diff NCBO_services/extract.java @ 20:1910c878378c

get_ontology menu improved (Automatically generated), source added, readme improved

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/extract.java	Wed Jan 25 19:49:20 2012 +0100
@@ -0,0 +1,65 @@
+package es.upm.fi.dia.oeg.ncbo.galaxy;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.DefaultHttpClient;
+
+public class extract {
+
+	/**
+	 * @param args
+	 * @throws IOException 
+	 * @throws ClientProtocolException 
+	 */
+	public static void main(String[] args) throws ClientProtocolException, IOException {
+		
+//		http://www.bioontology.org/wiki/index.php/View_Extraction
+//		./viewextractor/{ontology version id}[?{args}]&apikey={YourAPIKey} 
+			    
+		String api_key = args [0]; 
+	    String ontologyversionid =  args [1]; // 35686
+	    String conceptid = args [2]; // E800-E999.9
+	    String filterrelations = args [3]; // PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass,[R]SIB,SI
+	    String ontologyname = args [4]; // http://who.int/icd9
+	    
+		HttpClient client = new DefaultHttpClient();
+		
+//		HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/35686/" +
+//				"?conceptid=E800-E999.9&filterrelations=PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass," +
+//				"[R]SIB,SIB&existontology=true&ontologyname=http://who.int/icd9&apikey=74c12fc6-9423-455a-a619-b94f47d1951b");
+		
+		HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/" + ontologyversionid +
+				"/?conceptid="+ conceptid +"&filterrelations=" + filterrelations +
+				"&existontology=true&ontologyname="+ ontologyname + "&apikey=" + api_key);
+
+		HttpResponse response = client.execute(get);
+		HttpEntity entity = response.getEntity();
+		if (entity != null) {	
+			InputStream instream = entity.getContent();
+			InputStreamReader is=new InputStreamReader(instream);
+			BufferedReader br=new BufferedReader(is);
+			String read=br.readLine();
+			BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));
+			while(read!=null){
+//			    System.out.println(read);
+				bw.write(read);
+				bw.newLine();
+			    read=br.readLine();
+			}
+			bw.close();
+			instream.close();
+		}
+
+	}
+
+}