations){n.$el.append(d.citations());var q=new j.ToolCitationCollection();q.tool_id=n.options.id;var r=new a.CitationListView({collection:q});r.render();q.fetch()}n.setElement(n.portlet.content());n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}}); \ No newline at end of file diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.log(d);b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.message(a.success(e));c._refreshHdas()},function(e){console.debug(e);if(e&&e.message&&e.message.data){var g=c.app.tree.matchResponse(e.message.data);for(var f in g){c._foundError(f,g[f])}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress"});b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{c.app.modal.show({title:g.statusText,body:a.error(d),closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}})}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(j){function d(l,m,k){g("GET",l,{},m,k)}function g(p,l,m,o,k){if(p=="GET"||p=="DELETE"){if(l.indexOf("?")==-1){l+="?"}else{l+="&"}l+=$.param(m)}var n=new XMLHttpRequest();n.open(p,l,true);n.setRequestHeader("Accept","application/json");n.setRequestHeader("Cache-Control","no-cache");n.setRequestHeader("X-Requested-With","XMLHttpRequest");n.setRequestHeader("Content-Type","application/json");n.onloadend=function(){var q=n.status;try{response=jQuery.parseJSON(n.responseText)}catch(r){response=n.responseText}if(q==200){o&&o(response)}else{k&&k(response)}};if(p=="GET"||p=="DELETE"){n.send()}else{n.send(JSON.stringify(m))}}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file +define(["libs/underscore"],function(j){function d(l,m,k){g("GET",l,{},m,k)}function g(p,m,n,o,l){var k={url:m,type:p,contentType:"application/json"};if(p=="GET"||p=="DELETE"){if(m.indexOf("?")==-1){m+="?"}else{m+="&"}m+=$.param(n)}else{k.data=JSON.stringify(n);k.dataType="json"}$.ajax(k).done(function(q){o&&o(q)}).fail(function(r){var q=null;try{q=jQuery.parseJSON(r.responseText)}catch(s){q=r.responseText}l&&l(q,r)})}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -13,6 +13,12 @@ // generic function to send json to url function request (method, url, data, success, error) { + // configure + var ajaxConfig = { + url : url, + type : method, + 'contentType' : 'application/json' + } // encode data into url if (method == 'GET' || method == 'DELETE') { @@ -22,40 +28,25 @@ url += '&'; } url += $.param(data) + } else { + ajaxConfig['data'] = JSON.stringify(data); + ajaxConfig['dataType'] = 'json'; } - // prepare request - var xhr = new XMLHttpRequest(); - xhr.open(method, url, true); - xhr.setRequestHeader('Accept', 'application/json'); - xhr.setRequestHeader('Cache-Control', 'no-cache'); - xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest'); - xhr.setRequestHeader('Content-Type', 'application/json'); - xhr.onloadend = function() { - // get status - var status = xhr.status; - - // read response + // make request + $.ajax(ajaxConfig) + .done(function(response) { + success && success(response); + }) + .fail(function(response) { + var response_text = null; try { - response = jQuery.parseJSON(xhr.responseText); + response_text = jQuery.parseJSON(response.responseText); } catch (e) { - response = xhr.responseText; + response_text = response.responseText; } - - // parse response - if (status == 200) { - success && success(response); - } else { - error && error(response); - } - }; - - // make request - if (method == 'GET' || method == 'DELETE') { - xhr.send(); - } else { - xhr.send(JSON.stringify(data)); - } + error && error(response_text, response); + }); }; // get css value Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Fix data column parameters pointed at multiple data parameters.
by commits-noreply＠bitbucket.org 26 Sep '14

26 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/95bcb99ad2b4/ Changeset: 95bcb99ad2b4 User: jmchilton Date: 2014-09-26 14:49:43+00:00 Summary: Fix data column parameters pointed at multiple data parameters. Before it would just die with an unhelpful server side exception - now it attempts to build, validate, and use a useful set of columns. Affected #: 4 files diff -r d27e8692adadf069e30d454cdb7a634526a6ba45 -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1170,34 +1170,47 @@ Generate a select list containing the columns of the associated dataset (if found). """ - column_list = [] # No value indicates a configuration error, the named DataToolParameter # must preceed this parameter in the config assert self.data_ref in other_values, "Value for associated DataToolParameter not found" # Get the value of the associated DataToolParameter (a dataset) dataset = other_values[ self.data_ref ] # Check if a dataset is selected - if dataset is None or dataset == '': + if dataset is None or dataset == '' or dataset == []: # NOTE: Both of these values indicate that no dataset is selected. # However, 'None' indicates that the dataset is optional # while '' indicates that it is not. Currently column # parameters do not work well with optional datasets - return column_list - # Generate options - if not dataset.metadata.columns: - if self.accept_default: - column_list.append( self.default_value or '1' ) - return column_list - if not self.force_select: + return [] + column_list = None + for dataset in util.listify( dataset ): + # Handle columns not available. + if not dataset.metadata.columns: + default_column_list = [] + if self.accept_default: + default_column_list.append( self.default_value or '1' ) + return default_column_list + + # Build up possible columns for this dataset + this_column_list = [] + if self.numerical: + # If numerical was requested, filter columns based on metadata + for i, col in enumerate( dataset.metadata.column_types ): + if col == 'int' or col == 'float': + this_column_list.append( str( i + 1 ) ) + else: + for i in range(0, dataset.metadata.columns): + this_column_list.append( str( i + 1 ) ) + + # Take the intersection of these columns with the other columns. + if column_list is None: + column_list = this_column_list + else: + column_list = filter(lambda c: c in this_column_list, column_list) + + if not self.force_select and 'None' not in column_list: column_list.append( 'None' ) - if self.numerical: - # If numerical was requested, filter columns based on metadata - for i, col in enumerate( dataset.metadata.column_types ): - if col == 'int' or col == 'float': - column_list.append( str( i + 1 ) ) - else: - for i in range(0, dataset.metadata.columns): - column_list.append( str( i + 1 ) ) + return column_list def get_options( self, trans, other_values ): @@ -1249,14 +1262,15 @@ if self.data_ref not in context: return False # Get the selected dataset if selected - dataset = context[ self.data_ref ] - if dataset: - # Check if the dataset does not have the expected metadata for columns - if not dataset.metadata.columns: - # Only allow late validation if the dataset is not yet ready - # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending or not dataset.datatype.matches_any( self.ref_input.formats ): - return True + datasets = util.listify( context[ self.data_ref ] ) + for dataset in datasets: + if dataset: + # Check if the dataset does not have the expected metadata for columns + if not dataset.metadata.columns: + # Only allow late validation if the dataset is not yet ready + # (since we have reason to expect the metadata to be ready eventually) + if dataset.is_pending or not dataset.datatype.matches_any( self.ref_input.formats ): + return True # No late validation return False diff -r d27e8692adadf069e30d454cdb7a634526a6ba45 -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f test/functional/tools/column_multi_param.xml --- /dev/null +++ b/test/functional/tools/column_multi_param.xml @@ -0,0 +1,25 @@ +<tool id="column_multi_param" name="Column Param Multi"> + <command> + #for $input in $input1# + cut -f '$col' '$input' >> 'col_output'; + #end for# + </command> + <inputs> + <param type="data" format="tabular" name="input1" label="Input 1" multiple="true" /> + <param name="col" type="data_column" data_ref="input1" label="Column to Use" /> + </inputs> + <outputs> + <data name="output1" type="tabular" from_work_dir="col_output" /> + </outputs> + <tests> + <test> + <param name="input1" value="2.tabular,2.tabular" /> + <param name="col" value="2" /> + <output name="outpu1"> + <assert_contents> + <has_line line="68" /> + </assert_contents> + </output> + </test> + </tests> +</tool> diff -r d27e8692adadf069e30d454cdb7a634526a6ba45 -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f test/functional/tools/column_param.xml --- /dev/null +++ b/test/functional/tools/column_param.xml @@ -0,0 +1,23 @@ +<tool id="column_param" name="Column Param"> + <command> + cut -f '$col' '$input1' > 'col_output' + </command> + <inputs> + <param type="data" format="tabular" name="input1" label="Input 1" /> + <param name="col" type="data_column" data_ref="input1" label="Column to Use" /> + </inputs> + <outputs> + <data name="output1" type="tabular" from_work_dir="col_output" /> + </outputs> + <tests> + <test> + <param name="input1" value="2.tabular" /> + <param name="col" value="2" /> + <output name="output1"> + <assert_contents> + <has_line line="68" /> + </assert_contents> + </output> + </test> + </tests> +</tool> diff -r d27e8692adadf069e30d454cdb7a634526a6ba45 -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -20,6 +20,8 @@ <tool file="parallelism_optional.xml" /><tool file="implicit_default_conds.xml" /><tool file="multi_data_param.xml" /> + <tool file="column_param.xml" /> + <tool file="column_multi_param.xml" /><tool file="special_params.xml" /><tool file="validation_default.xml" /><tool file="validation_sanitizer.