lens2.js

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editor":"Associate Editor","series-editor":"Series Editor",contributor:"Contributor",chairman:"Chairman","monographs-editor":"Monographs Editor","contrib-author":"Contributing Author",organizer:"Organizer",chair:"Chair",discussant:"Discussant",presenter:"Presenter","guest-issue-editor":"Guest Issue Editor",participant:"Participant",translator:"Translator","section-editor":"Section Editor","section-author":"Section Author","chapter-author":"Chapter Author"},this.isAnnotation=function(t){return void 0!==this._annotationTypes[t]},this.isParagraphish=function(t){for(var e=0;e<t.childNodes.length;e++){var n=t.childNodes[e];if(n.nodeType!==Node.TEXT_NODE&&!this.isAnnotation(n.tagName.toLowerCase()))return!1}return!0},this.test=function(t,e){return!0},this.getName=function(t){if(!t)return"N/A";var e=[],n=t.querySelector("surname"),r=t.querySelector("given-names"),i=t.querySelector("suffix");return r&&e.push(r.textContent),n&&e.push(n.textContent),i?[e.join(" "),i.textContent].join(", "):e.join(" ")},this.toHtml=function(t){if(!t)return"";var e=document.createElement("DIV");return e.appendChild(t.cloneNode(!0)),e.innerHTML},this.mmlToHtmlString=function(t){var e=this.toHtml(t);return e=e.replace(/<(\/)?mml:([^>]+)>/g,"<$1$2>")},this.selectDirectChildren=function(t,e){for(var n=[],r=t.querySelectorAll(e),i=0;i<r.length;i++){var o=r[i];o.parentElement===t&&n.push(o)}return n},this.import=function(t){var e;b.isString(t)?e=(new DOMParser).parseFromString(t,"text/xml"):e=t;this.sanitizeXML(e);var n=this.createDocument();window.doc=n;var r=this.createState(e,n);return this.document(r,e)},this.sanitizeXML=function(t){},this.createState=function(t,e){return new i.State(this,t,e)},this.createDocument=function(){return new r},this.show=function(e,t){b.each(t,function(t){this.showNode(e,t)},this)},this.extractDate=function(t){if(!t)return null;var e=t.querySelector("year"),n=t.querySelector("month"),r=t.querySelector("day"),i=null!==e?[e.textContent]:[];return n&&i.push(n.textContent),r&&i.push(r.textContent),i.join("-")},this.extractURLSuffix=function(t){return t=t.replace("https://doi.org/","")},this.extractPublicationInfo=function(t,e){for(var n=t.doc,r=e.querySelector("article-meta"),i=r.querySelector("pub-date"),o=r.querySelectorAll("history date"),s=e.querySelector("journal-title"),a=e.querySelector("article-id[pub-id-type=doi]"),c=e.querySelector("related-article"),u=this.extractArticleInfo(t,e),l={id:"publication_info",type:"publication_info",published_on:this.extractDate(i),journal:s?s.textContent:"",related_article:c?c.getAttribute("xlink:href"):"",doi:a?this.extractURLSuffix(a.textContent):"",article_info:u.id,article_type:"",keywords:[],links:[],subjects:[],supplements:[],history:[],research_organisms:[],provider:""},p=0;p<o.length;p++){var h=o[p],d={type:h.getAttribute("date-type"),date:this.extractDate(h)};l.history.push(d)}n.create(l),n.show("info",l.id,0),this.enhancePublicationInfo(t,l)},this.extractArticleInfo=function(t,e){var n={id:"articleinfo",type:"paragraph"},r=t.doc,i=[];return i=(i=(i=(i=(i=(i=i.concat(this.extractEditor(t,e))).concat(this.extractDatasets(t,e))).concat(this.extractCustomMetaGroup(t,e))).concat(this.extractAcknowledgements(t,e))).concat(this.extractCopyrightAndLicense(t,e))).concat(this.extractNotes(t,e)),n.children=i,r.create(n),n},this.extractEditor=function(t,e){var n=[],r=t.doc,i=e.querySelector("contrib[contrib-type=editor]");if(i){var o=[],s=this.getName(i.querySelector("name"));s&&o.push(s);var a=i.querySelector("institution");a&&o.push(a.textContent);var c=i.querySelector("country");c&&o.push(c.textContent);var u={type:"heading",id:t.nextId("heading"),level:3,content:"Reviewing Editor"};r.create(u),n.push(u.id);var l={type:"text",id:t.nextId("text"),content:o.join(", ")};r.create(l),n.push(l.id)}return n},this.extractDatasets=function(t,e){for(var n=[],r=t.doc,i=e.querySelectorAll("sec"),o=0;o<i.length;o++){var s=i[o];if("datasets"===s.getAttribute("sec-type")){var a={type:"heading",id:t.nextId("heading"),level:3,content:"Major Datasets"};r.create(a),n.push(a.id);for(var c=this.datasets(t,f.dom.getChildren(s)),u=0;u<c.length;u++)c[u]&&n.push(c[u])}}return n};var n=function(t,e){return e?t.split(" ").map(function(t){return n(t)}).join(" "):t.charAt(0).toUpperCase()+t.slice(1)};this.capitalized=function(t,e){return n(t,e)},this.extractAcknowledgements=function(i,t){var o=[],s=i.doc,e=t.querySelectorAll("ack");return e&&0<e.length&&b.each(e,function(t){var e=t.querySelector("title"),n={type:"heading",id:i.nextId("heading"),level:3,content:e?this.capitalized(e.textContent.toLowerCase(),"all"):"Acknowledgements"};s.create(n),o.push(n.id);var r=this.bodyNodes(i,f.dom.getChildren(t),{ignore:["title"]});b.each(r,function(t){o.push(t.id)})},this),o},this.extractNotes=function(){return[]},this.__ignoreCustomMetaNames=[],this.extractCustomMetaGroup=function(t,e){var n=[],r=t.doc,i=e.querySelectorAll("article-meta-group custom-meta");if(0===i.length)return n;for(var o=0;o<i.length;o++){var s=i[o],a=s.querySelector("meta-name"),c=s.querySelector("meta-value");if(!b.include(this.