/** Gets the initial list of ids */
private SearchResult getIds(String term, int start, int pacing) {
String baseUrl = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils";
String medlineUrl =
baseUrl
+ "/esearch.fcgi?db=pubmed&retmax="
+ Integer.toString(pacing)
+ "&retstart="
+ Integer.toString(start)
+ "&term=";
Pattern idPattern = Pattern.compile("<Id>(\\d+)</Id>");
Pattern countPattern = Pattern.compile("<Count>(\\d+)<\\/Count>");
Pattern retMaxPattern = Pattern.compile("<RetMax>(\\d+)<\\/RetMax>");
Pattern retStartPattern = Pattern.compile("<RetStart>(\\d+)<\\/RetStart>");
boolean doCount = true;
SearchResult result = new SearchResult();
try {
URL ncbi = new URL(medlineUrl + term);
// get the ids
BufferedReader in = new BufferedReader(new InputStreamReader(ncbi.openStream()));
String inLine;
while ((inLine = in.readLine()) != null) {
// get the count
Matcher idMatcher = idPattern.matcher(inLine);
if (idMatcher.find()) {
result.addID(idMatcher.group(1));
}
Matcher retMaxMatcher = retMaxPattern.matcher(inLine);
if (retMaxMatcher.find()) {
result.retmax = Integer.parseInt(retMaxMatcher.group(1));
}
Matcher retStartMatcher = retStartPattern.matcher(inLine);
if (retStartMatcher.find()) {
result.retstart = Integer.parseInt(retStartMatcher.group(1));
}
Matcher countMatcher = countPattern.matcher(inLine);
if (doCount && countMatcher.find()) {
result.count = Integer.parseInt(countMatcher.group(1));
doCount = false;
}
}
} catch (MalformedURLException e) { // new URL() failed
System.out.println("bad url");
e.printStackTrace();
} catch (IOException e) { // openConnection() failed
System.out.println("connection failed");
e.printStackTrace();
}
return result;
}
