86 lines
3.2 KiB
JavaScript
86 lines
3.2 KiB
JavaScript
{
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"translatorID":"e16095ae-986c-4117-9cb6-20f3b7a52f64",
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"translatorType":4,
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"label":"Protein Data Bank",
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"creator":"Michael Berkowitz",
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"target":"http://www.pdb.org/",
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"minVersion":"1.0.0b4.r5",
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"maxVersion":"",
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"priority":100,
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"inRepository":true,
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"lastUpdated":"2009-01-08 08:19:07"
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}
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function detectWeb(doc, url) {
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if (doc.title.indexOf("Query Results") != -1) {
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return "multiple";
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} else if (url.indexOf("structureId") != -1) {
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return "journalArticle";
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}
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}
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function doWeb(doc, url) {
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var proteins = new Array();
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if (detectWeb(doc, url) == "multiple") {
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//search results
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var items = new Object();
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var xpath = '//a[@class="qrb_title"]';
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var titles = doc.evaluate(xpath, doc, null, XPathResult.ANY_TYPE, null);
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var next_title;
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while (next_title = titles.iterateNext()) {
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items[next_title.href.match(/structureId=(.*)/)[1]] = next_title.textContent;
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}
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items = Zotero.selectItems(items);
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for (var i in items) {
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proteins.push(i);
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}
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} else {
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proteins = [url.match(/structureId=(.*)/)[1]];
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}
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Zotero.debug(proteins);
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for (var p in proteins) {
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var xmlstr = 'http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=xml&headerOnly=YES&structureId=' + proteins[p];
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Zotero.debug(xmlstr);
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Zotero.Utilities.HTTP.doGet(xmlstr, function(text) {
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var item = new Zotero.Item("journalArticle");
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text = text.replace(/<!DOCTYPE[^>]*>/, "").replace(/<\?xml[^>]*\?>/, "").replace(/PDBx\:/g, "");
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var article = text.split('<citation id="primary">');
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var art = article[1].split(/<\/citation>\n/);
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art = "<citation>" + art[0] + "</citation>";
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var xml = new XML(art);
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var info = text.split('<database_PDB_revCategory>')[1].split('</database_PDB_revCategory>')[0];
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var xml2 = new XML("<PDB_revCategory>" + info + "</PDB_revCategory>");
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var aus = text.split('<citation_authorCategory>')[1].split('</citation_authorCategory>')[0];
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aus = "<authors>" + aus + "</authors>";
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var xml3 = new XML(aus);
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item.title = xml..title.text().toString();
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item.publicationTitle = xml..journal_abbrev.text().toString();
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item.volume = xml..journal_volume.text().toString();
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item.pages = xml..page_first.text().toString() + "-" + xml..page_last.text().toString();
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item.ISSN = xml..journal_id_ISSN.text().toString();
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item.extra = "PubMed ID: " + xml..pdbx_database_id_PubMed.text().toString();
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if (xml..pdbx_database_id_DOI.length()) {
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item.DOI = xml..pdbx_database_id_DOI.text().toString();
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}
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item.date = xml2..date_original.text().toString();
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item.url = 'http://www.pdb.org/pdb/explore/explore.do?structureId=' + xml2..replaces.text().toString();
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var authors = xml3..citation_author.toString().split(/\n/);
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for (var i in authors) {
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var name = authors[i].match(/name=\"([^"]+)\"/)[1].split(", ");;
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Zotero.debug(name);
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item.creators.push({firstName:name[1], lastName:name[0], creatorType:"author"});
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}
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item.attachments = [
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{url:item.url, title:"PDB Snapshot", mimeType:"text/html"},
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{url:'http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=' + proteins[p], title:"Protein Data Bank .pdb File", mimeType:"chemical/x-pdb"}
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]
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item.complete();
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});
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Zotero.done();
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}
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Zotero.wait();
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} |