__ignoreCustomMetaNames,a.textContent)){var u={type:"heading",id:t.nextId("heading"),level:3,content:""};u.content=this.annotatedText(t,a,[u.id,"content"]),r.create(u);var l=this.paragraphGroup(t,c);n.push(u.id),n=n.concat(b.pluck(l,"id"))}}return n},this.extractCopyrightAndLicense=function(t,e){var n=[],r=t.doc,i=e.querySelector("permissions");if(i){var o,s={type:"heading",id:t.nextId("heading"),level:3,content:"Copyright & License"};r.create(s),n.push(s.id);var a,c=i.querySelector("copyright-statement");if(c&&(o=this.paragraphGroup(t,c))&&o.length&&(n=n.concat(b.map(o,function(t){return t.id})),"."!==c.textContent.trim().slice(-1))){var u=b.last(b.last(o).children);r.nodes[u].content+=". "}var l=i.querySelectorAll("license");for(a=0;a<l.length;a++)if((1==l[a].length||"en"==l[a].getAttribute("xml:lang"))&&l[a])for(var p=l[a].firstElementChild;p;p=p.nextElementSibling){var h=f.dom.getNodeType(p);"p"!==h&&"license-p"!==h||(o=this.paragraphGroup(t,p))&&o.length&&(n=n.concat(b.pluck(o,"id")))}}return n},this.extractCover=function(o,t){var s=o.doc,e=s.get("document"),n=t.querySelector("article-meta"),r=this._abstract(o,n),a={id:"cover",type:"cover",title:e.title,authors:[],abstract:void 0!==r?r.id:""},c=!1;b.each(e.authors,function(t){s.get(t).contributor_type.toLowerCase()==="Translator".toLowerCase()&&(c=!0)},this),b.each(e.authors,function(t){var e=s.get(t),n=e.name;!0===c&&(n+="("+e.contributor_type+")");var r={id:"text_"+t+"_reference",type:"text",content:n};s.create(r),a.authors.push(r.id);var i={id:o.nextId("contributor_reference"),type:"contributor_reference",path:["text_"+t+"_reference","content"],range:[0,n.length],target:t};s.create(i)},this),this.enhanceCover(o,a,t),s.create(a),s.show("content",a.id,0)},this.contribGroup=function(t,e){var n,r=[],i=e.querySelectorAll("contrib");for(n=0;n<i.length;n++){var o=this.contributor(t,i[n]);r.push(o)}var s=t.doc,a=e.querySelector("on-behalf-of");return a&&(s.on_behalf_of=a.textContent.trim()),r},this.affiliation=function(t,e){var n=t.doc,r=e.querySelector("institution"),i=e.querySelector("country"),o=e.querySelector("label"),s=e.querySelector("addr-line named-content[content-type=department]"),a=e.querySelector("addr-line named-content[content-type=city]"),c={id:t.nextId("affiliation"),type:"affiliation",source_id:e.getAttribute("id"),label:o?o.textContent:null,department:s?s.textContent:null,city:a?a.textContent:null,institution:r?r.textContent:null,country:i?i.textContent:null};n.create(c)},this.contributor=function(i,t){var e=i.doc,n=i.nextId("contributor"),o={id:n,source_id:t.getAttribute("id"),type:"contributor",name:"",affiliations:[],fundings:[],bio:[],image:"",deceased:!1,emails:[],contribution:"",members:[]},r=t.getAttribute("contrib-type");o.contributor_type=this._contribTypeMapping[r];var s=t.querySelector("role");s&&(o.role=s.textContent);var a=t.querySelector("bio");a&&b.each(f.dom.getChildren(a),function(t){var e=t.querySelector("graphic");if(e){var n=e.getAttribute("xlink:href");o.image=n}else{var r=this.paragraphGroup(i,t);0<r.length&&(o.bio=[r[0].id])}},this),"yes"===t.getAttribute("deceased")&&(o.deceased=!0);var c=t.querySelector("uri[content-type=orcid]");c&&(o.orcid=c.getAttribute("xlink:href"));var u=t.querySelector("name");if(u)o.name=this.getName(u);else{var l=t.querySelector("collab");o.name=l?l.textContent:"N/A"}return this.extractContributorProperties(i,t,o),0===o.affiliations.length&&(o.affiliations=i.affiliations),1<o.competing_interests.length&&(o.competing_interests=b.filter(o.competing_interests,function(t){return t.indexOf("no competing")<0})),"author"===t.getAttribute("contrib-type")&&e.nodes.document.authors.push(n),"editor"===t.getAttribute("contrib-type")&&e.nodes.document.authors.push(n),"translator"===t.getAttribute("contrib-type")&&e.nodes.document.authors.push(n),"section-editor"===t.getAttribute("contrib-type")&&e.nodes.document.authors.push(n),"section-author"===t.getAttribute("contrib-type")&&e.nodes.document.authors.push(n),"chapter-author"===t.getAttribute("contrib-type")&&e.nodes.document.authors.push(n),e.create(o),e.show("info",o.id),o},this._getEqualContribs=function(t,n,e){var r=[],i=t.xmlDoc.querySelectorAll("xref[rid="+e+"]");return b.each(i,function(t){var e=t.parentNode;e!==n&&r.push(this.getName(e.querySelector("name")))},this),r},this.extractContributorProperties=function(d,f,g){var y=d.doc,m=[],v=[],t=f.querySelectorAll("xref");b.each(t,function(t){if("aff"===t.getAttribute("ref-type")){var e=t.getAttribute("rid"),n=y.getNodeBySourceId(e);n&&(g.affiliations.push(n.id),d.used[e]=!0)}else if("other"===t.getAttribute("ref-type")){console.log("FIXME: please add documentation about using 'other' as indicator for extracting an awardGroup.");var r=d.xmlDoc.getElementById(t.getAttribute("rid"));if(!r)return;var i=r.querySelector("funding-source");if(!i)return;var o=r.querySelector("award-id");o=o?", "+o.textContent:"";var s=i.childNodes[0].textContent;g.fundings.push([s,o].join(""))}else if("corresp"===t.getAttribute("ref-type")){var a=t.getAttribute("rid"),c=d.xmlDoc.getElementById(a);if(!c)return;var u=c.querySelector("email");if(!u)return;g.emails.push(u.textContent)}else if("fn"===t.getAttribute("ref-type")){var l=t.getAttribute("rid"),p=d.xmlDoc.getElementById(l),h=!0;if(p){switch(p.getAttribute("fn-type")){case"con":g.contribution=p.textContent;break;case"conflict":v.push(p.textContent.trim());break;case"present-address":g.present_address=p.querySelector("p").textContent;break;case"equal":console.log("FIXME: isn't fnElem.getAttribute(id) === fnId?"),m=this._getEqualContribs(d,f,p.getAttribute("id"));break;case"other":console.log("FIXME: isn't fnElem.getAttribute(id) === fnId?"),0<=p.getAttribute("id").indexOf("equal-contrib")?m=this._getEqualContribs(d,f,p.getAttribute("id")):h=!1;break;default:h=!1}h&&(d.used[l]=!0)}}else console.log("Skipping contrib's xref",t.textContent)},this),1<v.length&&(v=b.filter(v,function(t){return t.indexOf("no competing")<0})),g.competing_interests=v;var e=f.querySelector("xref[ref-type=other]");if(e){var n=e.getAttribute("rid"),r=d.xmlDoc.querySelectorAll("#"+n+" contrib");g.members=b.map(r,function(t){return this.getName(t.querySelector("name"))},this)}g.equal_contrib=m,g.competing_interests=v},this.document=function(t,e){var n=t.doc,r=e.querySelector("article");if(!r)throw new s("Expected to find an 'article' element.");return this.article(t,r),this.postProcess(t),b.each(n.containers,function(t){t.rebuild()}),n},this.postProcess=function(t){this.postProcessAnnotations(t)},this.postProcessAnnotations=function(t){for(var e=0;e<t.annotations.length;e++){var n=t.annotations[e];if(n.target){var r=t.doc.getNodeBySourceId(n.target);r&&(n.target=r.id)}t.doc.create(t.annotations[e])}},this.article=function(t,e){var n=t.doc,r=e.querySelector("article-id");n.id=r?r.textContent:f.uuid(),this.extractDefinitions(t,e),this.extractAffilitations(t,e),this.extractContributors(t,e),this.extractCitations(t,e),this.extractFootnotes(t,e),this.extractCover(t,e),this.extractArticleMeta(t,e),this.extractPublicationInfo(t,e);var i=e.querySelector("body");i&&this.body(t,i),this.extractFigures(t,e),this.enhanceArticle(t,e)},this.extractDefinitions=function(i){var t=i.xmlDoc.querySelectorAll("def-item");b.each(t,function(t){var e=t.querySelector("term"),n=t.querySelector("def"),r={id:n.id||n.getAttribute("hwp:id")||i.nextId("definition"),type:"definition",title:e.textContent,description:n.textContent};i.doc.create(r),i.doc.show("definitions",r.id)})},this.extractArticleMeta=function(t,e){var n=e.querySelector("article-meta");if(!n)throw new s("Expected element: 'article-meta'");var r=n.querySelectorAll("article-id");this.articleIds(t,r);var i=n.querySelector("title-group");i&&this.titleGroup(t,i);var o=n.querySelectorAll("pub-date");this.pubDates(t,o)},this.extractAffilitations=function(t,e){for(var n=e.querySelectorAll("aff"),r=0;r<n.length;r++)this.affiliation(t,n[r])},this.extractContributors=function(t,e){var n=e.querySelector("contrib-group");n&&this.contribGroup(t,n)},this.extractFigures=function(t,e){for(var n=e.querySelector("body").querySelectorAll("fig, table-wrap, supplementary-material, media[mimetype=video]"),r=[],i=0;i<n.length;i++){var o=n[i];if(!o._converted){var s=f.dom.getNodeType(o),a=null;"fig"===s?a=this.figure(t,o):"table-wrap"===s||("media"===s?a=this.video(t,o):"supplementary-material"===s&&(a=this.supplement(t,o))),a&&r.push(a)}}this.show(t,r)},this.extractCitations=function(t,e){var n=e.querySelector("ref-list");n&&this.refList(t,n)},this.extractFootnotes=function(t,e){var n=e.querySelector("fn-group");n&&this.fnList(t,n)},this.articleIds=function(t,e){var n=t.doc;0<e.length?n.id=e[0].textContent:n.id=f.uuid()},this.titleGroup=function(t,e){var n=t.doc,r=e.querySelector("article-title");r&&(n.title=this.annotatedText(t,r,["document","title"],{ignore:["xref"]}))},this.pubDates=function(t,e){var n=t.doc;if(0<e.length){var r=this.pubDate(t,e[0]);n.created_at=r.date}},this.pubDate=function(t,e){var r=-1,i=-1,o=-1;return b.each(f.dom.getChildren(e),function(t){var e=f.dom.getNodeType(t),n=t.textContent;"day"===e?r=parseInt(n,10):"month"===e?i=parseInt(n,10):"year"===e&&(o=parseInt(n,10))},this),{date:new Date(o,i,r)}},this.abstracts=function(e,t){var n=t.querySelectorAll("abstract");b.each(n,function(t){this.abstract(e,t)},this)},this._abstract=function(n,t){var e=t.querySelector("title"),r=n.doc,i={id:n.nextId("abstract"),type:"abstract",label:"",title:"",children:[]};if(null!==e&&0<e.textContent.length){for(var o=new f.dom.ChildNodeIterator(e);o.hasNext();){var s=o.next(),a=f.dom.getNodeType(s);if("text"===a||this.isAnnotation(a))var c={id:n.nextId("text"),type:"text",content:null}}n.stack.push({path:[c.id,"content"]});var u=this._annotatedText(n,o.back(),{offset:0,breakOnUnknown:!0});0<u.length&&(c.content=u,r.create(c)),i.title=c.id}var l=[],p=t.querySelectorAll("p");return b.each(p,function(t){var e=this.paragraph(n,t);e&&l.push(e.id)},this),0<p.length&&(i.children=l,r.create(i)),i},this.body=function(t,e){var n=t.doc,r={id:t.nextId("heading"),type:"heading",level:1,content:""};n.create(r);var i=[r].concat(this.bodyNodes(t,f.dom.getChildren(e)));0<i.length&&this.show(t,i)},this._ignoredBodyNodes={fig:!0,table:!0,speaker:!0},this._bodyNodes={},this.bodyNodes=function(t,e,n){for(var r,i=[],o=0;o<e.length;o++){var s=e[o],a=f.dom.getNodeType(s);if(this._bodyNodes[a]){var c=this._bodyNodes[a].call(this,t,s);b.isArray(c)?i=i.concat(c):c&&i.push(c)}else this._ignoredBodyNodes[a]||n&&n.ignore&&0<=n.ignore.indexOf(a)?