/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
/**
*
*/
package org.dspace.submit.lookup;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import gr.ekt.bte.core.MutableRecord;
import gr.ekt.bte.core.Record;
import gr.ekt.bte.core.StringValue;
import gr.ekt.bte.core.Value;
import org.apache.commons.lang.StringUtils;
import org.dspace.app.util.XMLUtils;
import org.dspace.submit.util.SubmissionLookupPublication;
import org.w3c.dom.Element;
/**
* @author Andrea Bollini
* @author Kostas Stamatis
* @author Luigi Andrea Pascarelli
* @author Panagiotis Koutsourakis
*/
public class PubmedUtils
{
public static Record convertPubmedDomToRecord(Element pubArticle)
{
MutableRecord record = new SubmissionLookupPublication("");
Map<String, String> monthToNum = new HashMap<String, String>();
monthToNum.put("Jan", "01");
monthToNum.put("Feb", "02");
monthToNum.put("Mar", "03");
monthToNum.put("Apr", "04");
monthToNum.put("May", "05");
monthToNum.put("Jun", "06");
monthToNum.put("Jul", "07");
monthToNum.put("Aug", "08");
monthToNum.put("Sep", "09");
monthToNum.put("Oct", "10");
monthToNum.put("Nov", "11");
monthToNum.put("Dec", "12");
Element medline = XMLUtils.getSingleElement(pubArticle,
"MedlineCitation");
Element article = XMLUtils.getSingleElement(medline, "Article");
Element pubmed = XMLUtils.getSingleElement(pubArticle, "PubmedData");
Element identifierList = XMLUtils.getSingleElement(pubmed,
"ArticleIdList");
if (identifierList != null)
{
List<Element> identifiers = XMLUtils.getElementList(identifierList,
"ArticleId");
if (identifiers != null)
{
for (Element id : identifiers)
{
if ("pubmed".equals(id.getAttribute("IdType")))
{
String pubmedID = id.getTextContent().trim();
if (pubmedID != null)
record.addValue("pubmedID", new StringValue(
pubmedID));
}
else if ("doi".equals(id.getAttribute("IdType")))
{
String doi = id.getTextContent().trim();
if (doi != null)
record.addValue("doi", new StringValue(doi));
}
}
}
}
String status = XMLUtils.getElementValue(pubmed, "PublicationStatus");
if (status != null)
record.addValue("publicationStatus", new StringValue(status));
String pubblicationModel = XMLUtils.getElementAttribute(medline,
"Article", "PubModel");
if (pubblicationModel != null)
record.addValue("pubModel", new StringValue(
pubblicationModel));
String title = XMLUtils.getElementValue(article, "ArticleTitle");
if (title != null)
record.addValue("articleTitle", new StringValue(title));
Element abstractElement = XMLUtils
.getSingleElement(article, "Abstract");
if (abstractElement == null)
{
abstractElement = XMLUtils.getSingleElement(medline,
"OtherAbstract");
}
if (abstractElement != null)
{
String summary = XMLUtils.getElementValue(abstractElement,
"AbstractText");
if (summary != null)
record.addValue("abstractText", new StringValue(summary));
}
List<String[]> authors = new LinkedList<String[]>();
Element authorList = XMLUtils.getSingleElement(article, "AuthorList");
if (authorList != null)
{
List<Element> authorsElement = XMLUtils.getElementList(authorList,
"Author");
if (authorsElement != null)
{
for (Element author : authorsElement)
{
if (StringUtils.isBlank(XMLUtils.getElementValue(author,
"CollectiveName")))
{
authors.add(new String[] {
XMLUtils.getElementValue(author, "ForeName"),
XMLUtils.getElementValue(author, "LastName") });
}
}
}
}
if (authors.size() > 0)
{
List<Value> values = new LinkedList<Value>();
for (String[] sArray : authors)
{
values.add(new StringValue(sArray[1] + ", " + sArray[0]));
}
record.addField("author", values);
}
Element journal = XMLUtils.getSingleElement(article, "Journal");
if (journal != null)
{
List<Element> jnumbers = XMLUtils.getElementList(journal, "ISSN");
if (jnumbers != null)
{
for (Element jnumber : jnumbers)
{
if ("Print".equals(jnumber.getAttribute("IssnType")))
{
String issn = jnumber.getTextContent().trim();
if (issn != null)
record.addValue("printISSN", new StringValue(issn));
}
else
{
String eissn = jnumber.getTextContent().trim();
if (eissn != null)
record.addValue("electronicISSN", new StringValue(eissn));
}
}
}
String journalTitle = XMLUtils.getElementValue(journal, "Title");
if (journalTitle != null)
record.addValue("journalTitle", new StringValue(journalTitle));
Element journalIssueElement = XMLUtils.getSingleElement(journal,
