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| import java.net .*;
import java.io. *;
import org.jdom.*;
import org.jdom.input.*;
import java.util.Iterator;
import java.util.List;
import jxl.*;
import jxl.read.biff.BiffException;
public class Projet {
private static int c = 0;
private static int c2 = 0;
public static void main(String[] args) throws IOException, BiffException, JDOMException
{
try{
InputStreamReader isr=new InputStreamReader (System.in);
BufferedReader br=new BufferedReader (isr);
System.out.println("Rentrez le chemin du classeur");
String url = br.readLine();
Workbook nomgpcr = Workbook.getWorkbook(new File(url));
Sheet feuille0 = nomgpcr.getSheet(0);
int Nb_gpcr=feuille0.getRows();
String[] tab_gpcr_exel=new String [Nb_gpcr];
tabexel(feuille0,Nb_gpcr,tab_gpcr_exel);
nomgpcr.close();
String[] Tab_Pubmed=new String [200];
CoOmim(Nb_gpcr,tab_gpcr_exel,Tab_Pubmed);
String tab_num_pubmed[] = new String [50];
CoPubmed(Tab_Pubmed,tab_num_pubmed);
}
catch (IOException e) {System.err.println("erreur");}
}
private static void tabexel (Sheet feuille0,int Nb_gpcr,String[] tab_gpcr_exel)
{
for ( int c=0 ; c<Nb_gpcr ; c++ )
{
tab_gpcr_exel[c]=feuille0.getCell(0,c).getContents();
}
}
private static void CoOmim(int Nb_gpcr,String []tab_gpcr,String []Tab_Pubmed) throws IOException, JDOMException
{
for ( c=0 ; c<Nb_gpcr ; c++ )
{
URL url = new URL("http://www.ncbi.nlm.nih.gov/sites/entrez?EntrezSystem2.PEntrez.Omim.SearchBar.Db=omim&EntrezSystem2.PEntrez.Omim.SearchBar.Term="+tab_gpcr[c]+"&EntrezSystem2.PEntrez.DbConnector.Db=omim&EntrezSystem2.PEntrez.DbConnector.LastDb=omim&EntrezSystem2.PEntrez.DbConnector.Term="+tab_gpcr[c]);
BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
String inputLine;
File fichier = new File("code_source_omim.xml") ;
PrintWriter out = new PrintWriter(new FileWriter(fichier)) ;
int compt=0;
while (((inputLine = in.readLine()) != null) )
{
compt++;
if (compt!=2)
{
out.write(inputLine);
out.println() ;
}
}
out.flush();
out.close() ;
in.close();
ParseOmim(Nb_gpcr,tab_gpcr,Tab_Pubmed);
}
}
private static void ParseOmim(int Nb_gpcr,String []tab_gpcr,String []tab_Pubmed) throws IOException, JDOMException
{
SAXBuilder sxb = new SAXBuilder();
org.jdom.Document document;
document = sxb.build(new File("code_source_omim.xml"));
Element racine;
racine = document.getRootElement();
Namespace nameSpace = Namespace.getNamespace("html", "http://www.w3.org/1999/xhtml");
Element body = racine.getChild("body",nameSpace);
Element form =body.getChild("form",nameSpace);
Object div = ((List) form.getChildren("div",nameSpace)).get(0);
Element div2 = ((Element) div).getChild("div",nameSpace);
Object div3 = ((List)div2.getChildren("div",nameSpace)).get(1);
Object div4 = ((Element) div3).getChildren("div",nameSpace).get(3);
Element div5 = ((Element) div4).getChild("div",nameSpace);
String resultat1 = (((Element) ((Element)div5).getChildren().get(1)).getTextTrim());
String resultat="The following term was not found in OMIM: "+tab_gpcr[c]+".See . No items found.";
if ( egal(resultat1,resultat)==true)
{
tab_Pubmed[c2]=tab_gpcr[c];
c2++;
}
else
System.out.println("no");
}
private static boolean egal (String p1,String p2)
{
boolean p = false;
int ph1=p1.length();
int ph2=p2.length();
if (ph1==ph2)
{
p=true;
for (int i=0;i<ph1;i++)
{
if (p1.charAt(i)!=p2.charAt(i))
{
p=false;
}
}
}
return p;
}
private static void CoPubmed(String[] Tab_Pubmed,String[]tab_num_pubmed) throws IOException, JDOMException
{
for ( c=0 ; c<c2 ; c++ )
{
OutputStreamWriter writer = null;
BufferedReader reader = null;
URL url = new URL(" http://www.ncbi.nlm.nih.gov/sites/entrez");
String data = ("EntrezSystem2.PEntrez.DbConnector.Db=pubmed&EntrezSystem2.PEntrez.DbConnector.LastDb=pubmed&EntrezSystem2.PEntrez.DbConnector.Term="+Tab_Pubmed[c]+"&EntrezSystem2.PEntrez.DbConnector.LastTabCmd=results&EntrezSystem2.PEntrez.DbConnector.LastQueryKey=1&EntrezSystem2.PEntrez.DbConnector.IdsFromResult=&EntrezSystem2.PEntrez.DbConnector.LastIdsFromResult=&EntrezSystem2.PEntrez.DbConnector.LinkName=&EntrezSystem2.PEntrez.DbConnector.LinkReadableName=&EntrezSystem2.PEntrez.DbConnector.Lin0kSrcDb=&EntrezSystem2.PEntrez.DbConnector.Cmd=Go&EntrezSystem2.PEntrez.DbConnector.TabCmd=&EntrezSystem2.PEntrez.DbConnector.QueryKey=&EntrezSystem2.PEntrez.Pubmed.Pubmed_SearchBar.SearchResourceList=pubmed&EntrezSystem2.PEntrez.Pubmed.Pubmed_SearchBar.Term="+Tab_Pubmed[c]+"&EntrezSystem2.PEntrez.Pubmed.Pubmed_SearchBar.FeedLimit=15&EntrezSystem2.PEntrez.Pubmed.Pubmed_SearchBar.FeedName="+Tab_Pubmed[c]+"&EntrezSystem2.PEntrez.Pubmed.Pubmed_SearchBar.CurrDb=pubmed&EntrezSystem2.PEntrez.Pubmed.Entrez_PageController.PreviousPageName=results&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.sPresentation=docsum&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.sSort=none&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.FFormat=docsum&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.FSort=&email_format=docsum&email_sort=&email_address=&email_add_text=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.FileFormat=docsum&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.LastPresentation=docsum&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.Presentation=docsum&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.PageSize=20&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