--- /dev/null
+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());
+ }
+ }
+
+}
git://source.jalview.org / jabaws.git / blobdiff