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Fix boolean handling
by commits-noreply＠bitbucket.org 26 Sep '14

26 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d27e8692adad/ Changeset: d27e8692adad User: guerler Date: 2014-09-26 13:52:32+00:00 Summary: ToolForm: Fix boolean handling Affected #: 3 files diff -r 38f6cf2629efd071b4e7cc3e420a4e5081ad51e0 -r d27e8692adadf069e30d454cdb7a634526a6ba45 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -109,16 +109,6 @@ } } break; - // handle boolean input - case 'boolean': - var value = self.app.field_list[input.id].value(); - if (value === 'true') { - value = input.truevalue; - } else { - value = input.falsevalue; - } - add (job_input_id, input.id, value); - break; default: // handle default value add (job_input_id, input.id, self.app.field_list[input.id].value()); diff -r 38f6cf2629efd071b4e7cc3e420a4e5081ad51e0 -r d27e8692adadf069e30d454cdb7a634526a6ba45 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -109,16 +109,6 @@ } } break; - // handle boolean input - case 'boolean': - var value = self.app.field_list[input.id].value(); - if (value === 'true') { - value = input.truevalue; - } else { - value = input.falsevalue; - } - add (job_input_id, input.id, value); - break; default: // handle default value add (job_input_id, input.id, self.app.field_list[input.id].value()); diff -r 38f6cf2629efd071b4e7cc3e420a4e5081ad51e0 -r d27e8692adadf069e30d454cdb7a634526a6ba45 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(j,m){for(var g in m){var e=m[g];if(e.input){var n=e.input;var h=j;if(j!=""){h+="|"}h+=n.name;switch(n.type){case"repeat":var d="section-";var q=[];var l=null;for(var p in e){var k=p.indexOf(d);if(k!=-1){k+=d.length;q.push(parseInt(p.substr(k)));if(!l){l=p.substr(0,k)}}}q.sort(function(r,i){return r-i});var g=0;for(var f in q){b(h+"_"+g++,e[l+q[f]])}break;case"conditional":var o=a.app.field_list[n.id].value();c(h+"|"+n.test_param.name,n.id,o);for(var f in n.cases){if(n.cases[f].value==o){b(h,m[n.id+"-section-"+f]);break}}break;case"boolean":var o=a.app.field_list[n.id].value();if(o==="true"){o=n.truevalue}else{o=n.falsevalue}c(h,n.id,o);break;default:c(h,n.id,a.app.field_list[n.id].value())}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(j,m){for(var g in m){var e=m[g];if(e.input){var n=e.input;var h=j;if(j!=""){h+="|"}h+=n.name;switch(n.type){case"repeat":var d="section-";var q=[];var l=null;for(var p in e){var k=p.indexOf(d);if(k!=-1){k+=d.length;q.push(parseInt(p.substr(k)));if(!l){l=p.substr(0,k)}}}q.sort(function(r,i){return r-i});var g=0;for(var f in q){b(h+"_"+g++,e[l+q[f]])}break;case"conditional":var o=a.app.field_list[n.id].value();c(h+"|"+n.test_param.name,n.id,o);for(var f in n.cases){if(n.cases[f].value==o){b(h,m[n.id+"-section-"+f]);break}}break;default:c(h,n.id,a.app.field_list[n.id].value())}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Tool test case demonstrating wrapping multiple data params in new meta-parameter wrapper.
by commits-noreply＠bitbucket.org 26 Sep '14

26 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/38f6cf2629ef/ Changeset: 38f6cf2629ef User: jmchilton Date: 2014-09-26 13:29:53+00:00 Summary: Tool test case demonstrating wrapping multiple data params in new meta-parameter wrapper. ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_multidata_param It was what was requested, but I am not sure I love this behavior - seems like for consistency that should maybe be a list of lists? I can see the other side of the argument though. Affected #: 1 file diff -r f52d7d6d64a671039a85959e1c720445f0ee672e -r 38f6cf2629efd071b4e7cc3e420a4e5081ad51e0 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -106,6 +106,23 @@ output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output ) assert output1_content == "--ex1,ex2" + @skip_without_tool( "multi_data_param" ) + def test_multidata_param( self ): + history_id = self.dataset_populator.new_history() + hda1 = dataset_to_param( self.dataset_populator.new_dataset( history_id, content='1\t2\t3' ) ) + hda2 = dataset_to_param( self.dataset_populator.new_dataset( history_id, content='4\t5\t6' ) ) + inputs = { + "f1": { 'batch': False, 'values': [ hda1, hda2 ] }, + "f2": { 'batch': False, 'values': [ hda2, hda1 ] }, + } + response = self._run( "multi_data_param", history_id, inputs, assert_ok=True ) + output1 = response[ "outputs" ][ 0 ] + output2 = response[ "outputs" ][ 1 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) + output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output2 ) + assert output1_content == "1\t2\t3\n4\t5\t6\n", output1_content + assert output2_content == "4\t5\t6\n1\t2\t3\n", output2_content + @skip_without_tool( "cat1" ) def test_run_cat1( self ): # Run simple non-upload tool with an input data parameter. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1a87b74d4f42/ Changeset: 1a87b74d4f42 Branch: next-stable User: natefoo Date: 2014-09-25 20:23:06+00:00 Summary: Fix bug in finding relocated tool_data_table_conf.xml Affected #: 1 file diff -r fdcefd1c3661ea71661584e7bcc03f33022641d1 -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -394,7 +394,7 @@ ) listify_defaults = dict( - tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], # rationale: # [0]: user has explicitly created config/tool_conf.xml but did not # move their existing shed_tool_conf.xml, don't use https://bitbucket.org/galaxy/galaxy-central/commits/f52d7d6d64a6/ Changeset: f52d7d6d64a6 User: natefoo Date: 2014-09-25 20:23:31+00:00 Summary: Merge next-stable. Affected #: 1 file diff -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 -r f52d7d6d64a671039a85959e1c720445f0ee672e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -394,7 +394,7 @@ ) listify_defaults = dict( - tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], # rationale: # [0]: user has explicitly created config/tool_conf.xml but did not # move their existing shed_tool_conf.xml, don't use Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Improve validation, minor fixes
