Mercurial > repos > mikel-egana-aranguren > ncbo_services

annotate NCBO_services/extract.java @ 23:02fd92020943

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author jose-minyarro
date Mon, 19 Mar 2012 08:17:58 -0400
parents 1910c878378c
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1910c878378c get_ontology menu improved (Automatically generated), source added, readme improved
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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1 package es.upm.fi.dia.oeg.ncbo.galaxy;
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2
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3 import java.io.BufferedReader;
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4 import java.io.BufferedWriter;
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5 import java.io.IOException;
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6 import java.io.InputStream;
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7 import java.io.InputStreamReader;
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8 import java.io.OutputStreamWriter;
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10 import org.apache.http.HttpEntity;
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11 import org.apache.http.HttpResponse;
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12 import org.apache.http.client.ClientProtocolException;
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13 import org.apache.http.client.HttpClient;
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14 import org.apache.http.client.methods.HttpGet;
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15 import org.apache.http.impl.client.DefaultHttpClient;
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17 public class extract {
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19 /**
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20 * @param args
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21 * @throws IOException
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22 * @throws ClientProtocolException
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23 */
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24 public static void main(String[] args) throws ClientProtocolException, IOException {
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26 // http://www.bioontology.org/wiki/index.php/View_Extraction
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27 // ./viewextractor/{ontology version id}[?{args}]&apikey={YourAPIKey}
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29 String api_key = args [0];
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30 String ontologyversionid = args [1]; // 35686
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31 String conceptid = args [2]; // E800-E999.9
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32 String filterrelations = args [3]; // PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass,[R]SIB,SI
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33 String ontologyname = args [4]; // http://who.int/icd9
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35 HttpClient client = new DefaultHttpClient();
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37 // HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/35686/" +
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38 // "?conceptid=E800-E999.9&filterrelations=PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass," +
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39 // "[R]SIB,SIB&existontology=true&ontologyname=http://who.int/icd9&apikey=74c12fc6-9423-455a-a619-b94f47d1951b");
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41 HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/" + ontologyversionid +
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42 "/?conceptid="+ conceptid +"&filterrelations=" + filterrelations +
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43 "&existontology=true&ontologyname="+ ontologyname + "&apikey=" + api_key);
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45 HttpResponse response = client.execute(get);
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46 HttpEntity entity = response.getEntity();
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47 if (entity != null) {
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48 InputStream instream = entity.getContent();
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49 InputStreamReader is=new InputStreamReader(instream);
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50 BufferedReader br=new BufferedReader(is);
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51 String read=br.readLine();
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52 BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));
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53 while(read!=null){
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54 // System.out.println(read);
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55 bw.write(read);
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56 bw.newLine();
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57 read=br.readLine();
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58 }
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59 bw.close();
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60 instream.close();
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61 }
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63 }
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65 }