.LastPageSize=20&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.Sort=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.LastSort=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.FileSort=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.Format=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.LastFormat=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_ResultsController.ResultCount=4&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_ResultsController.RunLastQuery=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.sPresentation2=docsum&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.sSort2=none&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.FFormat2=docsum&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DisplayBar.FSort2=&email_format2=docsum&email_sort2=&email_address2=&email_add_text2=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Entrez_Filters.CurrFilter=all&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Entrez_Filters.LastFilter=all&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_MultiItemSupl.RelatedDataLinks.rdDatabase=rddbto&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_MultiItemSupl.Discovery_SearchDetails.SearchDetailsTerm="+Tab_Pubmed[c]+"&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.HistoryDisplay.Cmd=Go&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.EmailTab.EmailReport=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.EmailTab.EmailFormat=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.EmailTab.EmailCount=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.EmailTab.EmailStart=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.EmailTab.EmailSort=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.EmailTab.Email=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.EmailTab.EmailText=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.EmailTab.EmailQueryKey=&EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.EmailTab.QueryDescription=&p%24a=EntrezSystem2.PEntrez.Pubmed.Pubmed_SearchBar.Search&p%24l=EntrezSystem2&p%24el=&p%24st=entrez");
URLConnection conn = url.openConnection();
conn.setDoOutput(true);
OutputStreamWriter osw = new OutputStreamWriter(conn.getOutputStream());
osw.write(data);
osw.flush();
osw.close();
BufferedReader br = new BufferedReader(new InputStreamReader(conn.getInputStream()));
File fichier = new File("code_source_Pubmed.xml") ;
PrintWriter out = new PrintWriter(new FileWriter(fichier)) ;
String line;
int c=0;
while (((line = br.readLine()) != null) )
{ c++;
if (c!=2)
{
out.write(line);
out.println() ;} }
out.close() ;
out.flush();
br.close();
ParsePubmed(tab_num_pubmed,Tab_Pubmed);
}
}
private static void ParsePubmed(String[]tab_num_pubmed,String[]Tab_Pubmed) throws IOException, JDOMException
{
SAXBuilder sxb = new SAXBuilder();
org.jdom.Document document;
document = sxb.build(new File("code_source_Pubmed.xml"));
Element racine;
racine = document.getRootElement();
Namespace nameSpace = Namespace.getNamespace("html", "http://www.w3.org/1999/xhtml");
Element body = racine.getChild("body",nameSpace);
Element form =body.getChild("form",nameSpace);
Object div = ((List) form.getChildren("div",nameSpace)).get(1);
Object div2 = ((List)((Element) div).getChildren("div",nameSpace)).get(2);
Element div3 =((Element) div2).getChild("div",nameSpace);
Element div4 = ((Element) div3).getChild("div",nameSpace);
Object div5 = ((List)((Element) div4).getChildren("div",nameSpace)).get(3);
List divs = ((Element) div5).getChildren("div",nameSpace);
Iterator i = divs.iterator();
while(i.hasNext()){
Element courant = (Element)i.next();
Element div6 = courant.getChild("div",nameSpace);
String res=div6.getChild("input",nameSpace).getAttribute("value").getValue();
Text_pubmed(res,Tab_Pubmed);
}
}
private static void Text_pubmed (String res,String[]Tab_Pubmed) throws IOException, JDOMException
{
URL url = new URL(" http://www.ncbi.nlm.nih.gov/sites/entrez/"+res);
BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
String inputLine;
File fichier = new File("t.xml") ;
PrintWriter out = new PrintWriter(new FileWriter(fichier)) ;
int compt=0;
while (((inputLine = in.readLine()) != null) )
{
compt++;
if (compt!=2)
{
out.write(inputLine);
out.println() ;
}
}
out.close() ;
out.flush();
in.close();
System.out.println(res);
SAXBuilder sxb = new SAXBuilder();
org.jdom.Document document;
document = sxb.build(new File("t.xml"));
Element racine;
racine = document.getRootElement();
Namespace nameSpace = Namespace.getNamespace("html", "http://www.w3.org/1999/xhtml");
Element body = racine.getChild("body",nameSpace);
Element form =body.getChild("form",nameSpace);
Object div = ((List) form.getChildren("div",nameSpace)).get(1);
Object div2 = ((List)((Element) div).getChildren("div",nameSpace)).get(2);
Object div3 = ((Element) div2).getChildren("div",nameSpace).get(0);
Element div4 =((Element) div3).getChild("div",nameSpace);
Object div5 = ((List) ((Element) div4).getChildren("div",nameSpace)).get(3);
Element div6 = ((Element) div5).getChild("div",nameSpace);
Element div7 = div6.getChild("div",nameSpace);
String line= div7.getChild("p",nameSpace).getText();
String tab[]=new String[50];
//tab[cpt]=line;
//cpt++;
System.out.println(line);
}
} |
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