+++ /dev/null
-package compbio.runner.structure;\r
-\r
-import static org.testng.Assert.assertFalse;\r
-import static org.testng.Assert.assertNotNull;\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.util.ArrayList;\r
-import java.util.Collections;\r
-import java.util.List;\r
-import java.util.Map;\r
-\r
-import javax.xml.bind.JAXBException;\r
-import javax.xml.bind.ValidationException;\r
-\r
-import org.apache.log4j.Level;\r
-import org.apache.log4j.Logger;\r
-import org.testng.annotations.BeforeMethod;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.data.sequence.RNAStructScoreManager;\r
-import compbio.data.sequence.ScoreManager;\r
-import compbio.engine.Configurator;\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.engine.client.Executable.ExecProvider;\r
-import compbio.engine.conf.RunnerConfigMarshaller;\r
-import compbio.engine.local.ExecutableWrapper;\r
-import compbio.engine.local.LocalRunner;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.JobExecutionException;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.Option;\r
-import compbio.metadata.Parameter;\r
-import compbio.metadata.Preset;\r
-import compbio.metadata.PresetManager;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.metadata.RunnerConfig;\r
-import compbio.runner.OptionCombinator;\r
-import compbio.runner.structure.RNAalifold;\r
-import compbio.util.FileUtil;\r
-\r
-\r
-public class RNAalifoldParametersTester {\r
-\r
- \r
- // should be: AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml"\r
- static final String rnaalifoldConfigFile = \r
- AllTestSuit.TEST_DATA_PATH + "RNAalifoldParameters.xml";\r
- public static String test_outfile = "rnaalifold.out.txt";\r
-\r
- private static Logger log = Logger\r
- .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);\r
- \r
- static {\r
- log.setLevel(Level.INFO);\r
- }\r
- \r
- RunnerConfig<RNAalifold> rnaalifoldConfig = null;\r
- OptionCombinator rnaalifoldOpc = null;\r
- \r
- @BeforeMethod(groups = { AllTestSuit.test_group_runner })\r
- @SuppressWarnings("unchecked")\r
- public void setup() {\r
- try {\r
- RunnerConfigMarshaller<RNAalifold> rnaalifoldmarsh = \r
- new RunnerConfigMarshaller<RNAalifold>(RunnerConfig.class);\r
- rnaalifoldConfig = rnaalifoldmarsh.read(new FileInputStream(new File(\r
- rnaalifoldConfigFile)), RunnerConfig.class);\r
- // set Name value separator\r
- rnaalifoldConfig.setPrmSeparator(" ");\r
- rnaalifoldOpc = new OptionCombinator(rnaalifoldConfig);\r
- \r
- \r
- \r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
- \r
- @Test\r
- public void testConfiguration() {\r
- try {\r
- this.rnaalifoldConfig.validate();\r
- } catch (ValidationException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IllegalStateException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
- public void testDefaultParameters() {\r
- RNAalifold rnaalifold = new RNAalifold();\r
- rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r
-\r
- try {\r
- // For local execution use relavive\r
- ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
- .configureExecutable(rnaalifold);\r
- LocalRunner lr = new LocalRunner(confRNAalifold);\r
- lr.executeJob();\r
- confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();\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
- \r
- @Test\r
- public void testOptions() {\r
- // populate list of incompatable pairs by their names. todo\r
- List<List<String>> failPairs = new ArrayList<List<String>>();\r
-\r
- \r
- // test the parameters without -g option\r
- test(removeParam(rnaalifoldOpc.getAllOptions(), "G-Quadruplex"));\r
- // now test without -c option\r
- test(removeParam(rnaalifoldOpc.getAllOptions(), "Circular"));\r
- }\r
- \r
-\r
- // Prints all the incompatible option pairs \r
- // (-c, -g) and (-p, -p0)\r
- \r
- @Test\r
- public void testOptionPairs() throws ResultNotAvailableException {\r
- List<Option<?>> pair = new ArrayList<Option<?>>();\r
- List<Option<?>> options = rnaalifoldOpc.getAllOptions();\r
- List<List<String>> failedOptionPairs = new ArrayList<List<String>>();\r
- \r
- boolean failed = true;\r
- for (int i = 0; i<options.size(); i++) {\r
- for (int j = i; j<options.size(); j++) {\r
- if (i != j) {\r
- pair.clear();\r
- pair.add(options.get(i)); pair.add(options.get(j));\r
