1 package compbio.runner.structure;
4 import static org.testng.Assert.assertEquals;
5 import static org.testng.Assert.assertFalse;
6 import static org.testng.Assert.assertNotNull;
7 import static org.testng.Assert.assertNull;
8 import static org.testng.Assert.assertTrue;
9 import static org.testng.Assert.fail;
12 import java.io.FileInputStream;
13 import java.io.FileNotFoundException;
14 import java.io.IOException;
15 import java.text.ParseException;
17 import javax.xml.bind.ValidationException;
19 import org.apache.log4j.*;
20 import org.ggf.drmaa.DrmaaException;
21 import org.ggf.drmaa.JobInfo;
22 import org.testng.annotations.BeforeMethod;
23 import org.testng.annotations.Test;
25 import compbio.data.sequence.Score;
26 import compbio.data.sequence.ScoreManager;
27 import compbio.data.sequence.ScoreManager.ScoreHolder;
28 import compbio.data.sequence.SequenceUtil;
29 import compbio.engine.AsyncExecutor;
30 import compbio.engine.Configurator;
31 import compbio.engine.SyncExecutor;
32 import compbio.engine.client.ConfExecutable;
33 import compbio.engine.client.ConfiguredExecutable;
34 import compbio.engine.client.Executable;
35 import compbio.engine.client.RunConfiguration;
36 import compbio.engine.cluster.drmaa.ClusterUtil;
37 import compbio.engine.cluster.drmaa.JobRunner;
38 import compbio.engine.cluster.drmaa.StatisticManager;
39 import compbio.engine.local.AsyncLocalRunner;
40 import compbio.engine.local.LocalExecutorService;
41 import compbio.engine.local.LocalRunner;
42 import compbio.metadata.AllTestSuit;
43 import compbio.metadata.JobExecutionException;
44 import compbio.metadata.JobStatus;
45 import compbio.metadata.JobSubmissionException;
46 import compbio.metadata.LimitsManager;
47 import compbio.metadata.PresetManager;
48 import compbio.metadata.ResultNotAvailableException;
49 import compbio.metadata.RunnerConfig;
50 import compbio.runner.msa.ClustalW;
51 import compbio.runner.structure.RNAalifold;
53 public class RNAalifoldTester {
55 private static Logger log = Logger
56 .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
59 private RNAalifold rnaalifold;
61 static final String rnaalifoldConfigFile = AllTestSuit.TEST_DATA_PATH
62 + "RNAalifoldParameters.xml";
63 public static String test_outfile = "rnaalifold.out";
65 @Test(groups = { AllTestSuit.test_group_runner })
66 public void testRunLocally() {
67 RNAalifold rnaalifold = new RNAalifold();
68 rnaalifold.setInput(AllTestSuit.test_alignment_input).setOutput(test_outfile);
71 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
72 .configureExecutable(rnaalifold, Executable.ExecProvider.Local);
73 LocalRunner lr = new LocalRunner(confRNAalifold);
75 confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
76 assertNotNull(confRNAalifold.getResults());
77 } catch (JobSubmissionException e) {
79 fail(e.getLocalizedMessage());
80 } catch (JobExecutionException e) {
82 fail(e.getLocalizedMessage());
83 } catch (ResultNotAvailableException e) {
85 fail(e.getLocalizedMessage());
90 public static void main(String[] args) throws JobSubmissionException,
91 JobExecutionException, InterruptedException {
94 log.warn("Logger test :- Run RNAalifold.main()");
96 RNAalifold rnaalifold = new RNAalifold();
97 rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput("test_outfile.txt");
99 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
100 .configureExecutable(rnaalifold);
101 AsyncExecutor lr = new AsyncLocalRunner();
102 lr.submitJob(confRNAalifold);
105 LocalExecutorService.shutDown();