Beispiel #1
0
  /** 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;
  }