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f02fcf8a931c/ Changeset: f02fcf8a931c User: guerler Date: 2014-09-25 20:14:56+00:00 Summary: ToolForm: Improve validation, minor fixes Affected #: 12 files diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -46,18 +46,35 @@ console.debug(response); if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); - for (var id in error_messages) { - var error_text = error_messages[id]; - if (!error_text) { - error_text = 'Please verify this parameter.'; - } - self.app.element_list[id].error(error_text); + for (var input_id in error_messages) { + self._foundError(input_id, error_messages[input_id]); } } } ); }, + /** Highlight and scroll to error + */ + _foundError: function (input_id, message) { + // get input field + var input_element = this.app.element_list[input_id]; + + // mark error + input_element.error(message || 'Please verify this parameter.'); + + // set flag + if (this.valid) { + // scroll to first input element + $(this.app.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + + // set error flag + this.valid = false; + } + }, + /** Validate job definition */ _validation: function(job_def) { @@ -65,30 +82,7 @@ var job_inputs = job_def.inputs; // validation flag - var valid = true; - - // link this - var self = this; - - /** Highlight and scroll to error */ - function foundError (input_id, message) { - // get input field - var input_element = self.app.element_list[input_id]; - - // mark error - input_element.error(message || 'Please verify this parameter.'); - - // set flag - if (valid) { - // scroll to first input element - $(self.app.container).animate({ - scrollTop: input_element.$el.offset().top - 20 - }, 500); - - // set error flag - valid = false; - } - } + this.valid = true; // counter for values declared in batch mode var n_values = -1; @@ -105,7 +99,7 @@ // check basic field validation if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) { - foundError(input_id); + this._foundError(input_id); } // check if input field is in batch mode @@ -115,15 +109,15 @@ n_values = n; } else { if (n_values !== n) { - foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); } } } } - // return result - return valid; + // return validation result + return this.valid; }, /** Refreshes the history panel diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -540,6 +540,10 @@ /** Slider field */ _field_slider: function(input_def) { + // set min/max + input_def.min = input_def.min || 0; + input_def.max = input_def.max || 100000; + // calculate step size var step = 1; if (input_def.type == 'float') { @@ -549,8 +553,8 @@ // create slider return new Ui.Slider.View({ id : 'field-' + input_def.id, - min : input_def.min || 0, - max : input_def.max || 1000, + min : input_def.min, + max : input_def.max, step : step }); }, diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -114,7 +114,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null' || !current[i]) { + if (current[i] === 'null') { return false; } } @@ -149,7 +149,7 @@ // get selected values var selected = this.$el.find(':checked'); if (selected.length == 0) { - return null; + return 'null'; } // return multiple or single value diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -91,7 +91,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null' || !current[i]) { + if (current[i] === 'null') { return false; } } diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -46,18 +46,35 @@ console.debug(response); if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); - for (var id in error_messages) { - var error_text = error_messages[id]; - if (!error_text) { - error_text = 'Please verify this parameter.'; - } - self.app.element_list[id].error(error_text); + for (var input_id in error_messages) { + self._foundError(input_id, error_messages[input_id]); } } } ); }, + /** Highlight and scroll to error + */ + _foundError: function (input_id, message) { + // get input field + var input_element = this.app.element_list[input_id]; + + // mark error + input_element.error(message || 'Please verify this parameter.'); + + // set flag + if (this.valid) { + // scroll to first input element + $(this.app.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + + // set error flag + this.valid = false; + } + }, + /** Validate job definition */ _validation: function(job_def) { @@ -65,30 +82,7 @@ var job_inputs = job_def.inputs; // validation flag - var valid = true; - - // link this - var self = this; - - /** Highlight and scroll to error */ - function foundError (input_id, message) { - // get input field - var input_element = self.app.element_list[input_id]; - - // mark error - input_element.error(message || 'Please verify this parameter.'); - - // set flag - if (valid) { - // scroll to first input element - $(self.app.container).animate({ - scrollTop: input_element.$el.offset().top - 20 - }, 500); - - // set error flag - valid = false; - } - } + this.valid = true; // counter for values declared in batch mode var n_values = -1; @@ -105,7 +99,7 @@ // check basic field validation if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) { - foundError(input_id); + this._foundError(input_id); } // check if input field is in batch mode @@ -115,15 +109,15 @@ n_values = n; } else { if (n_values !== n) { - foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); } } } } - // return result - return valid; + // return validation result + return this.valid; }, /** Refreshes the history panel diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -540,6 +540,10 @@ /** Slider field */ _field_slider: function(input_def) { + // set min/max + input_def.min = input_def.min || 0; + input_def.max = input_def.max || 100000; + // calculate step size var step = 1; if (input_def.type == 'float') { @@ -549,8 +553,8 @@ // create slider return new Ui.Slider.View({ id : 'field-' + input_def.id, - min : input_def.min || 0, - max : input_def.max || 1000, + min : input_def.min, + max : input_def.max, step : step }); }, diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -114,7 +114,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null' || !current[i]) { + if (current[i] === 'null') { return false; } } @@ -149,7 +149,7 @@ // get selected values var selected = this.$el.find(':checked'); if (selected.length == 0) { - return null; + return 'null'; } // return multiple or single value diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -91,7 +91,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null' || !current[i]) { + if (current[i] === 'null') { return false; } } diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.log(d);b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.message(a.success(e));c._refreshHdas()},function(e){console.debug(e);if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var g in h){var f=h[g];if(!f){f="Please verify this parameter."}c.app.element_list[g].error(f)}}})},_validation:function(h){var e=h.inputs;var c=true;var o=this;function m(n,p){var q=o.app.element_list[n];q.error(p||"Please verify this parameter.");if(c){$(o.app.container).animate({scrollTop:q.$el.offset().top-20},500);c=false}}var l=-1;for(var k in e){var f=e[k];var j=this.app.tree.match(k);var d=this.app.field_list[j];var i=this.app.input_list[j];if(i&&!i.optional&&d&&d.validate&&!d.validate()){m(j)}if(f.batch){var g=f.values.length;if(l===-1){l=g}else{if(l!==g){m(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+l+"</b>.")}}}}return c},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.log(d);b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.message(a.success(e));c._refreshHdas()},function(e){console.debug(e);if(e&&e.message&&e.message.data){var g=c.app.tree.matchResponse(e.message.data);for(var f in g){c._foundError(f,g[f])}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-dataset"],function(d,a,g,c,b){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new a.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_field_conditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(h){var i=this;var j=h.id;return new b.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(l){var v=l.values[0].id;var t=i.app.tree.references(j,"data_column");if(t.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}var o=i.app.datasets.filter(v);var x=null;if(o){console.debug("tool-form::field_data() - Selected dataset "+v+".");x=o.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+v+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+v+".")}for(var p in t){var r=i.app.input_list[t[p]];var s=i.app.field_list[t[p]];if(!r||!s){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=r.numerical;var m=[];for(var w in x){var u=x[w];var k=(parseInt(w)+1);var q="Text";if(u=="int"||u=="float"){q="Number"}if(u=="int"||u=="float"||!n){m.push({label:"Column: "+k+" ["+q+"]",value:k})}}if(s){s.update(m);if(!s.exists(s.value())){s.value(s.first())}}}}})},_field_select:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min||0,max:h.max||1000,step:i})},_field_hidden:function(h){return new g.Hidden({id:"field-"+h.id})},_field_boolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-dataset"],function(d,a,g,c,b){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new a.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_field_conditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(h){var i=this;var j=h.id;return new b.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(l){var v=l.values[0].id;var t=i.app.tree.references(j,"data_column");if(t.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}var o=i.app.datasets.filter(v);var x=null;if(o){console.debug("tool-form::field_data() - Selected dataset "+v+".");x=o.