(r=this.ignoredNode(t,s,a))&&i.push(r):console.warn("Node not yet supported as top-level node: "+a)}return i},this._bodyNodes.p=function(t,e){return this.paragraphGroup(t,e)},this._bodyNodes.sec=function(t,e){return this.section(t,e)},this._bodyNodes.list=function(t,e){return this.list(t,e)},this._bodyNodes["disp-formula"]=function(t,e){return this.formula(t,e)},this._bodyNodes.caption=function(t,e){return this.caption(t,e)},this._bodyNodes["boxed-text"]=function(t,e){return this.boxedText(t,e)},this._bodyNodes["disp-quote"]=function(t,e){return this.quoteText(t,e)},this._bodyNodes.attrib=function(t,e){return this.paragraphGroup(t,e)},this._bodyNodes.comment=function(t,e){return this.comment(t,e)},this._bodyNodes.fig=function(t,e){return this.figure(t,e)},this._bodyNodes.speech=function(t,e){return this.speechText(t,e)},this._bodyNodes["table-wrap"]=function(t,e){return this.tableWrap(t,e)},this._bodyNodes["sec-meta"]=function(t,e){return this.secMeta(t,e)},this._bodyNodes.abstract=function(t,e){return this._abstract(t,e)},this._bodyNodes["contrib-group"]=function(t,e){return this.contribGroup(t,e)},this.secMeta=function(o,t){var s,a=o.doc,e=a.get("document"),c=this.bodyNodes(o,f.dom.getChildren(t)),u={id:o.nextId("sec_meta"),type:"sec_meta",children:b.pluck(c,"id"),authors:[],abstract:[]},l=["Section Editor","Section 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n.create(i),i},this.childNodes=function(t,e){for(var n=[],r=0;r<e.length;r++){var i=e[r],o=f.dom.getNodeType(i);if(this.childNodes[o]){var s=this.childNodes[o].call(this,t,i);b.isArray(s)?n=n.concat(s):s&&n.push(s)}}return n},this.speakerName=function(t,e){return{type:"speaker",label:"Speaker",children:e.innerHTML}},this.quoteText=function(t,e){var n=t.doc,r=this.bodyNodes(t,f.dom.getChildren(e)),i={type:"quote",id:t.nextId("quote"),source_id:e.getAttribute("id"),label:"",children:b.pluck(r,"id")};return n.create(i),i},this.speechText=function(t,e){var n=t.doc,r=this.bodyNodes(t,f.dom.getChildren(e)),i={type:"speech",id:t.nextId("speech"),source_id:e.getAttribute("id"),label:"",speaker:e.querySelectorAll("speaker"),children:b.pluck(r,"id")};return n.create(i),i},this.datasets=function(t,e){for(var n=[],r=0;r<e.length;r++){var i=e[r];if("p"===f.dom.getNodeType(i)){var o=i.querySelector("related-object");if(o)n=n.concat(this.indivdata(t,o));else{var s=this.paragraphGroup(t,i);0<s.length&&n.push(s[0].id)}}}return n},this.indivdata=function(t,e){var n=t.doc,r={type:"paragraph",id:t.nextId("paragraph"),children:[]},i={type:"text",id:t.nextId("text"),content:""};r.children.push(i.id);for(var o=f.dom.getChildren(e),s=0;s<o.length;s++){var a,c=o[s];if("name"===f.dom.getNodeType(c))for(var u=f.dom.getChildren(c),l=0;l<u.length;l++){var p=u[l];if(0===l)a=this.paragraphGroup(t,p),r.children.push(a[0].children[0]);else{var h={type:"text",id:t.nextId("text"),content:", "};n.create(h),r.children.push(h.id),a=this.paragraphGroup(t,p),r.children.push(a[0].children[0])}}else(a=this.paragraphGroup(t,c))&&a[0]&&a[0].children&&r.children.push(a[0].children[0])}return n.create(r),n.create(i),r.id},this.section=function(t,e){t.sectionLevel++;var n=t.doc,r=f.dom.getChildren(e),i=[],o=this.selectDirectChildren(e,"label")[0],s=this.selectDirectChildren(e,"title")[0];if(s||console.warn("FIXME: every section should have a 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t.sectionLevel--,i},this.ignoredParagraphElements={comment:!0,"supplementary-material":!0,fig:!0,"fig-group":!0,media:!0},this.acceptedParagraphElements={"boxed-text":{handler:"boxedText"},"disp-quote":{handler:"quoteText"},list:{handler:"list"},"disp-formula":{handler:"formula"},speech:{handler:"speechText"},"table-wrap":{handler:"tableWrap"}},this.inlineParagraphElements={"inline-graphic":!0,"inline-formula":!0},this.segmentParagraphElements=function(t){for(var e=[],n="",r=new f.dom.ChildNodeIterator(t);r.hasNext();){var i=r.next(),o=f.dom.getNodeType(i);this.ignoredParagraphElements[o]||("text"===o||this.isAnnotation(o)||this.inlineParagraphElements[o]?("paragraph"!==n&&(e.push({handler:"paragraph",nodes:[]}),n="paragraph"),b.last(e).nodes.push(i)):(this.acceptedParagraphElements[o]&&e.push(b.extend({node:i},this.acceptedParagraphElements[o])),n=o))}return e},this.paragraphGroup=function(t,e){for(var n=[],r=this.segmentParagraphElements(e),i=0;i<r.length;i++){var o,s=r[i];"paragraph"===s.handler?(o=this.paragraph(t,s.nodes))&&(o.source_id=e.getAttribute("id"),o.attributes=e.attributes):o=this[s.handler](t,s.node),o&&n.push(o)}return n},this.paragraph=function(t,e){var n=t.doc;t.skipWS=!0;for(var r={id:t.nextId("paragraph"),type:"paragraph",children:null},i=[],o=new f.dom.ChildNodeIterator(e);o.hasNext();){var s=o.next(),a=f.dom.getNodeType(s);if("text"===a||this.isAnnotation(a)){var c={id:t.nextId("text"),type:"text",content:null};t.stack.push({path:[c.id,"content"]});var u=this._annotatedText(t,o.back(),{offset:0,breakOnUnknown:!0});0<u.length&&(c.content=u,n.create(c),i.push(c)),t.stack.pop()}else if("inline-graphic"===a){var l=s.getAttribute("xlink:href"),p={id:t.nextId("image"),type:"image",url:this.resolveURL(t,l)};n.create(p),i.push(p)}else if("inline-formula"===a){var h=this.formula(t,s,"inline");h?i.push(h):"table-wrap"===a&&this.tableWrap(t,s)}}return 0===i.length?null:(r.children=b.map(i,function(t){return 