private static void testWrapper() {
JNPhysiologyWrapper jpw = new JNPhysiologyWrapper();
jpw.extractReferences(
HtmlDocumentUtil.getHtmlDocumentFromFile(
"C:/Users/du/Projekte/SMAFIRA/git/data/html/fulltexts/18003881_jn.physiology.org.html"));
//
// jpw.extractReferences(HtmlDocumentUtil.getHtmlDocumentFromFile("C:/Users/du/Projekte/SMAFIRA/git/data/html/fulltexts/12686573_jn.physiology.org.html"));
}
private static void testWrapperOnAllPhysio() {
JNPhysiologyWrapper jpw = new JNPhysiologyWrapper();
String directory = "C:/Users/du/Projekte/SMAFIRA/git/data/html/fulltextsWithRefs/";
String[] fileNameList = (new File(directory)).list();
for (String fileName : fileNameList) {
// System.out.println("fileName: " + fileName);
if (fileName.contains("jn.physiology.org")) {
System.out.println("fileName_extracted: " + fileName);
jpw.extractReferences(HtmlDocumentUtil.getHtmlDocumentFromFile(directory + fileName));
}
}
}
public void extractReferences(Document htmlDoc) {
Elements references = htmlDoc.select(ContentXPath.REFERENCE.path);
Element firstAuthorSNM,
firstAuthorFNM,
authors,
citationAuthorsList,
source,
volume,
fpage,
lpage,
date,
citeComplete,
medline,
titleElement,
publisherName,
publisherLocation,
referenceUnstructured;
Elements citationAuthorsEntries, authorElements;
Document referenceHtml, authorsHtml;
Reference refInfo;
String authorsList,
firstPage,
lastPage,
completePages,
title,
completeCitation,
citeNodeText,
medlineLink,
authorClass,
firstName,
lastName;
if (references != null) {
for (Element reference : references) {
refInfo = new Reference();
// doi
refInfo.setDoi(reference.attr(ContentXPath.REFERENCE_DOI_ATTR.path));
// parse content of reference
referenceHtml = HtmlDocumentUtil.getHtmlDocumentFromString(reference.html());
// check if reference is unstructured
referenceUnstructured =
referenceHtml.select(ContentXPath.REFERENCE_UNSTRUCTURED.path).first();
if (referenceUnstructured != null) {
// TODO: handle unstructured Data
} else {
// authors
authorsList = "";
citationAuthorsList = referenceHtml.select(ContentXPath.AUTHORS2_ROOT.path).first();
if (citationAuthorsList != null) {
// citation version 2
authorsHtml = HtmlDocumentUtil.getHtmlDocumentFromString(citationAuthorsList.html());
citationAuthorsEntries = authorsHtml.select(ContentXPath.AUTHORS2_ENTRY.path);
for (Element authorEntry : citationAuthorsEntries) {
authorElements = authorEntry.children();
lastName = "";
firstName = "";
for (Element authorElement : authorElements) {
authorClass = authorElement.attr("class");
if (authorClass.contains(ContentXPath.AUTHORS2_SURNAME.path))
lastName = authorElement.text();
else if (authorClass.contains(ContentXPath.AUTHORS2_FIRSTNAME.path))
firstName = authorElement.text();
}
refInfo.addAuthor(refInfo.new Author(lastName, firstName));
}
} else {
// citation version 1
firstAuthorSNM = referenceHtml.select(ContentXPath.FIRST_AUTHOR_SURNAME.path).first();
firstAuthorFNM = referenceHtml.select(ContentXPath.FIRST_AUTHOR_FIRSTNAME.path).first();
refInfo.addAuthor(refInfo.new Author(firstAuthorSNM.text(), firstAuthorFNM.text()));
authors = referenceHtml.select(ContentXPath.AUTHORS.path).first();
authorsList = "";
if (authors != null) {
authorsList = authors.text();
addAuthorsToReference(authorsList, refInfo);
}
}
// reference source/journal
source = referenceHtml.select(ContentXPath.CITE_SOURCE.path).first();
if (source != null) {
refInfo.setSource(source.text());
} else {
source = referenceHtml.select(ContentXPath.CITE_SOURCE_JNL.path).first();
if (source != null) {
refInfo.setSource(source.text());
}
}
// reference volume
volume = referenceHtml.select(ContentXPath.CITE_VOLUME.path).first();
if (volume != null) refInfo.setVolume(volume.text());
// reference date
date = referenceHtml.select(ContentXPath.CITE_DATE.path).first();
if (date != null) refInfo.setDate(date.text());
// complete citation
citeComplete = referenceHtml.select(ContentXPath.CITE_COMPLETE.path).first();
completeCitation = citeComplete.text();
refInfo.setCompleteCitation(completeCitation);
// reference title
titleElement = referenceHtml.select(ContentXPath.CITE_TITLE.path).first();
if (titleElement != null) {
title = titleElement.text();
refInfo.setTitle(title);
} else {
citeNodeText = citeComplete.ownText();
title = extractTitleFromCitation(citeNodeText);
refInfo.setTitle(title);
}
// reference first page
fpage = referenceHtml.select(ContentXPath.CITE_FPAGE.path).first();
firstPage = "";
if (fpage != null) firstPage = fpage.text();
// reference last page
lpage = referenceHtml.select(ContentXPath.CITE_LPAGE.path).first();
if (lpage != null) {
lastPage = lpage.text();
completePages = firstPage + "-" + lastPage;
refInfo.setPages(completePages);
} else if (fpage != null) {
completePages = extractCompletePagesFromCitation(completeCitation, firstPage);
refInfo.setPages(completePages);
}
// pmid from medline link (if available)
medline = referenceHtml.select(ContentXPath.MEDLINE_LINK.path).first();
if (medline != null) {
medlineLink = medline.attr(ContentXPath.MEDLINE_LINK_ATTR.path);
refInfo.setPmid(extractPMIDFromMedlineLink(medlineLink));
}
// publisherName
publisherName = referenceHtml.select(ContentXPath.PUBL_NAME.path).first();
if (publisherName != null) refInfo.setPublisherName(publisherName.text());
// publisherLocation
publisherLocation = referenceHtml.select(ContentXPath.PUBL_LOC.path).first();
if (publisherLocation != null) refInfo.setPublisherLocation(publisherLocation.text());
}
// System.out.print("doi: " + refInfo.getDoi() + "; authors: ");
// for(Author author: refInfo.getAuthors()){
// System.out.print(author.getLastName() + ", " + author.getFirstName() + "; ");
// }
// System.out.print("source: " + refInfo.getSource() + "; volume: " + refInfo.getVolume()
// + "; date: " + refInfo.getDate() + "; pages: " + refInfo.getPages() + "; title: " +
// title);
// System.out.println();
// System.out.println("pages: " + refInfo.getPages());
// System.out.println("pmid: " + refInfo.getPmid());
// System.out.println("citeNode: " + citeNodeText);
// System.out.println("title: " + refInfo.getTitle());
// System.out.println("publisher: " + refInfo.getPublisherName() + "; loc: " +
// refInfo.getPublisherLocation());
}
}
}