1 package compbio.runner.structure;
3 import static org.testng.Assert.assertFalse;
4 import static org.testng.Assert.assertNotNull;
5 import static org.testng.Assert.assertTrue;
6 import static org.testng.Assert.fail;
9 import java.io.FileInputStream;
10 import java.io.FileNotFoundException;
11 import java.io.IOException;
12 import java.util.ArrayList;
13 import java.util.Collections;
14 import java.util.List;
17 import javax.xml.bind.JAXBException;
18 import javax.xml.bind.ValidationException;
20 import org.apache.log4j.Level;
21 import org.apache.log4j.Logger;
22 import org.testng.annotations.BeforeMethod;
23 import org.testng.annotations.Test;
25 import compbio.engine.Configurator;
26 import compbio.engine.client.ConfiguredExecutable;
27 import compbio.engine.client.Executable.ExecProvider;
28 import compbio.engine.conf.RunnerConfigMarshaller;
29 import compbio.engine.local.ExecutableWrapper;
30 import compbio.engine.local.LocalRunner;
31 import compbio.metadata.AllTestSuit;
32 import compbio.metadata.JobExecutionException;
33 import compbio.metadata.JobSubmissionException;
34 import compbio.metadata.Option;
35 import compbio.metadata.Parameter;
36 import compbio.metadata.Preset;
37 import compbio.metadata.PresetManager;
38 import compbio.metadata.ResultNotAvailableException;
39 import compbio.metadata.RunnerConfig;
40 import compbio.runner.OptionCombinator;
41 import compbio.runner.structure.RNAalifold;
42 import compbio.util.FileUtil;
45 public class RNAalifoldParametersTester {
48 // should be: AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml"
49 static final String rnaalifoldConfigFile =
50 AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml";
51 public static String test_outfile = "rnaalifold.out.txt";
53 private static Logger log = Logger
54 .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
57 log.setLevel(Level.INFO);
60 RunnerConfig<RNAalifold> rnaalifoldConfig = null;
61 OptionCombinator rnaalifoldOpc = null;
63 @BeforeMethod(groups = { AllTestSuit.test_group_runner })
64 @SuppressWarnings("unchecked")
67 RunnerConfigMarshaller<RNAalifold> rnaalifoldmarsh =
68 new RunnerConfigMarshaller<RNAalifold>(RunnerConfig.class);
69 rnaalifoldConfig = rnaalifoldmarsh.read(new FileInputStream(new File(
70 rnaalifoldConfigFile)), RunnerConfig.class);
71 rnaalifoldOpc = new OptionCombinator(rnaalifoldConfig);
73 log.info("Num options: " + rnaalifoldOpc.getAllOptions().size());
74 log.info("Num params: " + rnaalifoldOpc.getAllParameters().size());
77 } catch (JAXBException e) {
79 fail(e.getLocalizedMessage());
80 } catch (FileNotFoundException e) {
82 fail(e.getLocalizedMessage());
87 public void testConfiguration() {
89 this.rnaalifoldConfig.validate();
90 } catch (ValidationException e) {
92 fail(e.getLocalizedMessage());
93 } catch (IllegalStateException e) {
95 fail(e.getLocalizedMessage());
99 @Test(groups = { AllTestSuit.test_group_runner })
100 public void testDefaultParameters() {
101 RNAalifold rnaalifold = new RNAalifold();
102 rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
105 // For local execution use relavive
106 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
107 .configureExecutable(rnaalifold);
108 LocalRunner lr = new LocalRunner(confRNAalifold);
110 confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
111 assertNotNull(confRNAalifold.getResults());
112 } catch (JobSubmissionException e) {
114 fail(e.getLocalizedMessage());
115 } catch (JobExecutionException e) {
117 fail(e.getLocalizedMessage());
118 } catch (ResultNotAvailableException e) {
120 fail(e.getLocalizedMessage());
124 @Test(groups = { AllTestSuit.test_group_runner })
125 public void testOptions() {
126 test(rnaalifoldOpc.getAllOptions());
129 @Test(groups = { AllTestSuit.test_group_runner })
130 public void testParameters() {
131 List<Parameter<?>> params = rnaalifoldOpc.getAllParameters();
132 Collections.shuffle(params);
136 @Test(groups = { AllTestSuit.test_group_runner })
137 public void testArguments() {
138 List<Option<?>> options = rnaalifoldOpc.getAllOptions();
139 options.addAll(rnaalifoldOpc.getAllParameters());
140 Collections.shuffle(options);
144 void test(Map<Parameter<?>, String> paramValue) {
145 List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(paramValue
147 for (int i = 0; i < paramValue.size(); i++) {
148 List<String> args = rnaalifoldOpc.parametersToCommandString(paramList,
151 Collections.shuffle(paramList);
153 log.info("NUMBER OF COMBINATION TESTED: " + paramValue.size());
156 void test(List<? extends Option<?>> params) {
157 for (int i = 0; i < params.size(); i++) {
158 List<String> args = rnaalifoldOpc.argumentsToCommandString(params);
160 Collections.shuffle(params);
162 log.info("NUMBER OF COMBINATION TESTED: " + params.size());
165 void singleTest(List<String> params) {
167 log.info("Using arguments: " + params);
168 RNAalifold rnaalifold = new RNAalifold();
169 rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);
171 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
172 .configureExecutable(rnaalifold, ExecProvider.Local);
173 // Add options to the executable
174 confRNAalifold.addParameters(params);
175 LocalRunner lr = new LocalRunner(confRNAalifold);
177 confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();
178 assertNotNull(confRNAalifold.getResults());
179 File errors = new File(confRNAalifold.getWorkDirectory(),
180 ExecutableWrapper.PROC_ERR_FILE);
181 if (errors.length() != 0) {
182 log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));
184 assertTrue(errors.length() == 0, "Run with arguments : " + params
186 Collections.shuffle(params);
187 } catch (JobSubmissionException e) {
189 fail(e.getLocalizedMessage());
190 } catch (JobExecutionException e) {
192 fail(e.getLocalizedMessage());
193 } catch (IOException e) {
195 fail(e.getLocalizedMessage());
196 } catch (ResultNotAvailableException e) {
198 fail(e.getLocalizedMessage());