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c&&(r.position=c||""),this.enhanceFigure(t,r,e),n.create(r),e._converted=!0,r},this.supplement=function(t,e){var n=t.doc,r=e.querySelector("label"),i=e.querySelector("media"),o=i?i.getAttribute("xlink:href"):null,s=e.querySelector("object-id[pub-id-type='doi']");s=s?s.textContent:"";var a={id:t.nextId("supplement"),source_id:e.getAttribute("id"),type:"supplement",label:r?r.textContent:"",url:o,caption:null},c=e.querySelector("caption");if(c){var u=this.caption(t,c);u&&(a.caption=u.id)}return this.enhanceSupplement(t,a,e),n.create(a),a},this.caption=function(n,r){var t=n.doc,e={id:n.nextId("caption"),source_id:r.getAttribute("id"),type:"caption",title:"",children:[]},i=r.querySelector("title");if(i){var o=this.paragraph(n,i);o&&(e.title=o.id)}var s=[],a=r.querySelectorAll("p");return b.each(a,function(t){if(t.parentNode===r){var e=this.paragraph(n,t);e&&s.push(e.id)}},this),e.children=s,t.create(e),e},this.video=function(t,e){var n=t.doc,r=e.querySelector("label").textContent,i={id:t.nextId("video"),source_id:e.getAttribute("id"),type:"video",label:r,title:"",caption:null,poster:""},o=e.querySelector("caption");if(o){var s=this.caption(t,o);s&&(i.caption=s.id)}var a=e.querySelector("object-id");return a&&"poster"===a.getAttribute("specific-use")&&(i.poster=a.textContent),this.enhanceVideo(t,i,e),n.create(i),i},this.tableWrap=function(t,e){for(var n=t.doc,r=e.querySelector("label"),i=e.querySelector("table"),o={},s={},a={},c=i.children,u=0;u<c.length;u++){for(var l=c[u].children,p=0;p<l.length;p++){for(var h=l[p].childNodes,d=0;d<h.length;d++){var f=h[d];if(a[d]={},"#text"===f.nodeName){var g=f.data.trim();if(0<g.length){var y=document.createElement("p"),m=document.createTextNode(g);y.appendChild(m),a[d].nodes=this.paragraphGroup(t,y)}}else"p"===f.nodeName&&(a[d].nodes=this.paragraphGroup(t,f));a[d].attributes=l[p].attributes}s[p]=a,a={}}o[u]=s,s={}}var 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this.factor=t/e,this.visibleArea=i(".visible-area"),this.scrollTop=this.surface.$el.scrollTop(),this.el.innerHTML="",this.el.appendChild(this.visibleArea),this.updateVisibleArea(),this},this.updateVisibleArea=function(){$(this.visibleArea).css({top:this.scrollTop/this.factor,height:this.surface.$el.height()/this.factor})},this.addOverlay=function(t){var e=$("<div>").addClass("node overlay");return this.overlays.push({el:t,$overlay:e}),this.$el.append(e),e},this.updateOverlay=function(t,e){var n=$(t),r=n.outerHeight(!0)/this.factor,i=(n.offset().top-this.surfaceTop)/this.factor;r<o.OverlayMinHeight&&(i-=.5*(r=o.OverlayMinHeight)),e.css({height:r,top:i})},this.addHighlight=function(t,e){var n=this.surface.findNodeView(t);if(n){var r=this.addOverlay(n);return this.updateOverlay(n,r),r.addClass(e),r[0]}},this.addHighlights=function(t,e){for(var n=[],r=0;r<t.length;r++){var i=this.addHighlight(t[r],e);n.push(i)}return this.update(),n},this.removeHighlights=function(){for(var t=0;t<this.overlays.length;t++){this.overlays[t].$overlay.remove()}},this.update=function(){var t=this.$nodes.height(),e=this.surface.$el.height();e<t?$(this.el).removeClass("hidden"):$(this.el).addClass("hidden"),this.factor=t/e,this.surfaceTop=this.$nodes.offset().top,this.scrollTop=this.surface.$el.scrollTop(),this.updateVisibleArea();for(var n=0;n<this.overlays.length;n++){var r=this.overlays[n];this.updateOverlay(r.el,r.$overlay)}},this.mouseDown=function(t){this._mouseDown=!0;var e=t.pageY;return t.target!==this.visibleArea?(this.offset=$(this.visibleArea).height()/2,this.mouseMove(t)):this.offset=e-$(this.visibleArea).position().top,!1},this.mouseUp=function(){this._mouseDown=!1},this.mouseMove=function(t){if(this._mouseDown){var e=(t.pageY-this.offset)*this.factor;this.scrollTop=this.surface.$el.scrollTop(e),this.updateVisibleArea()}},this.onScroll=function(){this.surface&&(this.scrollTop=this.surface.$el.scrollTop(),this.updateVisibleArea())}}).prototype=r.prototype,o.prototype=new o.Prototype,o.OverlayMinHeight=5,e.exports=o},{"../../substance/application":161,underscore:131}],153:[function(t,e,n){"use strict";function r(e,t,n){this.__document=e,this.options=n||{},this.panels=n.panels,this.contentPanel=new a(e),this.panelCtrls={},this.panelCtrls.content=this.contentPanel.createController(e),i.each(this.panels,function(t){this.panelCtrls[t.getName()]=t.createController(e)},this),this.workflows=n.workflows||[],this.state=t,this.currentPanel="toc"}var i=t("underscore"),o=t("../substance/application").Controller,s=t("./reader_view"),a=t("./panels/content");(r.Prototype=function(){this.createView=function(){return this.view||(this.view=new s(this)),this.view},this.switchPanel=function(t){this.currentPanel=t,this.modifyState({panel:t,focussedNode:null,fullscreen:!1})},this.getDocument=function(){return this.__document}}).prototype=o.prototype,r.prototype=new r.Prototype,e.exports=r},{"../substance/application":161,"./panels/content":145,"./reader_view":154,underscore:131}],154:[function(t,e,n){"use strict";function r(r){i.call(this),this.readerCtrl=r,this.doc=this.readerCtrl.getDocument(),this.$el.addClass("article"),this.