X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Fcompbio%2Frunner%2Fstructure%2FRNAalifoldParametersTester.java;fp=testsrc%2Fcompbio%2Frunner%2Fstructure%2FRNAalifoldParametersTester.java;h=9c15537700a0f5ac9e40956e6496146a4776de37;hb=424e935319103a35bea321a15911ad51fc78ebaf;hp=0000000000000000000000000000000000000000;hpb=8f275a6850e693e670e77dc6c8c83b77b2c0d25a;p=jabaws.git

diff --git a/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java b/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java
new file mode 100644
index 0000000..9c15537
--- /dev/null
+++ b/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java
@@ -0,0 +1,202 @@
+package compbio.runner.structure;
+
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.ValidationException;
+
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import compbio.engine.Configurator;
+import compbio.engine.client.ConfiguredExecutable;
+import compbio.engine.client.Executable.ExecProvider;
+import compbio.engine.conf.RunnerConfigMarshaller;
+import compbio.engine.local.ExecutableWrapper;
+import compbio.engine.local.LocalRunner;
+import compbio.metadata.AllTestSuit;
+import compbio.metadata.JobExecutionException;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.Option;
+import compbio.metadata.Parameter;
+import compbio.metadata.Preset;
+import compbio.metadata.PresetManager;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.metadata.RunnerConfig;
+import compbio.runner.OptionCombinator;
+import compbio.runner.structure.RNAalifold;
+import compbio.util.FileUtil;
+
+
+public class RNAalifoldParametersTester {
+
+	
+	// should be: AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml"
+	static final String rnaalifoldConfigFile = 
+			AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml";
+	public static String test_outfile = "rnaalifold.out.txt";
+
+	private static Logger log = Logger
+			.getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
+	
+	static {
+		log.setLevel(Level.INFO);
+	}
+	
+	RunnerConfig<RNAalifold> rnaalifoldConfig = null;
+	OptionCombinator rnaalifoldOpc = null;
+	
+	@BeforeMethod(groups = { AllTestSuit.test_group_runner })
+	@SuppressWarnings("unchecked")
+	public void setup() {
+		try {
+			RunnerConfigMarshaller<RNAalifold> rnaalifoldmarsh = 
+					new RunnerConfigMarshaller<RNAalifold>(RunnerConfig.class);
+			rnaalifoldConfig = rnaalifoldmarsh.read(new FileInputStream(new File(
+					rnaalifoldConfigFile)), RunnerConfig.class);
+			rnaalifoldOpc = new OptionCombinator(rnaalifoldConfig);
+			
+			log.info("Num options: " + rnaalifoldOpc.getAllOptions().size());
+			log.info("Num params: " + rnaalifoldOpc.getAllParameters().size());
+			
+			
+		} catch (JAXBException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		}
+	}
+	
+	@Test
+	public void testConfiguration() {
+		try {
+			this.rnaalifoldConfig.validate();
+		} catch (ValidationException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (IllegalStateException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		}
+	}
+
+	@Test(groups = { AllTestSuit.test_group_runner })
+	public void testDefaultParameters() {
+		RNAalifold rnaalifold = new RNAalifold();
+		rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
+
+		try {
+			// For local execution use relavive
+			ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
+					.configureExecutable(rnaalifold);
+			LocalRunner lr = new LocalRunner(confRNAalifold);
+			lr.executeJob();
+			confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
+			assertNotNull(confRNAalifold.getResults());
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (JobExecutionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (ResultNotAvailableException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		}
+	}
+	
+	@Test(groups = { AllTestSuit.test_group_runner })
+	public void testOptions() {
+		test(rnaalifoldOpc.getAllOptions());
+	}
+
+	@Test(groups = { AllTestSuit.test_group_runner })
+	public void testParameters() {
+		List<Parameter<?>> params = rnaalifoldOpc.getAllParameters();
+		Collections.shuffle(params);
+		test(params);
+	}
+
+	@Test(groups = { AllTestSuit.test_group_runner })
+	public void testArguments() {
+		List<Option<?>> options = rnaalifoldOpc.getAllOptions();
+		options.addAll(rnaalifoldOpc.getAllParameters());
+		Collections.shuffle(options);
+		test(options);
+	}
+	
+	void test(Map<Parameter<?>, String> paramValue) {
+		List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(paramValue
+				.keySet());
+		for (int i = 0; i < paramValue.size(); i++) {
+			List<String> args = rnaalifoldOpc.parametersToCommandString(paramList, 
+					paramValue);
+			singleTest(args);
+			Collections.shuffle(paramList);
+		}
+		log.info("NUMBER OF COMBINATION TESTED: " + paramValue.size());
+	}
+	
+	void test(List<? extends Option<?>> params) {
+		for (int i = 0; i < params.size(); i++) {
+			List<String> args = rnaalifoldOpc.argumentsToCommandString(params);
+			singleTest(args);
+			Collections.shuffle(params);
+		}
+		log.info("NUMBER OF COMBINATION TESTED: " + params.size());
+	}
+	
+	void singleTest(List<String> params) {
+		try {
+			log.info("Using arguments: " + params);
+			RNAalifold rnaalifold = new RNAalifold();
+			rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
+			
+			ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
+					.configureExecutable(rnaalifold, ExecProvider.Local);
+			// Add options to the executable
+			confRNAalifold.addParameters(params);
+			LocalRunner lr = new LocalRunner(confRNAalifold);
+			lr.executeJob();
+			confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
+			assertNotNull(confRNAalifold.getResults());
+			File errors = new File(confRNAalifold.getWorkDirectory(),
+					ExecutableWrapper.PROC_ERR_FILE);
+			if (errors.length() != 0) {
+				log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));
+			}
+			assertTrue(errors.length() == 0, "Run with arguments : " + params
+					+ " FAILED!");
+			Collections.shuffle(params);
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (JobExecutionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (IOException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (ResultNotAvailableException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		}
+	}
+	
+}