/*
* 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");
}
}
}
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);
}