Add testing dirs

[proteocache.git] / testsrc / compbio / casscode / structure / RNAalifoldTester.java

diff --git a/testsrc/compbio/casscode/structure/RNAalifoldTester.java b/testsrc/compbio/casscode/structure/RNAalifoldTester.java
new file mode 100644 (file)
index 0000000..370d040
--- /dev/null
+++ b/testsrc/compbio/casscode/structure/RNAalifoldTester.java
@@ -0,0 +1,119 @@
+package compbio.runner.structure;\r
+\r
+\r
+import static org.testng.Assert.assertEquals;\r
+import static org.testng.Assert.assertFalse;\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.assertNull;\r
+import static org.testng.Assert.assertTrue;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.text.ParseException;\r
+\r
+import javax.xml.bind.ValidationException;\r
+\r
+import org.apache.log4j.*;\r
+import org.ggf.drmaa.DrmaaException;\r
+import org.ggf.drmaa.JobInfo;\r
+import org.testng.annotations.BeforeMethod;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.ScoreManager.ScoreHolder;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.SyncExecutor;\r
+import compbio.engine.client.ConfExecutable;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.RunConfiguration;\r
+import compbio.engine.cluster.drmaa.ClusterEngineUtil;\r
+import compbio.engine.cluster.drmaa.ClusterRunner;\r
+import compbio.engine.cluster.drmaa.StatisticManager;\r
+import compbio.engine.local.AsyncLocalRunner;\r
+import compbio.engine.local.LocalExecutorService;\r
+import compbio.engine.local.LocalRunner;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.JobExecutionException;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.runner.msa.ClustalW;\r
+import compbio.runner.structure.RNAalifold;\r
+\r
+public class RNAalifoldTester {\r
+\r
+       private static Logger log = Logger\r
+                       .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);\r
+       \r
+       \r
+       private RNAalifold rnaalifold;\r
+       \r
+       static final String rnaalifoldConfigFile = AllTestSuit.TEST_DATA_PATH\r
+                       + "RNAalifoldParameters.xml";\r
+       public static String test_outfile = "rnaalifold.out";\r
+       \r
+       \r
+       @Test(groups = { AllTestSuit.test_group_runner })\r
+       public void testRunLocally() {\r
+               RNAalifold rnaalifold = new RNAalifold();\r
+               rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r
+               try{\r
+                       \r
+                       ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
+                                       .configureExecutable(rnaalifold, Executable.ExecProvider.Local);\r
+                       LocalRunner lr = new LocalRunner(confRNAalifold);\r
+                       lr.executeJob();\r
+                       confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();\r
+                       \r
+                       System.out.println("TEST");\r
+                       System.out.println(((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
+                       \r
+                       assertNotNull(confRNAalifold.getResults()); \r
+               } catch (JobSubmissionException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (JobExecutionException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               } catch (ResultNotAvailableException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getLocalizedMessage());\r
+               }\r
+       }\r
+       \r
+       \r
+       public static void main(String[] args) throws JobSubmissionException,\r
+                       JobExecutionException, InterruptedException, ResultNotAvailableException {\r
+\r
+               \r
+               log.warn("Logger test :- Run RNAalifold.main()");\r
+\r
+               RNAalifold rnaalifold = new RNAalifold();\r
+               rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput("test_outfile.txt");\r
+               \r
+               ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
+                                       .configureExecutable(rnaalifold);\r
+               AsyncExecutor lr = new AsyncLocalRunner();\r
+               lr.submitJob(confRNAalifold);\r
+               \r
+               \r
+               System.out.println(((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
+\r
+               \r
+               Thread.sleep(3000);\r
+               LocalExecutorService.shutDown();\r
+               \r
+       }\r
+       \r
+}\r