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+v+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+v+".")}for(var p in t){var r=i.app.input_list[t[p]];var s=i.app.field_list[t[p]];if(!r||!s){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=r.numerical;var m=[];for(var w in x){var u=x[w];var k=(parseInt(w)+1);var q="Text";if(u=="int"||u=="float"){q="Number"}if(u=="int"||u=="float"||!n){m.push({label:"Column: "+k+" ["+q+"]",value:k})}}if(s){s.update(m);if(!s.exists(s.value())){s.value(s.first())}}}}})},_field_select:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_field_hidden:function(h){return new g.Hidden({id:"field-"+h.id})},_field_boolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$error=$(this._templateError(g));this.$options=$(this._template(g));this.$el.append(this.$error);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if(g[f]==="null"||!g[f]){return false}}return true},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){var f=this.$el.find(".ui-option").length;if(f==0){this.$error.show();this.$options.hide()}else{this.$error.hide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return null}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_templateError:function(f){return'<div class="ui-error" style="display: none;">'+f.empty+"</div>"}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$error=$(this._templateError(g));this.$options=$(this._template(g));this.$el.append(this.$error);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if(g[f]==="null"){return false}}return true},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){var f=this.$el.find(".ui-option").length;if(f==0){this.$error.show();this.$options.hide()}else{this.$error.hide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_templateError:function(f){return'<div class="ui-error" style="display: none;">'+f.empty+"</div>"}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if(d[c]==="null"||!d[c]){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if(d[c]==="null"){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b737af143fce/ Changeset: b737af143fce Branch: next-stable User: jmchilton Date: 2014-09-25 17:49:04+00:00 Summary: Fix various BibTex styling problems. Need to get out of the BibTeX formatting game as quickly as possible this is a loosing battle, but until then plugging holes in the ship. Affected #: 2 files diff -r f3284eb7ec210d50a3e9f2c0d393cffcb24894da -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 client/galaxy/scripts/libs/bibtex.js --- a/client/galaxy/scripts/libs/bibtex.js +++ b/client/galaxy/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'online' : 998 // Galaxy MOD: Handle @online entries for preprints. ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { diff -r f3284eb7ec210d50a3e9f2c0d393cffcb24894da -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 client/galaxy/scripts/mvc/citation/citation-view.js --- a/client/galaxy/scripts/mvc/citation/citation-view.js +++ b/client/galaxy/scripts/mvc/citation/citation-view.js @@ -24,11 +24,12 @@ var pages = fields.pages ? ("pp. " + fields.pages) : ""; var address = fields.address; if( entryType == "article" ) { + var volume = (fields.volume ? fields.volume : "") + + (fields.number ? ( " (" + fields.number + ")" ) : "") + + (pages ? ", " + pages : ""); ref = authorsAndYear + this._asSentence(title) + (fields.journal ? ("In <em>" + fields.journal + ", ") : "") + - (fields.volume ? fields.volume : "") + - (fields.number ? ( "(" + fields.number + "), " ) : ", " ) + - this._asSentence(pages) + + this._asSentence(volume) + this._asSentence(fields.address) + "<\/em>"; } else if( entryType == "inproceedings" || entryType == "proceedings" ) { @@ -43,14 +44,14 @@ (fields.howpublished ? fields.howpublished + ". " : "") + (fields.note ? fields.note + "." : ""); } else if( entryType == "techreport" ) { - ref = authorsAndYear + ". " + this._asSentence(title) + + ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type); } else if( entryType == "book" || entryType == "inbook" || entryType == "incollection" ) { - ref = this._asSentence(authorsAndYear) + " " + this._formatBookInfo(fields); + ref = authorsAndYear + " " + this._formatBookInfo(fields); } else { - ref = this._asSentence(authorsAndYear) + " " + this._asSentence(title) + + ref = authorsAndYear + " " + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note); } https://bitbucket.org/galaxy/galaxy-central/commits/fdcefd1c3661/ Changeset: fdcefd1c3661 Branch: next-stable User: jmchilton Date: 2014-09-25 17:49:04+00:00 Summary: Grunting at the scripts. Affected #: 4 files diff -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 -r fdcefd1c3661ea71661584e7bcc03f33022641d1 static/scripts/libs/bibtex.js --- a/static/scripts/libs/bibtex.js +++ b/static/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'online' : 998 // Galaxy MOD: Handle @online entries for preprints. ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { diff -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 -r fdcefd1c3661ea71661584e7bcc03f33022641d1 static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -24,11 +24,12 @@ var pages = fields.pages ? ("pp. " + fields.pages) : ""; var address = fields.address; if( entryType == "article" ) { + var volume = (fields.volume ? fields.volume : "") + + (fields.number ? ( " (" + fields.number + ")" ) : "") + + (pages ? ", " + pages : ""); ref = authorsAndYear + this._asSentence(title) + (fields.journal ? ("In <em>" + fields.journal + ", ") : "") + - (fields.volume ? fields.volume : "") + - (fields.number ? ( "(" + fields.number + "), " ) : ", " ) + - this._asSentence(pages) + + this._asSentence(volume) + this._asSentence(fields.address) + "<\/em>"; } else if( entryType == "inproceedings" || entryType == "proceedings" ) { @@ -43,14 +44,14 @@ (fields.howpublished ? fields.howpublished + ". " : "") + (fields.note ? fields.note + "." : ""); } else if( entryType == "techreport" ) { - ref = authorsAndYear + ". " + this._asSentence(title) + + ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type); } else if( entryType == "book" || entryType == "inbook" || entryType == "incollection" ) { - ref = this._asSentence(authorsAndYear) + " " + this._formatBookInfo(fields); + ref = authorsAndYear + " " + this._formatBookInfo(fields); } else { - ref = this._asSentence(authorsAndYear) + " " + this._asSentence(title) + + ref = authorsAndYear + " " + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note); } diff -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 -r fdcefd1c3661ea71661584e7bcc03f33022641d1 static/scripts/packed/libs/bibtex.js --- a/static/scripts/packed/libs/bibtex.js +++ b/static/scripts/packed/libs/bibtex.js @@ -1,1 +1,1 @@ -function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser construction."}this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5};this.DATA_={};this.CALLBACK_=c;this.CHAR_=0;this.LINE_=1;this.CHAR_IN_LINE_=0;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={};this.SKIPTILLEOL_=false;this.VALBRACES_=null;this.BRACETYPE_=null;this.BRACECOUNT_=0;this.STATE_=this.STATES_.ENTRY_OR_JUNK;this.ERRORS_=[];this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16,data:999};this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"};this.getErrors=function(){return this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for object.");this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;f=true;this.STATE_=this.STATES_.KV_KEY;this.PARSETMP_.Key="";this.DATA_.Fields={}}}}else{this.DATA_.EntryKey+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}break;case this.STATES_.KV_KEY:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(/[\-A-Za-z:]/.test(l)){this.PARSETMP_.Key+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{if(this.PARSETMP_.Key.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.EQUALS;f=true}}break;case this.STATES_.EQUALS:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no value.');this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(l=="="){this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.KV_VALUE;this.PARSETMP_.Value="";this.VALBRACES_={'"':[],"{":[]}}break;case this.STATES_.KV_VALUE:var k=this.VALBRACES_;var j=this.PARSETMP_.Value;var h=false;if(l=='"'||l=="{"||l=="}"||l==","){if(l==","){if(0===k['"'].length+k["{"].length){var g=this.PARSETMP_.Value.trim();if(g in this.MACROS_){this.PARSETMP_.Value=this.MACROS_[g]}else{this.error_("Reference to an undefined macro: "+g)}h=true}}if(l=='"'){if(0===k['"'].length+k["{"].length){k['"'].