$el.addClass(this.doc.schema.id),this.bodyScroll={},this.contentView=r.panelCtrls.content.createView(),this.tocView=this.contentView.getTocView(),this.panelViews={},this.panelForRef={},l.each(r.panels,function(t){var e=t.getName(),n=r.panelCtrls[e];this.panelViews[e]=n.createView(),l.each(t.config.references,function(t){this.panelForRef[t]=e},this)},this),this.panelViews.toc=this.tocView,this.resources=new o(this.readerCtrl.getDocument(),{types:["resource_reference"],property:"target"}),this.lastWorkflow=null,this.lastPanel="toc",this._onTogglePanel=l.bind(this.switchPanel,this),this.listenTo(this.readerCtrl,"state-changed",this.updateState),this.listenTo(this.tocView,"toggle",this._onTogglePanel),l.each(this.panelViews,function(t){this.listenTo(t,"toggle",this._onTogglePanel),this.listenTo(t,"toggle-resource",this.onToggleResource),this.listenTo(t,"toggle-resource-reference",this.onToggleResourceReference),this.listenTo(t,"toggle-fullscreen",this.onToggleFullscreen)},this),this.listenTo(this.contentView,"toggle",this._onTogglePanel),this.listenTo(this.contentView,"toggle-resource",this.onToggleResource),this.listenTo(this.contentView,"toggle-resource-reference",this.onToggleResourceReference),this.listenTo(this.contentView,"toggle-fullscreen",this.onToggleFullscreen),l.each(this.readerCtrl.workflows,function(t){t.attach(this.readerCtrl,this)},this),$(window).resize(l.debounce(l.bind(function(){this.contentView.scrollbar.update();var t=this.panelViews[this.readerCtrl.state.panel];t&&t.hasScrollbar()&&t.scrollbar.update()},this),1))}var l=t("underscore"),i=t("../substance/application").View,o=t("../substance/data").Graph.Index,c=t("../substance/application").$$;(r.Prototype=function(){this.render=function(){var t=document.createDocumentFragment();t.appendChild(this.contentView.render().el);var e=c(".scrollbar-cover"),n=parseInt($(".panel.content.document").width(),10),r=parseInt($(".surface.resource-view.content").width(),10),i=parseInt($(".scrollbar-cover").width(),10);parseInt(10*(n+r+i)/100,10),$(".scrollbar-cover").offset(),$(".surface.resource-view.content");this.contentView.el.appendChild(e);var o=c(".context-toggles");o.appendChild(this.tocView.getToggleControl()),this.tocView.on("toggle",this._onClickPanel),l.each(this.readerCtrl.panels,function(t){var e=this.panelViews[t.getName()],n=e.getToggleControl();o.appendChild(n),e.on("toggle",this._onClickPanel)},this);var s=c(".resources");s.appendChild(this.tocView.render().el),l.each(this.readerCtrl.panels,function(t){var e=this.panelViews[t.getName()];s.appendChild(e.render().el)},this);var a=c(".menu-bar");return a.appendChild(o),s.appendChild(a),t.appendChild(s),this.el.appendChild(t),l.delay(l.bind(function(){this.updateState();var t=this;window.MathJax&&(window.MathJax.Hub.Queue(["Typeset",window.MathJax.Hub]),window.MathJax.Hub.Queue(function(){t.updateState()}))},this),1),this},this.dispose=function(){l.each(this.workflows,function(t){t.detach()}),this.contentView.dispose(),l.each(this.panelViews,function(t){t.off("toggle",this._onClickPanel),t.dispose()},this),this.resources.dispose(),this.stopListening()},this.getState=function(){return this.readerCtrl.state},this.switchPanel=function(t){this.readerCtrl.switchPanel(t),this.lastPanel=t},this.updateState=function(){var t,e=this,n=this.readerCtrl.state,r={focussedNode:n.focussedNode?this.doc.get(n.focussedNode):null},i="content"===n.panel?this.contentView:this.panelViews[n.panel];if(l.each(this.panelViews,function(t){t.isHidden()||t.hide()}),this.contentView.removeHighlights(),l.each(this.panelViews,function(t){t.removeHighlights()}),n.focussedNode){var o=["focussed","highlighted"];n.fullscreen&&o.push("fullscreen"),this.contentView.addHighlight(n.focussedNode,o.concat("main-occurrence").join(" ")),i.addHighlight(n.focussedNode,o.join(" ")),i.scrollTo(n.focussedNode)}if(this.lastWorkflow&&(t=this.lastWorkflow.handleStateUpdate(n,r)),!t)for(var s=0;s<this.readerCtrl.workflows.length;s++){var a=this.readerCtrl.workflows[s];if(a!==this.lastWorkflow&&a.handlesStateUpdate&&(t=a.handleStateUpdate(n,r))){this.lastWorkflow=a;break}}if(!t)if("content"!==n.panel){var c=this.panelViews[n.panel];if(this.showPanel(n.panel),n.focussedNode){var u=this.resources.get(n.focussedNode);l.each(u,function(t){this.contentView.addHighlight(t.id,"highlighted "),this.contentView.scrollTo(t.target)},this),c.hasScrollbar()&&c.scrollTo(n.focussedNode)}}else this.showPanel("toc");e.updateScrollbars(),l.delay(function(){e.updateScrollbars()},2e3)},this.updateScrollbars=function(){this.readerCtrl.state;this.contentView.scrollbar.update(),l.each(this.panelViews,function(t){t.hasScrollbar()&&t.scrollbar.update()})},this.showPanel=function(t){this.panelViews[t]?(this.panelViews[t].activate(),this.el.dataset.context=t):"content"===t&&(this.panelViews.toc.activate(),this.el.dataset.context=t)},this.getPanelView=function(t){return this.panelViews[t]},this.onToggleResource=function(t,e,n){n.classList.contains("highlighted")?this.readerCtrl.modifyState({panel:t,focussedNode:null,fullscreen:!1}):this.readerCtrl.modifyState({panel:t,focussedNode:e})},this.onToggleResourceReference=function(t,e,n){n.classList.contains("highlighted")||this.readerCtrl.modifyState({panel:"content",focussedNode:e,fullscreen:!1})},this.onToggleFullscreen=function(t,e){var n=!this.readerCtrl.state.fullscreen;this.readerCtrl.modifyState({panel:t,focussedNode:e,fullscreen:n})}}).prototype=i.prototype,(r.prototype=new r.Prototype).constructor=r,e.exports=r},{"../substance/application":161,"../substance/data":167,underscore:131}],155:[function(t,e,n){"use strict";function r(){o.apply(this,arguments),this._followCrossReference=i.bind(this.followCrossReference,this)}var i=t("underscore"),o=t("./workflow");(r.Prototype=function(){this.registerHandlers=function(){this.readerView.