Remove JABAWS testing code

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

diff --git a/testsrc/compbio/casscode/structure/RNAalifoldTester.java b/testsrc/compbio/casscode/structure/RNAalifoldTester.java
deleted file mode 100644 (file)
index 370d040..0000000
--- a/testsrc/compbio/casscode/structure/RNAalifoldTester.java
+++ /dev/null
@@ -1,119 +0,0 @@
-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