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false;break}if(k['"'].length==1&&k["{"].length==0&&(j.length==0||j[j.length-1]!="\\")){h=true}else{}}if(l=="{"){if(j.length==0||j[j.length-1]!="\\"){k["{"].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{}}if(l=="}"){if(0===k['"'].length+k["{"].length){var g=this.PARSETMP_.Value.trim();if(g in this.MACROS_){this.PARSETMP_.Value=this.MACROS_[g]}else{this.error_("Reference to an undefined macro: "+g)}f=true;h=true}else{if(j.length==0||j[j.length-1]!="\\"){if(k["{"].length>0){k["{"].splice(k["{"].length-1,1);if(0==k["{"].length+k['"'].length){h=true}else{}}}else{}}}}if(h){this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.KV_KEY;this.DATA_.Fields[this.PARSETMP_.Key]=this.PARSETMP_.Value;this.PARSETMP_={Key:""};this.VALBRACES_=null}else{this.PARSETMP_.Value+=l}break}}};this.CHARCONV_=[[/\\space /g,"\u0020"],[/\\textdollar /g,"\u0024"],[/\\textquotesingle /g,"\u0027"],[/\\ast /g,"\u002A"],[/\\textbackslash /g,"\u005C"],[/\\\^\{\}/g,"\u005E"],[/\\textasciigrave /g,"\u0060"],[/\\lbrace /g,"\u007B"],[/\\vert /g,"\u007C"],[/\\rbrace /g,"\u007D"],[/\\textasciitilde /g,"\u007E"],[/\\textexclamdown /g,"\u00A1"],[/\\textcent /g,"\u00A2"],[/\\textsterling /g,"\u00A3"],[/\\textcurrency /g,"\u00A4"],[/\\textyen 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/g,"\u29A0"],[/\\ElsevierGlyph\{E260\}/g,"\u29B5"],[/\\ElsevierGlyph\{E61B\}/g,"\u29B6"],[/\\ElzLap /g,"\u29CA"],[/\\Elzdefas /g,"\u29CB"],[/\\LeftTriangleBar /g,"\u29CF"],[/\\NotLeftTriangleBar /g,"\u29CF-00338"],[/\\RightTriangleBar /g,"\u29D0"],[/\\NotRightTriangleBar /g,"\u29D0-00338"],[/\\ElsevierGlyph\{E372\}/g,"\u29DC"],[/\\blacklozenge /g,"\u29EB"],[/\\RuleDelayed /g,"\u29F4"],[/\\Elxuplus /g,"\u2A04"],[/\\ElzThr /g,"\u2A05"],[/\\Elxsqcup /g,"\u2A06"],[/\\ElzInf /g,"\u2A07"],[/\\ElzSup /g,"\u2A08"],[/\\ElzCint /g,"\u2A0D"],[/\\clockoint /g,"\u2A0F"],[/\\ElsevierGlyph\{E395\}/g,"\u2A10"],[/\\sqrint /g,"\u2A16"],[/\\ElsevierGlyph\{E25A\}/g,"\u2A25"],[/\\ElsevierGlyph\{E25B\}/g,"\u2A2A"],[/\\ElsevierGlyph\{E25C\}/g,"\u2A2D"],[/\\ElsevierGlyph\{E25D\}/g,"\u2A2E"],[/\\ElzTimes /g,"\u2A2F"],[/\\ElsevierGlyph\{E25E\}/g,"\u2A34"],[/\\ElsevierGlyph\{E25E\}/g,"\u2A35"],[/\\ElsevierGlyph\{E259\}/g,"\u2A3C"],[/\\amalg /g,"\u2A3F"],[/\\ElzAnd /g,"\u2A53"],[/\\ElzOr /g,"\u2A54"],[/\\ElsevierGlyph\{E36E\}/g,"\u2A55"],[/\\ElOr /g,"\u2A56"],[/\\perspcorrespond /g,"\u2A5E"],[/\\Elzminhat /g,"\u2A5F"],[/\\ElsevierGlyph\{225A\}/g,"\u2A63"],[/\\stackrel\{*\}\{=\}/g,"\u2A6E"],[/\\Equal /g,"\u2A75"],[/\\leqslant /g,"\u2A7D"],[/\\nleqslant /g,"\u2A7D-00338"],[/\\geqslant /g,"\u2A7E"],[/\\ngeqslant /g,"\u2A7E-00338"],[/\\lessapprox /g,"\u2A85"],[/\\gtrapprox /g,"\u2A86"],[/\\lneq /g,"\u2A87"],[/\\gneq /g,"\u2A88"],[/\\lnapprox /g,"\u2A89"],[/\\gnapprox /g,"\u2A8A"],[/\\lesseqqgtr /g,"\u2A8B"],[/\\gtreqqless /g,"\u2A8C"],[/\\eqslantless /g,"\u2A95"],[/\\eqslantgtr /g,"\u2A96"],[/\\Pisymbol\{ppi020\}\{117\}/g,"\u2A9D"],[/\\Pisymbol\{ppi020\}\{105\}/g,"\u2A9E"],[/\\NestedLessLess /g,"\u2AA1"],[/\\NotNestedLessLess /g,"\u2AA1-00338"],[/\\NestedGreaterGreater /g,"\u2AA2"],[/\\NotNestedGreaterGreater /g,"\u2AA2-00338"],[/\\preceq /g,"\u2AAF"],[/\\not\\preceq /g,"\u2AAF-00338"],[/\\succeq /g,"\u2AB0"],[/\\not\\succeq /g,"\u2AB0-00338"],[/\\precneqq /g,"\u2AB5"],[/\\succneqq /g,"\u2AB6"],[/\\precapprox /g,"\u2AB7"],[/\\succapprox /g,"\u2AB8"],[/\\precnapprox /g,"\u2AB9"],[/\\succnapprox /g,"\u2ABA"],[/\\subseteqq /g,"\u2AC5"],[/\\nsubseteqq /g,"\u2AC5-00338"],[/\\supseteqq /g,"\u2AC6"],[/\\nsupseteqq/g,"\u2AC6-00338"],[/\\subsetneqq /g,"\u2ACB"],[/\\supsetneqq /g,"\u2ACC"],[/\\ElsevierGlyph\{E30D\}/g,"\u2AEB"],[/\\Elztdcol /g,"\u2AF6"],[/\\ElsevierGlyph\{300A\}/g,"\u300A"],[/\\ElsevierGlyph\{300B\}/g,"\u300B"],[/\\ElsevierGlyph\{3018\}/g,"\u3018"],[/\\ElsevierGlyph\{3019\}/g,"\u3019"],[/\\openbracketleft /g,"\u301A"],[/\\openbracketright /g,"\u301B"]];return this}if(typeof module!=="undefined"&&module.exports){module.exports=BibtexParser}; \ No newline at end of file +function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser construction."}this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5};this.DATA_={};this.CALLBACK_=c;this.CHAR_=0;this.LINE_=1;this.CHAR_IN_LINE_=0;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={};this.SKIPTILLEOL_=false;this.VALBRACES_=null;this.BRACETYPE_=null;this.BRACECOUNT_=0;this.STATE_=this.STATES_.ENTRY_OR_JUNK;this.ERRORS_=[];this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16,online:998,data:999};this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"};this.getErrors=function(){return this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for object.");this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;f=true;this.STATE_=this.STATES_.KV_KEY;this.PARSETMP_.Key="";this.DATA_.Fields={}}}}else{this.DATA_.EntryKey+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}break;case this.STATES_.KV_KEY:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(/[\-A-Za-z:]/.test(l)){this.PARSETMP_.Key+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{if(this.PARSETMP_.Key.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.EQUALS;f=true}}break;case this.STATES_.EQUALS:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no value.');this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(l=="="){this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.KV_VALUE;this.PARSETMP_.Value="";this.VALBRACES_={'"':[],"{":[]}}break;case this.STATES_.KV_VALUE:var k=this.VALBRACES_;var j=this.PARSETMP_.Value;var h=false;if(l=='"'||l=="{"||l=="}"||l==","){if(l==","){if(0===k['"'].length+k["{"].length){var g=this.PARSETMP_.Value.trim();if(g in this.MACROS_){this.PARSETMP_.Value=this.MACROS_[g]}else{this.error_("Reference to an undefined macro: "+g)}h=true}}if(l=='"'){if(0===k['"'].length+k["{"].length){k['"'].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false;break}if(k['"'].length==1&&k["{"].length==0&&(j.length==0||j[j.length-1]!="\\")){h=true}else{}}if(l=="{"){if(j.length==0||j[j.length-1]!="\\"){k["{"].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{}}if(l=="}"){if(0===k['"'].length+k["{"].length){var g=this.PARSETMP_.Value.trim();if(g in this.MACROS_){this.PARSETMP_.Value=this.MACROS_[g]}else{this.error_("Reference to an undefined macro: "+g)}f=true;h=true}else{if(j.length==0||j[j.length-1]!="\\"){if(k["{"].length>0){k["{"].splice(k["{"].length-1,1);if(0==k["{"].length+k['"'].length){h=true}else{}}}else{}}}}if(h){this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.KV_KEY;this.DATA_.Fields[this.PARSETMP_.Key]=this.PARSETMP_.Value;this.PARSETMP_={Key:""};this.VALBRACES_=null}else{this.PARSETMP_.Value+=l}break}}};this.CHARCONV_=[[/\\space /g,"\u0020"],[/\\textdollar /g,"\u0024"],[/\\textquotesingle /g,"\u0027"],[/\\ast /g,"\u002A"],[/\\textbackslash /g,"\u005C"],[/\\\^\{\}/g,"\u005E"],[/\\textasciigrave /g,"\u0060"],[/\\lbrace /g,"\u007B"],[/\\vert /g,"\u007C"],[/\\rbrace /g,"\u007D"],[/\\textasciitilde /g,"\u007E"],[/\\textexclamdown /g,"\u00A1"],[/\\textcent /g,"\u00A2"],[/\\textsterling /g,"\u00A3"],[/\\textcurrency /g,"\u00A4"],[/\\textyen 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Affected #: 6 files diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 client/galaxy/scripts/libs/bibtex.js --- a/client/galaxy/scripts/libs/bibtex.js +++ b/client/galaxy/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'online' : 998 // Galaxy MOD: Handle @online entries for preprints. ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 client/galaxy/scripts/mvc/citation/citation-view.js --- a/client/galaxy/scripts/mvc/citation/citation-view.js +++ b/client/galaxy/scripts/mvc/citation/citation-view.js @@ -24,11 +24,12 @@ var pages = fields.pages ? ("pp. " + fields.pages) : ""; var address = fields.address; if( entryType == "article" ) { + var volume = (fields.volume ? fields.volume : "") + + (fields.number ? ( " (" + fields.number + ")" ) : "") + + (pages ? ", " + pages : ""); ref = authorsAndYear + this._asSentence(title) + (fields.journal ? ("In <em>" + fields.journal + ", ") : "") + - (fields.volume ? fields.volume : "") + - (fields.number ? ( "(" + fields.number + "), " ) : ", " ) + - this._asSentence(pages) + + this._asSentence(volume) + this._asSentence(fields.address) + "<\/em>"; } else if( entryType == "inproceedings" || entryType == "proceedings" ) { @@ -43,14 +44,14 @@ (fields.howpublished ? fields.howpublished + ". " : "") + (fields.note ? fields.note + "." : ""); } else if( entryType == "techreport" ) { - ref = authorsAndYear + ". " + this._asSentence(title) + + ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type); } else if( entryType == "book" || entryType == "inbook" || entryType == "incollection" ) { - ref = this._asSentence(authorsAndYear) + " " + this._formatBookInfo(fields); + ref = authorsAndYear + " " + this._formatBookInfo(fields); } else { - ref = this._asSentence(authorsAndYear) + " " + this._asSentence(title) + + ref = authorsAndYear + " " + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note); } diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 static/scripts/libs/bibtex.js --- a/static/scripts/libs/bibtex.js +++ b/static/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'online' : 998 // Galaxy MOD: Handle @online entries for preprints. ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -24,11 +24,12 @@ var pages = fields.pages ? ("pp. " + fields.pages) : ""; var address = fields.address; if( entryType == "article" ) { + var volume = (fields.volume ? fields.volume : "") + + (fields.number ? ( " (" + fields.number + ")" ) : "") + + (pages ? ", " + pages : ""); ref = authorsAndYear + this._asSentence(title) + (fields.journal ? ("In <em>" + fields.journal + ", ") : "") + - (fields.volume ? fields.volume : "") + - (fields.number ? ( "(" + fields.number + "), " ) : ", " ) + - this._asSentence(pages) + + this._asSentence(volume) + this._asSentence(fields.address) + "<\/em>"; } else if( entryType == "inproceedings" || entryType == "proceedings" ) { @@ -43,14 +44,14 @@ (fields.howpublished ? fields.howpublished + ". " : "") + (fields.note ? fields.note + "." : ""); } else if( entryType == "techreport" ) { - ref = authorsAndYear + ". " + this._asSentence(title) + + ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type); } else if( entryType == "book" || entryType == "inbook" || entryType == "incollection" ) { - ref = this._asSentence(authorsAndYear) + " " + this._formatBookInfo(fields); + ref = authorsAndYear + " " + this._formatBookInfo(fields); } else { - ref = this._asSentence(authorsAndYear) + " " + this._asSentence(title) + + ref = authorsAndYear + " " + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note); } diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 static/scripts/packed/libs/bibtex.js --- a/static/scripts/packed/libs/bibtex.js +++ b/static/scripts/packed/libs/bibtex.js @@ -1,1 +1,1 @@ -function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var 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/g,"\u294F"],[/\\DownLeftRightVector /g,"\u2950"],[/\\LeftUpDownVector /g,"\u2951"],[/\\LeftVectorBar /g,"\u2952"],[/\\RightVectorBar /g,"\u2953"],[/\\RightUpVectorBar /g,"\u2954"],[/\\RightDownVectorBar /g,"\u2955"],[/\\DownLeftVectorBar /g,"\u2956"],[/\\DownRightVectorBar /g,"\u2957"],[/\\LeftUpVectorBar /g,"\u2958"],[/\\LeftDownVectorBar /g,"\u2959"],[/\\LeftTeeVector /g,"\u295A"],[/\\RightTeeVector /g,"\u295B"],[/\\RightUpTeeVector /g,"\u295C"],[/\\RightDownTeeVector /g,"\u295D"],[/\\DownLeftTeeVector /g,"\u295E"],[/\\DownRightTeeVector /g,"\u295F"],[/\\LeftUpTeeVector /g,"\u2960"],[/\\LeftDownTeeVector /g,"\u2961"],[/\\UpEquilibrium /g,"\u296E"],[/\\ReverseUpEquilibrium /g,"\u296F"],[/\\RoundImplies /g,"\u2970"],[/\\ElsevierGlyph\{E214\}/g,"\u297C"],[/\\ElsevierGlyph\{E215\}/g,"\u297D"],[/\\Elztfnc /g,"\u2980"],[/\\ElsevierGlyph\{3018\}/g,"\u2985"],[/\\Elroang /g,"\u2986"],[/\\ElsevierGlyph\{E291\}/g,"\u2994"],[/\\Elzddfnc /g,"\u2999"],[/\\Angle /g,"\u299C"],[/\\Elzlpargt /g,"\u29A0"],[/\\ElsevierGlyph\{E260\}/g,"\u29B5"],[/\\ElsevierGlyph\{E61B\}/g,"\u29B6"],[/\\ElzLap /g,"\u29CA"],[/\\Elzdefas /g,"\u29CB"],[/\\LeftTriangleBar /g,"\u29CF"],[/\\NotLeftTriangleBar /g,"\u29CF-00338"],[/\\RightTriangleBar /g,"\u29D0"],[/\\NotRightTriangleBar /g,"\u29D0-00338"],[/\\ElsevierGlyph\{E372\}/g,"\u29DC"],[/\\blacklozenge /g,"\u29EB"],[/\\RuleDelayed /g,"\u29F4"],[/\\Elxuplus /g,"\u2A04"],[/\\ElzThr /g,"\u2A05"],[/\\Elxsqcup /g,"\u2A06"],[/\\ElzInf /g,"\u2A07"],[/\\ElzSup /g,"\u2A08"],[/\\ElzCint /g,"\u2A0D"],[/\\clockoint /g,"\u2A0F"],[/\\ElsevierGlyph\{E395\}/g,"\u2A10"],[/\\sqrint /g,"\u2A16"],[/\\ElsevierGlyph\{E25A\}/g,"\u2A25"],[/\\ElsevierGlyph\{E25B\}/g,"\u2A2A"],[/\\ElsevierGlyph\{E25C\}/g,"\u2A2D"],[/\\ElsevierGlyph\{E25D\}/g,"\u2A2E"],[/\\ElzTimes /g,"\u2A2F"],[/\\ElsevierGlyph\{E25E\}/g,"\u2A34"],[/\\ElsevierGlyph\{E25E\}/g,"\u2A35"],[/\\ElsevierGlyph\{E259\}/g,"\u2A3C"],[/\\amalg /g,"\u2A3F"],[/\\ElzAnd /g,"\u2A53"],[/\\ElzOr /g,"\u2A54"],[/\\ElsevierGlyph\{E36E\}/g,"\u2A55"],[/\\ElOr /g,"\u2A56"],[/\\perspcorrespond /g,"\u2A5E"],[/\\Elzminhat /g,"\u2A5F"],[/\\ElsevierGlyph\{225A\}/g,"\u2A63"],[/\\stackrel\{*\}\{=\}/g,"\u2A6E"],[/\\Equal /g,"\u2A75"],[/\\leqslant /g,"\u2A7D"],[/\\nleqslant /g,"\u2A7D-00338"],[/\\geqslant /g,"\u2A7E"],[/\\ngeqslant /g,"\u2A7E-00338"],[/\\lessapprox /g,"\u2A85"],[/\\gtrapprox /g,"\u2A86"],[/\\lneq /g,"\u2A87"],[/\\gneq /g,"\u2A88"],[/\\lnapprox /g,"\u2A89"],[/\\gnapprox /g,"\u2A8A"],[/\\lesseqqgtr /g,"\u2A8B"],[/\\gtreqqless /g,"\u2A8C"],[/\\eqslantless /g,"\u2A95"],[/\\eqslantgtr /g,"\u2A96"],[/\\Pisymbol\{ppi020\}\{117\}/g,"\u2A9D"],[/\\Pisymbol\{ppi020\}\{105\}/g,"\u2A9E"],[/\\NestedLessLess /g,"\u2AA1"],[/\\NotNestedLessLess /g,"\u2AA1-00338"],[/\\NestedGreaterGreater /g,"\u2AA2"],[/\\NotNestedGreaterGreater /g,"\u2AA2-00338"],[/\\preceq /g,"\u2AAF"],[/\\not\\preceq /g,"\u2AAF-00338"],[/\\succeq /g,"\u2AB0"],[/\\not\\succeq /g,"\u2AB0-00338"],[/\\precneqq /g,"\u2AB5"],[/\\succneqq /g,"\u2AB6"],[/\\precapprox /g,"\u2AB7"],[/\\succapprox /g,"\u2AB8"],[/\\precnapprox /g,"\u2AB9"],[/\\succnapprox /g,"\u2ABA"],[/\\subseteqq /g,"\u2AC5"],[/\\nsubseteqq /g,"\u2AC5-00338"],[/\\supseteqq /g,"\u2AC6"],[/\\nsupseteqq/g,"\u2AC6-00338"],[/\\subsetneqq /g,"\u2ACB"],[/\\supsetneqq /g,"\u2ACC"],[/\\ElsevierGlyph\{E30D\}/g,"\u2AEB"],[/\\Elztdcol /g,"\u2AF6"],[/\\ElsevierGlyph\{300A\}/g,"\u300A"],[/\\ElsevierGlyph\{300B\}/g,"\u300B"],[/\\ElsevierGlyph\{3018\}/g,"\u3018"],[/\\ElsevierGlyph\{3019\}/g,"\u3019"],[/\\openbracketleft /g,"\u301A"],[/\\openbracketright /g,"\u301B"]];return this}if(typeof module!=="undefined"&&module.exports){module.exports=BibtexParser}; \ No newline at end of file +function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser construction."}this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5};this.DATA_={};this.CALLBACK_=c;this.CHAR_=0;this.LINE_=1;this.CHAR_IN_LINE_=0;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={};this.SKIPTILLEOL_=false;this.VALBRACES_=null;this.BRACETYPE_=null;this.BRACECOUNT_=0;this.STATE_=this.STATES_.ENTRY_OR_JUNK;this.ERRORS_=[];this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16,online:998,data:999};this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"};this.getErrors=function(){return this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for object.");this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;f=true;this.STATE_=this.STATES_.KV_KEY;this.PARSETMP_.Key="";this.DATA_.Fields={}}}}else{this.DATA_.EntryKey+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}break;case this.STATES_.KV_KEY:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(/[\-A-Za-z:]/.test(l)){this.PARSETMP_.Key+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{if(this.PARSETMP_.Key.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.EQUALS;f=true}}break;case this.STATES_.EQUALS:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no value.');this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(l=="="){this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.KV_VALUE;this.PARSETMP_.Value="";this.VALBRACES_={'"':[],"{":[]}}break;case this.STATES_.KV_VALUE:var k=this.VALBRACES_;var j=this.PARSETMP_.Value;var h=false;if(l=='"'||l=="{"||l=="}"||l==","){if(l==","){if(0===k['"'].length+k["{"].length){var g=this.PARSETMP_.Value.trim();if(g in this.MACROS_){this.PARSETMP_.Value=this.MACROS_[g]}else{this.error_("Reference to an undefined macro: "+g)}h=true}}if(l=='"'){if(0===k['"'].length+k["{"].length){k['"'].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false;break}if(k['"'].length==1&&k["{"].length==0&&(j.length==0||j[j.length-1]!="\\")){h=true}else{}}if(l=="{"){if(j.length==0||j[j.length-1]!="\\"){k["{"].