$el.on("click",".annotation.cross_reference",this._followCrossReference)},this.unRegisterHandlers=function(){this.readerView.$el.off("click",".annotation.cross_reference",this._followCrossReference)},this.followCrossReference=function(t){t.preventDefault(),t.stopPropagation();var e,n=t.currentTarget.dataset.id,r=this.readerCtrl.getDocument().get(n);void 0!==r&&(void 0!==r.target&&(e=r.target,this.readerView.contentView.scrollTo(e)),void 0===e&&void 0!==r.properties&&(e=r.properties.id,this.readerView.contentView.scrollTo(e)))}}).prototype=o.prototype,r.prototype=new r.Prototype,e.exports=r},{"./workflow":158,underscore:131}],156:[function(t,n,r){"use strict";function i(){s.apply(this,arguments),this._gotoTop=o.bind(this.gotoTop,this)}var o=t("underscore"),s=t("./workflow");(i.Prototype=function(){this.registerHandlers=function(){this.readerView.$el.on("click",".document .content-node.heading .top",this._gotoTop)},this.unRegisterHandlers=function(){this.readerView.$el.off("click",".document .content-node.heading .top",this._gotoTop)},this.gotoTop=function(){e.preventDefault(),e.stopPropagation(),this.readerCtrl.contentView.jumpToNode("cover")}}).prototype=s.prototype,i.prototype=new i.Prototype,n.exports=i},{"./workflow":158,underscore:131}],157:[function(t,e,n){"use strict";function r(){i.apply(this,arguments)}var c=t("underscore"),i=t("./workflow");(r.Prototype=function(){this.registerHandlers=function(){},this.unRegisterHandlers=function(){},this.handlesStateUpdate=!0,this.handleStateUpdate=function(t,e){if(e.focussedNode&&this.readerView.panelForRef[e.focussedNode.type]){var n=e.focussedNode,r=this.readerView.panelForRef[n.type],i=this.readerView.panelViews[r],o=this.readerView.contentView,s=n.target;i.activate();i.addHighlight(s,["highlighted"].join(" ")),i.scrollTo(s);var a=this.readerView.resources.get(s);return delete a[n.id],c.each(a,function(t){o.addHighlight(t.id,"highlighted")},this),!0}return!1}}).prototype=i.prototype,r.prototype=new r.Prototype,e.exports=r},{"./workflow":158,underscore:131}],158:[function(t,e,n){"use strict";function r(){this.readerController=null,this.readerView=null}r.Prototype=function(){this.attach=function(t,e){this.readerCtrl=t,this.readerView=e,this.registerHandlers()},this.detach=function(){this.unRegisterHandlers(),this.readerView=null,this.readerController=null},this.registerHandlers=function(){throw new Error("This method is abstract")},this.unRegisterHandlers=function(){throw new Error("This method is abstract")},this.handlesStateUpdate=!1,this.handleStateUpdate=function(t,e){throw new Error("This method is abstract")}},r.prototype=new r.Prototype,e.exports=r},{}],159:[function(t,e,n){"use strict";function r(t){i.call(this),this.config=t}var i=t("./view"),o=t("./router"),s=(t("../../substance/util"),t("underscore"));(r.Prototype=function(){this.initRouter=function(){this.router=new o,s.each(this.config.routes,function(t){this.router.route(t.route,t.name,s.bind(this.controller[t.command],this.controller))},this),o.history.start()},this.start=function(){this.$el=$("body"),this.el=this.$el[0],this.render(),this.initRouter()}}).prototype=i.prototype,r.prototype=new r.Prototype,e.exports=r},{"../../substance/util":183,"./router":163,"./view":164,underscore:131}],160:[function(t,e,n){"use strict";function r(t){this.state={},this.context=null}var i=t("../../substance/util"),o=t("underscore");(r.Prototype=function(){this.updateState=function(t,e){console.error("updateState is deprecated, use modifyState. State is now a rich object where context replaces the old state variable");var n=this.context;this.context=t,this.state=e,this.trigger("state-changed",this.context,n,e)},this.modifyState=function(t){var e=this.state.context;o.extend(this.state,t),t.context&&t.context!==e&&this.trigger("context-changed",t.context),this.trigger("state-changed",this.state.context)}}).prototype=i.Events,r.prototype=new r.Prototype,e.exports=r},{"../../substance/util":183,underscore:131}],161:[function(t,e,n){"use strict";var r=t("./application");r.View=t("./view"),r.Router=t("./router"),r.Controller=t("./controller"),r.ElementRenderer=t("./renderers/element_renderer"),r.$$=r.ElementRenderer.$$,e.exports=r},{"./application":159,"./controller":160,"./renderers/element_renderer":162,"./router":163,"./view":164}],162:[function(t,e,n){"use strict";function o(t){return this.attributes=t,this.tagName=t.tag,this.children=t.children||[],this.text=t.text||"",this.html=t.html,delete t.children,delete t.text,delete t.html,delete t.tag,this.render()}var r=t("../../../substance/util"),s=r.RegExp;o.Prototype=function(){this.render=function(){var t=document.createElement(this.tagName);for(var e in this.html?t.innerHTML=this.html:t.textContent=this.text,this.attributes){var n=this.attributes[e];t.setAttribute(e,n)}for(var r=0;r<this.children.length;r++){var i=this.children[r];t.appendChild(i)}return this.el=t}};o.