rendered paste bodypublic void endElement(String uri, String localName, String qName)
throws SAXException {
// boolean recognizedFlag = false;
String data = dataBuffer.toString();
if (qName.equals("MedlineCitationSet")) {
}
/** ** ELEMENT MedlineCitation begins *** */
else if (qName.equals("MedlineCitation")) {
bool_medlineCitation = false;
try {
String bionix_articleTitle = "<not available>";
String bionix_abstract_txt = "<not available>";
File file_bionix = new File(directory_bionix + "/"
+ pmid.trim() + ".txt");
if (!file_bionix.exists()) {
System.out.println(file_bionix.getCanonicalPath()
+ " not reaadable");
System.exit(0);
}
if (!file_bionix.canRead()) {
System.out.println(file_bionix.getCanonicalPath()
+ " not reaadable");
System.exit(0);
}
FileInputStream fis = new FileInputStream(file_bionix);
InputStreamReader isr = new InputStreamReader(fis);
BufferedReader br = new BufferedReader(isr);
String tmp_tmp;
boolean bool_tmp_abs = false;
while ((tmp_tmp = br.readLine()) != null) {
if (bool_tmp_abs == true && tmp_tmp.trim().length() > 0)
bionix_abstract_txt = bionix_abstract_txt + tmp_tmp;
if (tmp_tmp.startsWith("AB"))
bionix_abstract_txt = tmp_tmp.substring(4, tmp_tmp
.length());
if (tmp_tmp.startsWith("TI")) {
int tmp_place;
tmp_place = tmp_tmp.indexOf("AB");
if (tmp_place == -1)
bionix_articleTitle = tmp_tmp.substring(4, tmp_tmp
.length());
else {
bool_tmp_abs = true;
bionix_articleTitle = tmp_tmp.substring(4,
tmp_place);
bionix_abstract_txt = tmp_tmp.substring(
tmp_place + 4, tmp_tmp.length());
}
}
if (tmp_tmp.startsWith("AU"))
bool_tmp_abs = false;
}
bionix_abstract_txt.trim();
bionix_articleTitle.trim();
File file = new File(directory_write_txt + "/" + pmid + ".txt");
FileOutputStream fos = new FileOutputStream(file);
PrintStream ps = new PrintStream(fos);
ps.println("pmid - " + pmid);
ps.println("owner - " + owner);
if (status.length() > 0)
ps.println("status - " + status);
ps.println("dateCreated - " + dateCreated);
if (pubModel.length() > 0)
ps.println("pumModel - " + pubModel);
if (dateCompleted.length() > 0)
ps.println("dateCompleted - " + dateCompleted);
if (dateCreated.length() > 0)
ps.println("dateRevised - " + dateRevised);
ps.println("datepubDate - " + datepubDate);
ps.println("datepubDate_display - " + datepubDate_display);
if (issn.length() >= 1)
ps.println("issn - " + issn);
if (volume.length() >= 1)
ps.println("volume - " + volume);
if (issue.length() >= 1)
ps.println("issue - " + issue);
if (coden.length() >= 1)
ps.println("coden - " + coden);
if (title.length() >= 1)
ps.println("title - " + title);
if (iso.length() >= 1)
ps.println("iso - " + iso);
if (medlinePgn.length() >= 1)
ps.println("medlinePgn - " + medlinePgn);
if (chemicalList.length() > 0)
ps.println("chemicalList - " + chemicalList);
if (publicationTitleList.length() > 0)
ps
.println("publicationTitleList - "
+ publicationTitleList);
if (dataBankList.length() > 0)
ps.println("dataBankList - " + dataBankList);
if (grantList.length() > 0)
ps.println("grantList - " + grantList);
if (personalNameSubList.length() > 0)
ps.println("personalNameSubList - " + personalNameSubList);
ps.println("citationSubset - " + citationSubset);
if (commentOn.length() > 0)
ps.println("CommentOn - " + commentOn);
if (commentIn.length() > 0)
ps.println("commentIn - " + commentIn);
if (erratumIn.length() > 0)
ps.println("erratumIn - " + erratumIn);
if (erratumFor.length() > 0)
ps.println("erratumFor - " + erratumFor);
if (repFrom.length() > 0)
ps.println("repFrom - " + repFrom);
if (repIn.length() > 0)
ps.println("repIn - " + repIn);
if (retOf.length() > 0)
ps.println("retOf - " + retOf);
if (retIn.length() > 0)
ps.println("retIn - " + retIn);
if (summPatIn.length() > 0)
ps.println("summPatIn - " + summPatIn);
if (orgRepIn.length() > 0)
ps.println("orgRepIn - " + orgRepIn);
if (spaceFlightMission.length() > 0)
ps.println("spaceFlightMission - " + spaceFlightMission);
if (geneSymbolList.length() > 0)
ps.println("geneSymbolList - " + geneSymbolList);
if (numberofRef.length() > 0)
ps.println("numberofRef - " + numberofRef);
if (otherID.length() > 0)
ps.println("otherID - " + otherID);
if (generalNote.length() > 0)
ps.println("generalNote - " + generalNote);
if (country.length() > 0)
ps.println("country - " + country);
if (medlineTA.length() > 0)
ps.println("medlineTA - " + medlineTA);
if (medlineCode.length() > 0)
ps.println("medlineCode - " + medlineCode);
if (nlmUniqueID.length() > 0)
ps.println("nlmUniqueID - " + nlmUniqueID);
if (articleTitle.length() > 0)
ps.println("articleTitle - " + articleTitle);
if (bionix_articleTitle.length() > 0)
ps.println("bionix_articleTitle - " + bionix_articleTitle);
if (abstract_txt.length() > 0)
ps.println("abstract_txt - " + abstract_txt);
if (bionix_abstract_txt.length() > 0)
ps.println("bionix_abstract_txt - " + bionix_abstract_txt);
if (copyright.length() > 0)
ps.println("copyright - " + copyright);
if (affiliation.length() > 0)
ps.println("affiliation - " + affiliation);
if (authorList.length() > 0)
ps.println("authorList - " + authorList);
if (language.length() > 0)
ps.println("language - " + language);
if (meshHeadingList.length() > 0)
ps.println("meshHeadingList - " + meshHeadingList);
if (vernacularTitle.length() > 0)
ps.println("vernacularTitle - " + vernacularTitle);
if (investigatorList.length() > 0)
ps.println("investigatorList - " + investigatorList);
if (articleDate.length() > 0)
ps.println("articleDate - " + articleDate);
if (keywordOwner.length() > 0)
ps.println("keywordOwner- " + keywordOwner);
if (keywordList.length() > 0)
ps.println("keywordList - " + keywordList);
source = medlineTA + ". " + datepubDate_display + ";";
if (volume.trim().length() > 0)
source = source + volume;
if (issue.length() > 0)
source = source + "(" + issue + ")";
source = source + ":" + medlinePgn + ".";
ps.println("source - " + source);
if (publicationStatus.length() > 0)
ps.println("publicationStatus - " + publicationStatus);
if (articleIdList.length() > 0)
ps.println("articleIdList - " + articleIdList);
if (edat.length() > 0)
ps.println("edat - " + edat);
if (mhda.length() > 0)
ps.println("mhda - " + mhda);
System.out.println(" Writing " + file.getCanonicalPath());
} catch (Exception e_file) {
e_file.printStackTrace();
}
}