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{}}if(l=="}"){if(0===k['"'].length+k["{"].length){var 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Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file +define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var k=this.model;var i=k.entryType();var l=k.fields();var g="";var o=this._asSentence((l.author?l.author:"")+(l.year?(" ("+l.year+")"):""))+" ";var n=l.title||"";var h=l.pages?("pp. "+l.pages):"";var p=l.address;if(i=="article"){var j=(l.volume?l.volume:"")+(l.number?(" ("+l.number+")"):"")+(h?", "+h:"");g=o+this._asSentence(n)+(l.journal?("In <em>"+l.journal+", "):"")+this._asSentence(j)+this._asSentence(l.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=o+this._asSentence(n)+(l.booktitle?("In <em>"+l.booktitle+", "):"")+(h?h:"")+(p?", "+p:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=o+this._asSentence(n)+(l.howpublished?l.howpublished+". ":"")+(l.note?l.note+".":"")}else{if(i=="techreport"){g=o+this._asSentence(n)+this._asSentence(l.institution)+this._asSentence(l.number)+this._asSentence(l.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=o+" "+this._formatBookInfo(l)}else{g=o+" "+this._asSentence(n)+this._asSentence(l.howpublished)+this._asSentence(l.note)}}}}}var m="";if(l.doi){m="http://dx.doi.org/"+l.doi;g+='[<a href="'+m+'">doi:'+l.doi+"</a>]"}var f=l.url||m;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0880211749b/ Changeset: a0880211749b Branch: next-stable User: saketkc Date: 2014-09-25 06:10:51+00:00 Summary: Update tool_list to reflect recent change in use of envirnoment variables tool_list.py now makese use of GALAXY_TEST_TOOL_CONF and exits throwing an appropriate error Affected #: 1 file diff -r 5296d69134bddeb11246c70347d83c6073da646f -r a0880211749b1f65c4fa78f9c121fa2234decc67 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -1,9 +1,15 @@ -import os,sys +import os +import sys #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml", "r"): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) +if not os.path.isfile(tool_conf_file): + sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) + sys.exit(1) + +for line in open(tool_conf_file, "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: https://bitbucket.org/galaxy/galaxy-central/commits/f3284eb7ec21/ Changeset: f3284eb7ec21 Branch: next-stable User: jmchilton Date: 2014-09-25 13:00:38+00:00 Summary: Fixes to tool_list.py for legacy configurations and modified tool confs. Now uses roughly the same order of precedence as Galaxy proper's config. Affected #: 1 file diff -r a0880211749b1f65c4fa78f9c121fa2234decc67 -r f3284eb7ec210d50a3e9f2c0d393cffcb24894da tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -4,8 +4,15 @@ #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) -if not os.path.isfile(tool_conf_file): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', None ) + +if tool_conf_file is None: + for possible_tool_file in [ 'config/tool_conf.xml', 'tool_conf.xml', 'config/tool_conf.xml.sample' ]: + tool_conf_file = possible_tool_file + if os.path.isfile( possible_tool_file ): + break + +if tool_conf_file is None or not os.path.isfile(tool_conf_file): sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) sys.exit(1) https://bitbucket.org/galaxy/galaxy-central/commits/1db1d66229db/ Changeset: 1db1d66229db User: jmchilton Date: 2014-09-25 13:03:21+00:00 Summary: Merge latest next-stable. Affected #: 1 file diff -r bcd98385d0af97c1dd5d4ba7944da49ff28158e1 -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -4,8 +4,15 @@ #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) -if not os.path.isfile(tool_conf_file): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', None ) + +if tool_conf_file is None: + for possible_tool_file in [ 'config/tool_conf.xml', 'tool_conf.xml', 'config/tool_conf.xml.sample' ]: + tool_conf_file = possible_tool_file + if os.path.isfile( possible_tool_file ): + break + +if tool_conf_file is None or not os.path.isfile(tool_conf_file): sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) sys.exit(1) 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: saketkc: Update tool_list to reflect recent change in use of envirnoment variables
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bcd98385d0af/ Changeset: bcd98385d0af User: saketkc Date: 2014-09-25 06:10:51+00:00 Summary: Update tool_list to reflect recent change in use of envirnoment variables tool_list.py now makese use of GALAXY_TEST_TOOL_CONF and exits throwing an appropriate error Affected #: 1 file diff -r a3d10d4db962d762d045bf3e46163508d3572e95 -r bcd98385d0af97c1dd5d4ba7944da49ff28158e1 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -1,9 +1,15 @@ -import os,sys +import os +import sys #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml", "r"): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) +if not os.path.isfile(tool_conf_file): + sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) + sys.exit(1) + +for line in open(tool_conf_file, "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Fix datatype mapping, provide data mapping through api
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3d10d4db962/ Changeset: a3d10d4db962 User: guerler Date: 2014-09-25 01:13:45+00:00 Summary: ToolForm: Fix datatype mapping, provide data mapping through api Affected #: 7 files diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 client/galaxy/scripts/mvc/tools/tools-datasets.js --- a/client/galaxy/scripts/mvc/tools/tools-datasets.js +++ b/client/galaxy/scripts/mvc/tools/tools-datasets.js @@ -1,38 +1,58 @@ -define([ 'mvc/history/history-contents' ], function( HISTORY_CONTENTS ){ +define([ 'mvc/history/history-contents', 'utils/utils' ], function( HistoryContents, Utils ){ return Backbone.Model.extend({ // initialize initialize: function(options) { // create history contents container - this.currHistoryContents = new HISTORY_CONTENTS.HistoryContents({}); + this.currHistoryContents = new HistoryContents.HistoryContents({}); // identify current history id this.currHistoryContents.historyId = options.history_id; - // make request + // prepare datatype structure + this.typedict = {}; + + // link this var self = this; - var xhr = this.currHistoryContents.fetchAllDetails() - .done( function(){ - // log request success - console.debug('tools-datasets::initialize() - Completed.'); + + // request datatypes + Utils.get(galaxy_config.root + 'api/datatypes/mapping', + // success + function(typedict) { + // backup datatype dictionary + self.typedict = typedict; - // callback - options.success && options.success(); - }) - .fail( function(){ + // make request + var xhr = self.currHistoryContents.fetchAllDetails() + .done( function(){ + // log request success + console.debug('tools-datasets::initialize() - Completed.'); + + // callback + options.success && options.success(); + }) + .fail( function(){ + // log request failure + console.debug('tools-datasets::initialize() - Ajax request for history datasets failed.'); + }); + }, + // error + function(response) { // log request failure - console.debug('tools-datasets::initialize() - Ajax request failed.'); - }); + console.debug('tools-datasets::initialize() - Ajax request for datatype dictionary failed.'); + } + ); }, /** Filters datasets by data type. */ filterType: function(options) { options = options || {}; + var self = this; return this.currHistoryContents.filter(function(content){ // match datatypes var found = false; for (var i in options.data_types) { - if (content.get('data_type').indexOf(options.data_types[i]) != -1) { + if (self._matchType(content.get('data_type'), options.data_types[i])) { found = true; break; } @@ -48,6 +68,26 @@ */ filter: function(filter_id) { return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) ); + }, + + /** Check if datatypes match + */ + _matchType: function(reference, target) { + // check if target class is available + var target_class = this.typedict.ext_to_class_name[target]; + if (!target_class) { + console.debug('tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.'); + return true; + } + + // check reference group + var reference_group = this.typedict.class_to_classes[reference]; + if (reference_group[target_class]) { + return true; + } + + // classes do not match + return false; } }); }); \ No newline at end of file diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 lib/galaxy/webapps/galaxy/api/datatypes.py --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/lib/galaxy/webapps/galaxy/api/datatypes.py @@ -5,6 +5,7 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController from galaxy.util import asbool +from galaxy.datatypes.data import Data import logging log = logging.getLogger( __name__ ) @@ -43,6 +44,37 @@ return { 'error': str( exception ) } @web.expose_api_anonymous + def mapping( self, trans ): + ''' + GET /api/datatypes/mapping + Return a dictionary of class to class mappings. + ''' + try: + ext_to_class_name = dict() + classes = [] + for k, v in trans.app.datatypes_registry.datatypes_by_extension.iteritems(): + c = v.