- List<String> args = rnaalifoldOpc.argumentsToCommandString(pair);\r
- try { \r
- failed = singleRun(args);\r
- } catch (ResultNotAvailableException e) {\r
- System.out.println("Results not available: " + e.getMessage());\r
- failed = true;\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- if (failed == true) {\r
- failedOptionPairs.add(args);\r
- }\r
- }\r
- }\r
- }\r
- System.out.println("failedOptionPairs: " + failedOptionPairs);\r
- \r
- }\r
- \r
- // tests for incompatible Pairs of Parameters \r
- // there are none however the --betascale parameter requires -p\r
- \r
- @Test\r
- public void testParameterPairs() throws ResultNotAvailableException {\r
- List<Parameter<?>> pair = new ArrayList<Parameter<?>>();\r
- List<Parameter<?>> Parameters = rnaalifoldOpc.getAllParameters();\r
- List<List<String>> failedParameterPairs = new ArrayList<List<String>>();\r
- \r
- \r
- boolean failed = true;\r
- for (int i = 0; i<Parameters.size(); i++) {\r
- for (int j = i; j<Parameters.size(); j++) {\r
- if (i != j) {\r
- pair.clear();\r
- pair.add(Parameters.get(i)); pair.add(Parameters.get(j));\r
- List<String> args = rnaalifoldOpc.argumentsToCommandString(pair);\r
- args.add("-p"); // --betascale requires -p\r
- try { \r
- failed = singleRun(args);\r
- } catch (ResultNotAvailableException e) {\r
- System.out.println("Results not available: " + e.getMessage());\r
- failed = true;\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- if (failed == true) {\r
- failedParameterPairs.add(args);\r
- }\r
- }\r
- }\r
- }\r
- System.out.println("failedParameterPairs: " + failedParameterPairs);\r
- \r
- }\r
- \r
- \r
- // removes an argument from the list by name\r
- public <U extends Option<?>> List<U> removeParam(List<U> optionList, String name) {\r
- List<U> newL = new ArrayList<U>();\r
- for (int i = 0; i < optionList.size(); i++) {\r
- System.out.println(name.equals(optionList.get(i).getName()));\r
- if (!name.equals(optionList.get(i).getName())) {\r
- \r
- newL.add(optionList.get(i));\r
- }\r
- \r
- }\r
- return newL;\r
- }\r
- \r
- public <U extends Option<?>> List<U> removeParams(List<U> optionList, List<String> names) {\r
- for (int i = 0; i < names.size(); i++) {\r
- optionList = removeParam(optionList, names.get(i));\r
- }\r
- return optionList;\r
- }\r
- \r
- \r
- @Test(groups = { AllTestSuit.test_group_runner })\r
- public void testParameters() {\r
- List<Parameter<?>> params = rnaalifoldOpc.getAllParameters();\r
- System.out.println("param list: " + params);\r
- Collections.shuffle(params);\r
- // test with -p for betascale option\r
- List<String> precursor = new ArrayList<String>();\r
- precursor.add("-p");\r
- \r
- test(params, precursor);\r
- }\r
- \r
- // incompatible pairs of arguments are\r
- /*\r
- * the -c and -g options\r
- * the -d2 option and the -d option\r
- * the -p and -p0 option\r
- */\r
-\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
- public void testArguments() {\r
- List<Option<?>> options = rnaalifoldOpc.getAllOptions();\r
- options.addAll(rnaalifoldOpc.getAllParameters());\r
- Collections.shuffle(options);\r
- test(options);\r
- }\r
- \r
- // This test supercedes the testParameterPair() and testOptionPair()\r
- // tests by testing all pairs of arguments\r
- \r
- \r
- @Test\r
- public void testAllPairs() throws ResultNotAvailableException {\r
- List<Option<?>> pair = new ArrayList<Option<?>>();\r
- List<Option<?>> options = rnaalifoldOpc.getAllOptions();\r
- \r
- // take out -p options so it can be added to all commands later\r
- // options = removeParam(options, "Partition Function");\r
- \r
- options.addAll(rnaalifoldOpc.getAllParameters());\r
- List<List<String>> failedOptionPairs = new ArrayList<List<String>>();\r
- \r
- boolean failed = true;\r
- for (int i = 0; i<options.size(); i++) {\r
- for (int j = i; j<options.size(); j++) {\r
- if (i != j) {\r
- pair.clear();\r
- pair.add(options.get(i)); pair.add(options.get(j));\r
- List<String> args = rnaalifoldOpc.argumentsToCommandString(pair);\r
- // add -p\r
- // args.add("-p");\r
- try { \r
- failed = singleRun(args);\r
- } catch (ResultNotAvailableException e) {\r
- System.out.println("Results not available: " + e.getMessage());\r
- failed = true;\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- if (failed == true) {\r
