Esempio n. 1
0
  /*
   * Récupère les génomes des chimpanzés.
   * Le résultat de la requete est le bon mais c'est lent et une erreur sort du try catch ...
   * http://www.ncbi.nlm.nih.gov/books/NBK25498/ -> application 3
   */
  public static void SecondTest() {
    // chimpanzee peut etre remplacé par "human" par exemple.
    String query = "chimpanzee[orgn]+AND+biomol+mrna[prop]";

    // query = "human[orgn]";
    String url = base + "esearch.fcgi?db=nucleotide&term=" + query + "&usehistory=y";

    String data = getHTML(url);
    RenderXML(data);

    String webEnv = EUtilities.getWebEnv(data);
    String key = EUtilities.getQueryKey(data);
    String countS = EUtilities.getCount(data);
    int count = Integer.parseInt(countS);
    // open(OUT, ">chimp.fna") || die "Can't open file!\n";

    int retmax = 500;
    int retstart;

    long start = System.currentTimeMillis();
    long chrono = System.currentTimeMillis();

    for (retstart = 0; retstart < count; retstart += retmax) {
      String efetch_url = base + "efetch.fcgi?db=nucleotide&WebEnv=" + webEnv;
      efetch_url += "&query_key=" + key + "&retstart=" + retstart;
      efetch_url += "&retmax=" + retmax + "&rettype=gb&retmode=text";

      try {
        System.out.print("read : ");
        String content = getHTML(efetch_url);

        chrono = System.currentTimeMillis();
        PrintTime(chrono - start);
        System.out.print("write : ");

        start = System.currentTimeMillis();
        FilesUtils.SaveFile("" + retstart, content);
        chrono = System.currentTimeMillis();
        PrintTime(chrono - start);
        start = chrono;
        System.out.println();
      } catch (Exception e) {
        System.out.println("ERROR");
      }
    }
  }
Esempio n. 2
0
  public static void FirstTest() {
    EUtilities eUtils = new EUtilities();

    String db = "protein";
    String id_list = "194680922,50978626,28558982,9507199,6678417";
    id_list = "28558982";

    String base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/";
    String url = base + "epost.fcgi?db=" + db + "&id=" + id_list;

    String xml = getHTML(url);

    String web = EUtilities.getWebEnv(xml);
    String key = EUtilities.getQueryKey(xml);

    url = base + "esummary.fcgi?db=" + db + "&query_key=" + key + "&WebEnv=" + web;

    String docsums = getHTML(url);
    System.out.println("Docsums :");
    RenderXML(docsums);

    url = base + "efetch.fcgi?db=" + db + "&query_key=" + key + "&WebEnv=" + web;
    url += "&rettype=fasta&retmode=text";

    String data = getHTML(url);

    System.out.println("Data :");
    RenderXML(data);

    ArrayList<Species> species = new ArrayList<Species>();
    species = EUtilities.getSpecies(data);

    for (Species spe : species) {
      System.out.println(spe);
    }

    System.out.println("\n phase 2 \n");

    String dbGene = "gene";
    String linkname = "protein_gene";

    url = base + "elink.fcgi?dbfrom=" + db + "&db=" + dbGene + "&id=" + id_list;
    url += "&linkname=" + linkname + "&cmd=neighbor_history";

    xml = getHTML(url);

    web = EUtilities.getWebEnv(xml);
    key = EUtilities.getQueryKey(xml);

    url = base + "esummary.fcgi?db=" + db + "&query_key=" + key + "&WebEnv=" + web;

    System.out.println("\n xml \n");
    System.out.println(key);
    xml = getHTML(url);
    RenderXML(xml);

    url =
        base
            + "efetch.fcgi?db="
            + dbGene
            + "&query_key="
            + key
            + "&WebEnv="
            + web; // + "&id_list=" + id_list;
    url += "&rettype=xml&retmode=xml";

    System.out.println("\n data \n");
    System.out.println(url);
    data = getHTML(url);
    System.out.println("Render");
    // RenderXML(data);
    FilesUtils.SaveFile("test", data);
  }