$$=function(t,e){e=e||{};var n=/^([a-zA-Z0-9]*)/.exec(t);e.tag=n&&n[1]?n[1]:"div";var r=/#([a-zA-Z0-9_]*)/.exec(t);r&&r[1]&&(e.id=r[1]);var i=new s(/\.([a-zA-Z0-9_-]*)/g);return e.class||(e.class=i.match(t).map(function(t){return t.match[1]}).join(" ")),new o(e)},o.Prototype.prototype=r.Events,o.prototype=new o.Prototype,e.exports=o},{"../../../substance/util":183}],163:[function(t,e,n){"use strict";function s(t){t||(t={}),t.routes&&(this.routes=t.routes),this._bindRoutes(),this.initialize.apply(this,arguments)}var r=t("../../substance/util"),a=t("underscore"),i=/\((.*?)\)/g,o=/(\(\?)?:\w+/g,c=/\*\w+/g,u=/[\-{}\[\]+?.,\\\^$|#\s]/g;a.extend(s.prototype,r.Events,{initialize:function(){},route:function(n,r,i){a.isRegExp(n)||(n=this._routeToRegExp(n)),a.isFunction(r)&&(i=r,r=""),i||(i=this[r]);var o=this;return s.history.route(n,function(t){var e=o._extractParameters(n,t);i&&i.apply(o,e),o.trigger.apply(o,["route:"+r].concat(e)),o.trigger("route",r,e),s.history.trigger("route",o,r,e)}),this},navigate:function(t,e){return s.history.navigate(t,e),this},_bindRoutes:function(){if(this.routes){this.routes=a.result(this,"routes");for(var t,e=a.keys(this.routes);null!=(t=e.pop());)this.route(t,this.routes[t])}},_routeToRegExp:function(t){return t=t.replace(u,"\\$&").replace(i,"(?:$1)?").replace(o,function(t,e){return e?t:"([^/]+)"}).replace(c,"(.*?)"),new RegExp("^"+t+"$")},_extractParameters:function(t,e){var n=t.exec(e).slice(1);return a.map(n,function(t){return t?decodeURIComponent(t):null})}});var l=s.History=function(){this.handlers=[],a.bindAll(this,"checkUrl"),"undefined"!=typeof window&&(this.location=window.location,this.history=window.history)},p=/^[#\/]|\s+$/g,h=/^\/+|\/+$/g,d=/msie [\w.]+/,f=/\/$/;l.started=!1,a.extend(l.prototype,r.Events,{interval:50,getHash:function(t){var e=(t||this).location.href.match(/#(.*)$/);return e?e[1]:""},getFragment:function(t,e){if(null==t)if(this._hasPushState||!this._wantsHashChange||e){t=this.location.pathname;var n=this.root.replace(f,"");t.indexOf(n)||(t=t.substr(n.length))}else t=this.getHash();return t.replace(p,"")},start:function(t){if(l.started)throw new Error("Router.history has already been started");l.started=!0,this.options=a.extend({},{root:"/"},this.options,t),this.root=this.options.root,this._wantsHashChange=!1!==this.options.hashChange,this._wantsPushState=!!this.options.pushState,this._hasPushState=!!(this.options.pushState&&this.history&&this.history.pushState);var e=this.getFragment(),n=document.documentMode,r=d.exec(navigator.userAgent.toLowerCase())&&(!n||n<=7);this.root=("/"+this.root+"/").replace(h,"/"),r&&this._wantsHashChange&&(this.iframe=$('<iframe src="javascript:0" tabindex="-1" />').hide().appendTo("body")[0].contentWindow,this.navigate(e)),this._hasPushState?$(window).on("popstate",this.checkUrl):this._wantsHashChange&&"onhashchange"in window&&!r?$(window).on("hashchange",this.checkUrl):this._wantsHashChange&&(this._checkUrlInterval=setInterval(this.checkUrl,this.interval)),this.fragment=e;var i=this.location,o=i.pathname.replace(/[^\/]$/,"$&/")===this.root;return this._wantsHashChange&&this._wantsPushState&&!this._hasPushState&&!o?(this.fragment=this.getFragment(null,!0),this.location.replace(this.root+this.location.search+"#"+this.fragment),!0):(this._wantsPushState&&this._hasPushState&&o&&i.hash&&(this.fragment=this.getHash().replace(p,""),this.history.replaceState({},document.title,this.root+this.fragment+i.search)),this.options.silent?void 0:this.loadUrl())},stop:function(){$(window).off("popstate",this.checkUrl).off("hashchange",this.checkUrl),clearInterval(this._checkUrlInterval),l.started=!1},route:function(t,e){this.handlers.unshift({route:t,callback:e})},checkUrl:function(t){var e=this.getFragment();if(e===this.fragment&&this.iframe&&(e=this.getFragment(this.getHash(this.iframe))),e===this.fragment)return!1;this.iframe&&this.navigate(e),this.loadUrl()||this.loadUrl(this.getHash())},loadUrl:function(t){var e=this.fragment=this.getFragment(t);return a.any(this.handlers,function(t){if(t.route.test(e))return t.callback(e),!0})},navigate:function(t,e){if(!l.started)return!1;if(e&&!0!==e||(e={trigger:e}),t=this.getFragment(t||""),this.fragment!==t){this.fragment=t;var n=this.root+t;if(this._hasPushState)this.history[e.replace?"replaceState":"pushState"]({},document.title,n);else{if(!this._wantsHashChange)return this.location.assign(n);this._updateHash(this.location,t,e.replace),this.iframe&&t!==this.getFragment(this.getHash(this.iframe))&&(e.replace||this.iframe.document.open().close(),this._updateHash(this.iframe.location,t,e.replace))}e.trigger&&this.loadUrl(t)}},_updateHash:function(t,e,n){if(n){var r=t.href.replace(/(javascript:|#).*$/,"");t.replace(r+"#"+e)}else t.hash="#"+e}}),s.history=new l,e.exports=s},{"../../substance/util":183,underscore:131}],164:[function(t,e,n){"use strict";function r(t){t=t||{},this.el=t.el||window.document.createElement(t.elementType||"div"),this.$el=$(this.el),this.dispatchDOMEvents()}var i=t("../../substance/util");(r.Prototype=function(){this.$=function(t){return this.$el.find(t)},this.render=function(){return this},this.dispatchDOMEvents=function(){var r=this;this.$el.delegate("[sbs-click]","click",function(t){console.error("FIXME: sbs-click is deprecated. 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