Mercurial > repos > mikel-egana-aranguren > sadi_generic

annotate src/info/wilkinsonlab/sadi/galaxy/SADIGenericClient.java @ 2:977c838e3442 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
New dir structure, README improved, tests added and RDF merge tool created
author mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
date Fri, 25 Apr 2014 14:41:12 +0200
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
1 package info.wilkinsonlab.sadi.galaxy;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
2
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
3 import java.io.InputStream;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
4 import java.util.Collection;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
5
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
6 import org.apache.log4j.Logger;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
7
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
8 import org.sadiframework.SADIException;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
9 import org.sadiframework.client.Service;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
10 import org.sadiframework.client.ServiceFactory;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
11
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
12 import com.hp.hpl.jena.rdf.model.Model;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
13 import com.hp.hpl.jena.rdf.model.ModelFactory;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
14 import com.hp.hpl.jena.rdf.model.Resource;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
15 import com.hp.hpl.jena.util.FileManager;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
16
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
17 public class SADIGenericClient {
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
18
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
19 /**
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
20 * @param service_URL
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
21 * @param input_RDF
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
22 *
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
23 * Given an RDF input and a service URL, infers whether the RDF
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
24 * complies with the service and if so executes it
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
25 *
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
26 */
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
27
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
28 // private static final Logger log = Logger.getLogger(SADIGenericClient.class);
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
29 public static void main(String[] args) {
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
30 String service_URL = args[0];
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
31 String input_RDF = args[1];
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
32
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
33 Service service;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
34 try {
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
35 service = ServiceFactory.createService(service_URL.trim());
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
36 }
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
37 catch (SADIException e) {
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
38 System.out.println("[ERROR] Error creating service object: ");
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
39 System.out.println(e.getMessage());
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
40 e.printStackTrace();
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
41 service = null;
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
42 }
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
43
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
44 if (service != null) {
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
45
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
46 Model model = ModelFactory.createOntologyModel();
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
47 InputStream in = FileManager.get().open(input_RDF);
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
48 model.read(in, null);
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
49
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
50 try {
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
51 Collection<Resource> inputs = service.discoverInputInstances(model);
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
52 Model output = service.invokeService(inputs);
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
53 output.write(System.out, "RDF/XML");
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
54 output.close();
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
55 }
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
56 catch (SADIException e) {
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
57 System.out.println("[ERROR] Error invoking service: ");
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
58 System.out.println(e.getMessage());
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
59 e.printStackTrace();
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
60 }
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
61 }
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
62 }
977c838e3442 New dir structure, README improved, tests added and RDF merge tool created
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
63 }