4 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d7bf7ad5c578/ Changeset: d7bf7ad5c578 Branch: next-stable User: jmchilton Date: 2014-08-07 15:35:43 Summary: Bugfix: Deal with BibTeX fields in a case insensitive fashion. Would have thought the parser would have done this already - oh well. Affected #: 2 files
diff -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 -r d7bf7ad5c578e7d27a4a94c559ef336b2eb3eab0 static/scripts/mvc/citation/citation-model.js --- a/static/scripts/mvc/citation/citation-model.js +++ b/static/scripts/mvc/citation/citation-model.js @@ -18,12 +18,19 @@ var bibtex = this.attributes.content; var entry = new BibtexParser(bibtex).entries[0]; this.entry = entry; + this._fields = {}; + var rawFields = entry.Fields; + for(key in rawFields) { + var value = rawFields[ key ]; + var lowerKey = key.toLowerCase(); + this._fields[ lowerKey ] = value; + } }, entryType: function() { return this.entry.EntryType; }, fields: function() { - return this.entry.Fields; + return this._fields; } } );
diff -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 -r d7bf7ad5c578e7d27a4a94c559ef336b2eb3eab0 static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -55,9 +55,9 @@ this._asSentence(fields.note); } var doiUrl = ""; - if( fields.DOI ) { - doiUrl = 'http://dx.doi.org/' + fields.DOI; - ref += '[<a href="' + doiUrl + '">doi:' + fields.DOI + "</a>]"; + if( fields.doi ) { + doiUrl = 'http://dx.doi.org/' + fields.doi; + ref += '[<a href="' + doiUrl + '">doi:' + fields.doi + "</a>]"; } var url = fields.url || doiUrl; if( url ) {
https://bitbucket.org/galaxy/galaxy-central/commits/ee8efcfd787f/ Changeset: ee8efcfd787f Branch: next-stable User: jmchilton Date: 2014-08-07 15:35:43 Summary: Relax BibTeX parsing and accept header to handle figshare DOIs. For instance 10.6084/m9.figshare.979190 reported by Michael Crusoe. JavaScript parser didn't like @data entries produced by figshare and when requesting the entry dx.doi.org returns a 403 response for type accept type text/bibliography, also allowing application/x-bibtex fixes this. Interestingly dx.doi.org throws 500 exceptions if application/x-bibtex is the only acceptable type or appears first for some other DOIs. Affected #: 2 files
diff -r d7bf7ad5c578e7d27a4a94c559ef336b2eb3eab0 -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e lib/galaxy/managers/citations.py --- a/lib/galaxy/managers/citations.py +++ b/lib/galaxy/managers/citations.py @@ -49,7 +49,7 @@
def _raw_get_bibtex( self, doi ): dx_url = "http://dx.doi.org/" + doi - headers = {'Accept': "text/bibliography; style=bibtex" } + headers = {'Accept': 'text/bibliography; style=bibtex, application/x-bibtex'} req = urllib2.Request(dx_url, data="", headers=headers) response = urllib2.urlopen(req) bibtex = response.read()
diff -r d7bf7ad5c578e7d27a4a94c559ef336b2eb3eab0 -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e 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 + ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { 'jan' : 'January',
https://bitbucket.org/galaxy/galaxy-central/commits/990bc0688199/ Changeset: 990bc0688199 Branch: next-stable User: jmchilton Date: 2014-08-07 15:36:18 Summary: Pack scripts. Affected #: 3 files
diff -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e -r 990bc0688199410ab08d5e8a418770b516c6f4e2 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};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 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/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
diff -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e -r 990bc0688199410ab08d5e8a418770b516c6f4e2 static/scripts/packed/mvc/citation/citation-model.js --- a/static/scripts/packed/mvc/citation/citation-model.js +++ b/static/scripts/packed/mvc/citation/citation-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var h=new BibtexParser(g).entries[0];this.entry=h},entryType:function(){return this.entry.EntryType},fields:function(){return this.entry.Fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",partial:true,model:f,});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:false,});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var i=new BibtexParser(g).entries[0];this.entry=i;this._fields={};var k=i.Fields;for(key in k){var j=k[key];var h=key.toLowerCase();this._fields[h]=j}},entryType:function(){return this.entry.EntryType},fields:function(){return this._fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",partial:true,model:f,});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:false,});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file