__class__ + ext_to_class_name[k] = c.__module__ + "." + c.__name__ + classes.append( c ) + class_to_classes = dict() + + def visit_bases( types, cls ): + for base in cls.__bases__: + if issubclass( base, Data ): + types.add( base.__module__ + "." + base.__name__ ) + visit_bases( types, base ) + for c in classes: + n = c.__module__ + "." + c.__name__ + types = set( [ n ] ) + visit_bases( types, c ) + class_to_classes[ n ] = dict( ( t, True ) for t in types ) + return dict( ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes ) + except Exception, exception: + log.error( 'could not get datatype mapping: %s', str( exception ), exc_info=True ) + trans.response.status = 500 + return { 'error': str( exception ) } + + @web.expose_api_anonymous def sniffers( self, trans, **kwd ): ''' GET /api/datatypes/sniffers diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -192,7 +192,7 @@ webapp.mapper.resource( 'datatype', 'datatypes', path_prefix='/api', - collection={ 'sniffers': 'GET' }, + collection={ 'sniffers': 'GET', 'mapping' : 'GET' }, parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1179,28 +1179,6 @@ use_panels=True, myexperiment_target_url=myexperiment_target_url ) - @web.json - def get_datatypes( self, trans ): - ext_to_class_name = dict() - classes = [] - for k, v in trans.app.datatypes_registry.datatypes_by_extension.iteritems(): - c = v.__class__ - ext_to_class_name[k] = c.__module__ + "." + c.__name__ - classes.append( c ) - class_to_classes = dict() - - def visit_bases( types, cls ): - for base in cls.__bases__: - if issubclass( base, Data ): - types.add( base.__module__ + "." + base.__name__ ) - visit_bases( types, base ) - for c in classes: - n = c.__module__ + "." + c.__name__ - types = set( [ n ] ) - visit_bases( types, c ) - class_to_classes[ n ] = dict( ( t, True ) for t in types ) - return dict( ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes ) - @web.expose def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None ): user = trans.get_user() diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 static/scripts/mvc/tools/tools-datasets.js --- a/static/scripts/mvc/tools/tools-datasets.js +++ b/static/scripts/mvc/tools/tools-datasets.js @@ -1,38 +1,58 @@ -define([ 'mvc/history/history-contents' ], function( HISTORY_CONTENTS ){ +define([ 'mvc/history/history-contents', 'utils/utils' ], function( HistoryContents, Utils ){ return Backbone.Model.extend({ // initialize initialize: function(options) { // create history contents container - this.currHistoryContents = new HISTORY_CONTENTS.HistoryContents({}); + this.currHistoryContents = new HistoryContents.HistoryContents({}); // identify current history id this.currHistoryContents.historyId = options.history_id; - // make request + // prepare datatype structure + this.typedict = {}; + + // link this var self = this; - var xhr = this.currHistoryContents.fetchAllDetails() - .done( function(){ - // log request success - console.debug('tools-datasets::initialize() - Completed.'); + + // request datatypes + Utils.get(galaxy_config.root + 'api/datatypes/mapping', + // success + function(typedict) { + // backup datatype dictionary + self.typedict = typedict; - // callback - options.success && options.success(); - }) - .fail( function(){ + // make request + var xhr = self.currHistoryContents.fetchAllDetails() + .done( function(){ + // log request success + console.debug('tools-datasets::initialize() - Completed.'); + + // callback + options.success && options.success(); + }) + .fail( function(){ + // log request failure + console.debug('tools-datasets::initialize() - Ajax request for history datasets failed.'); + }); + }, + // error + function(response) { // log request failure - console.debug('tools-datasets::initialize() - Ajax request failed.'); - }); + console.debug('tools-datasets::initialize() - Ajax request for datatype dictionary failed.'); + } + ); }, /** Filters datasets by data type. */ filterType: function(options) { options = options || {}; + var self = this; return this.currHistoryContents.filter(function(content){ // match datatypes var found = false; for (var i in options.data_types) { - if (content.get('data_type').indexOf(options.data_types[i]) != -1) { + if (self._matchType(content.get('data_type'), options.data_types[i])) { found = true; break; } @@ -48,6 +68,26 @@ */ filter: function(filter_id) { return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) ); + }, + + /** Check if datatypes match + */ + _matchType: function(reference, target) { + // check if target class is available + var target_class = this.typedict.ext_to_class_name[target]; + if (!target_class) { + console.debug('tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.'); + return true; + } + + // check reference group + var reference_group = this.typedict.class_to_classes[reference]; + if (reference_group[target_class]) { + return true; + } + + // classes do not match + return false; } }); }); \ No newline at end of file diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 static/scripts/packed/mvc/tools/tools-datasets.js --- a/static/scripts/packed/mvc/tools/tools-datasets.js +++ b/static/scripts/packed/mvc/tools/tools-datasets.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-contents"],function(a){return Backbone.Model.extend({initialize:function(c){this.currHistoryContents=new a.HistoryContents({});this.currHistoryContents.historyId=c.history_id;var b=this;var d=this.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request failed.")})},filterType:function(b){b=b||{};return this.currHistoryContents.filter(function(d){var e=false;for(var c in b.data_types){if(d.get("data_type").indexOf(b.data_types[c])!=-1){e=true;break}}return(d.get("history_content_type")===b.content_type||!b.content_type)&&(e||!b.data_types)&&!d.get("deleted")})},filter:function(b){return _.first(this.currHistoryContents.filter(function(c){return c.get("id")===b}))}})}); \ No newline at end of file +define(["mvc/history/history-contents","utils/utils"],function(b,a){return Backbone.Model.extend({initialize:function(d){this.currHistoryContents=new b.HistoryContents({});this.currHistoryContents.historyId=d.history_id;this.typedict={};var c=this;a.get(galaxy_config.root+"api/datatypes/mapping",function(e){c.typedict=e;var f=c.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");d.success&&d.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request for history datasets failed.")})},function(e){console.debug("tools-datasets::initialize() - Ajax request for datatype dictionary failed.")})},filterType:function(d){d=d||{};var c=this;return this.currHistoryContents.filter(function(f){var g=false;for(var e in d.data_types){if(c._matchType(f.get("data_type"),d.data_types[e])){g=true;break}}return(f.get("history_content_type")===d.content_type||!d.content_type)&&(g||!d.data_types)&&!f.get("deleted")})},filter:function(c){return _.first(this.currHistoryContents.filter(function(d){return d.get("id")===c}))},_matchType:function(c,f){var d=this.typedict.ext_to_class_name[f];if(!d){console.debug("tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var e=this.typedict.class_to_classes[c];if(e[d]){return true}return false}})}); \ No newline at end of file diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -41,7 +41,7 @@ // URLs used by galaxy.workflows.js var tool_search_url = "${h.url_for( controller='root', action='tool_search' )}", - get_datatypes_url = "${h.url_for( controller='workflow', action='get_datatypes' )}", + get_datatypes_url = "${h.url_for( '/api/datatypes/mapping' )}", load_workflow_url = "${h.url_for( controller='workflow', action='load_workflow' )}", run_workflow_url = "${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(stored.id))}", rename_async_url = "${h.url_for( controller='workflow', action='rename_async', id=trans.security.encode_id(stored.id) )}", Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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