- failedOptionPairs.add(args);\r
- }\r
- }\r
- }\r
- }\r
- System.out.println("failedOptionPairs: " + failedOptionPairs);\r
- }\r
- \r
- /*\r
- * This test method stolen from the other parameter testing classes\r
- * the only purpose of the Collections.shuffle(params) and the for loop\r
- * is to test giving the executable the parameters in different orders\r
- * which leads to a lot of (unnecessary?) tests with an argument list\r
- * as long as this one.\r
- * \r
- */\r
- \r
- \r
- void test(List<? extends Option<?>> params) {\r
- for (int i = 0; i < params.size(); i++) {\r
- List<String> args = rnaalifoldOpc.argumentsToCommandString(params);\r
- singleTest(args);\r
- Collections.shuffle(params);\r
- }\r
- log.info("NUMBER OF COMBINATION TESTED: " + params.size());\r
- }\r
- \r
- // because some parameters presuppose the -p option\r
- \r
- void test(List<? extends Option<?>> params, List<String> precursor) {\r
-\r
- for (int i = 0; i < params.size(); i++) {\r
- List<String> args = rnaalifoldOpc.argumentsToCommandString(params);\r
- args.addAll(precursor);\r
- singleTest(args);\r
- Collections.shuffle(params);\r
- }\r
- log.info("NUMBER OF COMBINATION TESTED: " + params.size());\r
- }\r
- @Test\r
- void singleParamTest() {\r
- //List<Parameter<?>> params = rnaalifoldOpc.getAllParameters();\r
- //System.out.println("special: params: " + params);\r
- \r
- //List<String> args = rnaalifoldOpc.argumentsToCommandString(params);\r
- List<String> args = new ArrayList<String>();\r
- //args.add("-T 37"); args.add("-S 1.07"); args.add("--stochBT_en 10");\r
- // replace "=" with " " to fail test\r
- args.add("--MEA=1");\r
- args.add("-p");\r
- singleTest(args);\r
- \r
- }\r
- \r
- void singleTest(List<String> params) {\r
- try {\r
- log.info("Using arguments: " + params);\r
- RNAalifold rnaalifold = new RNAalifold();\r
- rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r
- \r
- ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
- .configureExecutable(rnaalifold, ExecProvider.Local);\r
- // Add options to the executable\r
- confRNAalifold.addParameters(params);\r
- LocalRunner lr = new LocalRunner(confRNAalifold);\r
- lr.executeJob();\r
- confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();\r
- assertNotNull(confRNAalifold.getResults(), "results is null");\r
- \r
- System.out.println("Results: \n" \r
- + ((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
- \r
- File errors = new File(confRNAalifold.getWorkDirectory(),\r
- ExecutableWrapper.PROC_ERR_FILE);\r
- if (errors.length() != 0) {\r
- log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));\r
- }\r
- assertTrue(errors.length() == 0, "Run with arguments : " + params\r
- + " FAILED!");\r
- Collections.shuffle(params);\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
- \r
- /* A version of singleTest that continues running instead of calling\r
- * fail() when it encounters a problem\r
- * \r
- * Used to identify incompatible options and parameters\r
- * returns -1 on failure\r
- * \r
- * Bad Progamming practice? \r
- */\r
- \r
- \r
- boolean singleRun(List<String> params) throws JobSubmissionException,\r
- JobExecutionException, IOException, ResultNotAvailableException {\r
- boolean fail = true;\r
- log.info("Using arguments: " + params);\r
- RNAalifold rnaalifold = new RNAalifold();\r
- rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r
-\r
- ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
- .configureExecutable(rnaalifold, ExecProvider.Local);\r
- // Add options to the executable\r
- confRNAalifold.addParameters(params);\r
- LocalRunner lr = new LocalRunner(confRNAalifold);\r
- lr.executeJob();\r
- confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();\r
- \r
- System.out.println("Results: \n" \r
- + ((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
- if (confRNAalifold.getResults() != null) fail = false;\r
- File errors = new File(confRNAalifold.getWorkDirectory(),\r
- ExecutableWrapper.PROC_ERR_FILE);\r
- if (errors.length() != 0) {\r
- log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));\r
- }\r
- assertTrue(errors.length() == 0, "Run with arguments : " + params\r
- + " FAILED!");\r
- Collections.shuffle(params);\r
- return fail;\r
- }\r
-}\r
git://source.jalview.org / proteocache.git / blobdiff