diff -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e -r 990bc0688199410ab08d5e8a418770b516c6f4e2 static/scripts/packed/mvc/citation/citation-view.js --- a/static/scripts/packed/mvc/citation/citation-view.js +++ b/static/scripts/packed/mvc/citation/citation-view.js @@ -1,1 +1,1 @@ -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.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/%22+k.DOI;g+=%27%5B<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".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.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file +define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.doi){l="http://dx.doi.org/%22+k.doi;g+=%27%5B<a href="'+l+'">doi:'+k.doi+"</a>]"}var f=k.url||l;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
https://bitbucket.org/galaxy/galaxy-central/commits/103697ebdd33/ Changeset: 103697ebdd33 User: jmchilton Date: 2014-08-07 15:36:41 Summary: Merge next-stable. Affected #: 7 files
diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c lib/galaxy/managers/citations.py --- a/lib/galaxy/managers/citations.py +++ b/lib/galaxy/managers/citations.py @@ -49,7 +49,7 @@
def _raw_get_bibtex( self, doi ): dx_url = "http://dx.doi.org/" + doi - headers = {'Accept': "text/bibliography; style=bibtex" } + headers = {'Accept': 'text/bibliography; style=bibtex, application/x-bibtex'} req = urllib2.Request(dx_url, data="", headers=headers) response = urllib2.urlopen(req) bibtex = response.read()
diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c 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 + ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { 'jan' : 'January',
diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c static/scripts/mvc/citation/citation-model.js --- a/static/scripts/mvc/citation/citation-model.js +++ b/static/scripts/mvc/citation/citation-model.js @@ -18,12 +18,19 @@ var bibtex = this.attributes.content; var entry = new BibtexParser(bibtex).entries[0]; this.entry = entry; + this._fields = {}; + var rawFields = entry.Fields; + for(key in rawFields) { + var value = rawFields[ key ]; + var lowerKey = key.toLowerCase(); + this._fields[ lowerKey ] = value; + } }, entryType: function() { return this.entry.EntryType; }, fields: function() { - return this.entry.Fields; + return this._fields; } } );
diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -55,9 +55,9 @@ this._asSentence(fields.note); } var doiUrl = ""; - if( fields.DOI ) { - doiUrl = 'http://dx.doi.org/' + fields.DOI; - ref += '[<a href="' + doiUrl + '">doi:' + fields.DOI + "</a>]"; + if( fields.doi ) { + doiUrl = 'http://dx.doi.org/' + fields.doi; + ref += '[<a href="' + doiUrl + '">doi:' + fields.doi + "</a>]"; } var url = fields.url || doiUrl; if( url ) {
diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c 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};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 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diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c static/scripts/packed/mvc/citation/citation-model.js --- a/static/scripts/packed/mvc/citation/citation-model.js +++ b/static/scripts/packed/mvc/citation/citation-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var h=new BibtexParser(g).entries[0];this.entry=h},entryType:function(){return this.entry.EntryType},fields:function(){return this.entry.Fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",partial:true,model:f,});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:false,});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var i=new BibtexParser(g).entries[0];this.entry=i;this._fields={};var k=i.Fields;for(key in k){var j=k[key];var h=key.toLowerCase();this._fields[h]=j}},entryType:function(){return this.entry.EntryType},fields:function(){return this._fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",partial:true,model:f,});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:false,});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file
diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c static/scripts/packed/mvc/citation/citation-view.js --- a/static/scripts/packed/mvc/citation/citation-view.js +++ b/static/scripts/packed/mvc/citation/citation-view.js @@ -1,1 +1,1 @@ -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 j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/%22+k.DOI;g+=%27%5B<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;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 +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.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.doi){l="http://dx.doi.org/%22+k.doi;g+=%27%5B<a href="'+l+'">doi:'+k.doi+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".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
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