"JournalIssue");
if (journalIssueElement != null)
{
String volume = XMLUtils.getElementValue(journalIssueElement,
"Volume");
if (volume != null)
record.addValue("journalVolume", new StringValue(volume));
String issue = XMLUtils.getElementValue(journalIssueElement,
"Issue");
if (issue != null)
record.addValue("journalIssue", new StringValue(issue));
Element pubDateElement = XMLUtils.getSingleElement(
journalIssueElement, "PubDate");
String pubDate = null;
if (pubDateElement != null)
{
pubDate = XMLUtils.getElementValue(pubDateElement, "Year");
String mounth = XMLUtils.getElementValue(pubDateElement,
"Month");
String day = XMLUtils
.getElementValue(pubDateElement, "Day");
if (StringUtils.isNotBlank(mounth)
&& monthToNum.containsKey(mounth))
{
pubDate += "-" + monthToNum.get(mounth);
if (StringUtils.isNotBlank(day))
{
pubDate += "-" + (day.length() == 1 ? "0" + day : day);
}
}
}
if (pubDate == null){
pubDate = XMLUtils.getElementValue(pubDateElement, "MedlineDate");
}
if (pubDate != null)
record.addValue("pubDate", new StringValue(pubDate));
}
String language = XMLUtils.getElementValue(article, "Language");
if (language != null)
record.addValue("language", new StringValue(language));
List<String> type = new LinkedList<String>();
Element publicationTypeList = XMLUtils.getSingleElement(article,
"PublicationTypeList");
if (publicationTypeList != null)
{
List<Element> publicationTypes = XMLUtils.getElementList(
publicationTypeList, "PublicationType");
for (Element publicationType : publicationTypes)
{
type.add(publicationType.getTextContent().trim());
}
}
if (type.size() > 0)
{
List<Value> values = new LinkedList<Value>();
for (String s : type)
{
values.add(new StringValue(s));
}
record.addField("publicationType", values);
}
List<String> primaryKeywords = new LinkedList<String>();
List<String> secondaryKeywords = new LinkedList<String>();
Element keywordsList = XMLUtils.getSingleElement(medline,
"KeywordList");
if (keywordsList != null)
{
List<Element> keywords = XMLUtils.getElementList(keywordsList,
"Keyword");
for (Element keyword : keywords)
{
if ("Y".equals(keyword.getAttribute("MajorTopicYN")))
{
primaryKeywords.add(keyword.getTextContent().trim());
}
else
{
secondaryKeywords.add(keyword.getTextContent().trim());
}
}
}
if (primaryKeywords.size() > 0)
{
List<Value> values = new LinkedList<Value>();
for (String s : primaryKeywords)
{
values.add(new StringValue(s));
}
record.addField("primaryKeyword", values);
}
if (secondaryKeywords.size() > 0)
{
List<Value> values = new LinkedList<Value>();
for (String s : secondaryKeywords)
{
values.add(new StringValue(s));
}
record.addField("secondaryKeyword", values);
}
List<String> primaryMeshHeadings = new LinkedList<String>();
List<String> secondaryMeshHeadings = new LinkedList<String>();
Element meshHeadingsList = XMLUtils.getSingleElement(medline,
"MeshHeadingList");
if (meshHeadingsList != null)
{
List<Element> meshHeadings = XMLUtils.getElementList(
meshHeadingsList, "MeshHeading");
for (Element meshHeading : meshHeadings)
{
if ("Y".equals(XMLUtils.getElementAttribute(meshHeading,
"DescriptorName", "MajorTopicYN")))
{
primaryMeshHeadings.add(XMLUtils.getElementValue(
meshHeading, "DescriptorName"));
}
else
{
secondaryMeshHeadings.add(XMLUtils.getElementValue(
meshHeading, "DescriptorName"));
}
}
}
if (primaryMeshHeadings.size() > 0)
{
List<Value> values = new LinkedList<Value>();
for (String s : primaryMeshHeadings)
{
values.add(new StringValue(s));
}
record.addField("primaryMeshHeading", values);
}
if (secondaryMeshHeadings.size() > 0)
{
List<Value> values = new LinkedList<Value>();
for (String s : secondaryMeshHeadings)
{
values.add(new StringValue(s));
}
record.addField("secondaryMeshHeading", values);
}
Element paginationElement = XMLUtils.getSingleElement(article,
"Pagination");
if (paginationElement != null)
{
String startPage = XMLUtils.getElementValue(paginationElement,
"StartPage");
String endPage = XMLUtils.getElementValue(paginationElement,
"EndPage");
if (StringUtils.isBlank(startPage))
{
startPage = XMLUtils.getElementValue(paginationElement,
"MedlinePgn");
}
if (startPage != null)
record.addValue("startPage", new StringValue(startPage));
if (endPage != null)
record.addValue("endPage", new StringValue(endPage));
}
}
return record;
}
}