[galaxy-commits] commit/galaxy-central: 3 new changesets

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 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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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":""}});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/82f8d68414f5/ Changeset: 82f8d68414f5 User: jmchilton Date: 2014-09-25 17:49:29+00:00 Summary: Merge latest next-stable. 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 e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser 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/g,"\u27F5"],[/\\longrightarrow /g,"\u27F6"],[/\\longleftrightarrow /g,"\u27F7"],[/\\Longleftarrow /g,"\u27F8"],[/\\Longrightarrow /g,"\u27F9"],[/\\Longleftrightarrow /g,"\u27FA"],[/\\longmapsto /g,"\u27FC"],[/\\sim\\joinrel\\leadsto/g,"\u27FF"],[/\\ElsevierGlyph\{E212\}/g,"\u2905"],[/\\UpArrowBar /g,"\u2912"],[/\\DownArrowBar /g,"\u2913"],[/\\ElsevierGlyph\{E20C\}/g,"\u2923"],[/\\ElsevierGlyph\{E20D\}/g,"\u2924"],[/\\ElsevierGlyph\{E20B\}/g,"\u2925"],[/\\ElsevierGlyph\{E20A\}/g,"\u2926"],[/\\ElsevierGlyph\{E211\}/g,"\u2927"],[/\\ElsevierGlyph\{E20E\}/g,"\u2928"],[/\\ElsevierGlyph\{E20F\}/g,"\u2929"],[/\\ElsevierGlyph\{E210\}/g,"\u292A"],[/\\ElsevierGlyph\{E21C\}/g,"\u2933"],[/\\ElsevierGlyph\{E21D\}/g,"\u2933-00338"],[/\\ElsevierGlyph\{E21A\}/g,"\u2936"],[/\\ElsevierGlyph\{E219\}/g,"\u2937"],[/\\Elolarr /g,"\u2940"],[/\\Elorarr /g,"\u2941"],[/\\ElzRlarr /g,"\u2942"],[/\\ElzrLarr /g,"\u2944"],[/\\Elzrarrx /g,"\u2947"],[/\\LeftRightVector /g,"\u294E"],[/\\RightUpDownVector /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 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