import org.testng.annotations.BeforeMethod;\r
import org.testng.annotations.Test;\r
\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.metadata.PresetManager;\r
import compbio.metadata.ResultNotAvailableException;\r
import compbio.metadata.RunnerConfig;\r
+import compbio.runner.msa.Mafft;\r
import compbio.util.SysPrefs;\r
\r
public class IUPredTester {\r
\r
- public static String test_outfile = "output";\r
-\r
private IUPred iupred;\r
\r
@BeforeMethod(alwaysRun = true)\r
void init() {\r
iupred = new IUPred();\r
- iupred.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
+ iupred.setInput(AllTestSuit.test_input);\r
}\r
\r
@Test(groups = {AllTestSuit.test_group_cluster,\r
}\r
}\r
\r
+ \r
+ @Test(enabled = false, groups = {AllTestSuit.test_group_runner})\r
+ public void testSetParameter() {\r
+ assertEquals(iupred.getInput(), AllTestSuit.test_input);\r
+ assertTrue(iupred.getParameters(null).getCommandString().trim().endsWith(AllTestSuit.test_input));\r
+ iupred.setParameter("all");\r
+ assertEquals(iupred.getInput(), AllTestSuit.test_input);\r
+ String cmd = iupred.getParameters(null).getCommandString().trim(); \r
+ assertTrue(cmd.endsWith("all"));\r
+ assertTrue(cmd.contains(AllTestSuit.test_input)); \r
+ }\r
+ \r
+ \r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testReadResults() {\r
+ ScoreManager scoreMan;\r
+ try {\r
+ scoreMan = iupred.getResults(AllTestSuit.TEST_DATA_PATH_ABSOLUTE);\r
+ System.out.println(scoreMan.asMap());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+ \r
@Test(groups = {AllTestSuit.test_group_runner})\r
public void testRunLocally() {\r
try {\r
ScoreManager al2 = confIUPred.getResults();\r
assertNotNull(al2);\r
assertEquals(al2.asMap().size(), 3);\r
+ assertEquals(al2.getNumberOfSeq(),3);\r
+ ScoreHolder sch = al2.getAnnotationForSequence("Foobar");\r
+ Score sc = sch.getScoreByMethod("Long");\r
+ \r
+ assertEquals(sc.getMethod(), "Long");\r
+ assertTrue(sc.getRanges().isEmpty());\r
+ assertNotNull(sc.getScores());\r
+ assertEquals(sc.getScores().size(), 481);\r
assertEquals(al1.getResults(), al2);\r
+\r
+ \r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
fail(e.getLocalizedMessage());\r
}\r
}\r
\r
- @Test(groups = {AllTestSuit.test_group_runner})\r
- public void readStatistics() {\r
- // No execution statistics is available!\r
+ @Test(enabled=false, groups = {AllTestSuit.test_group_runner})\r
+ public void testRunLocallyWithParams() {\r
+ try {\r
+ iupred.setParameter("all");\r
+ ConfiguredExecutable<IUPred> confIUPred = Configurator\r
+ .configureExecutable(iupred, Executable.ExecProvider.Local);\r
+\r
+ // For local execution use relative\r
+ LocalRunner lr = new LocalRunner(confIUPred);\r
+ lr.executeJob();\r
+ ConfiguredExecutable<?> al1 = lr.waitForResult();\r
+ assertNotNull(al1.getResults());\r
+ ScoreManager al2 = confIUPred.getResults();\r
+ \r
+ System.out.println("!!!"+al2.asMap());\r
+ \r
+ /*\r
+ assertNotNull(al2);\r
+ assertEquals(al2.asSet().size(), 1);\r
+ assertEquals(al2.getNumberOfSeq(),1);\r
+ Score sc = al2.asSet().iterator().next(); \r
+ assertEquals(sc.getMethod(), "Long");\r
+ assertTrue(sc.getRanges().isEmpty());\r
+ assertNotNull(sc.getScores());\r
+ assertEquals(sc.getScores().size(), 568);\r
+ assertEquals(al1.getResults(), al2);\r
+*/\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
}\r
\r
@Test(groups = {AllTestSuit.test_group_runner})\r
public void testPersistance() {\r
try {\r
- IUPred disembl = new IUPred();\r
- disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
- .setOutput("outtt.txt");\r
- assertEquals(disembl.getInput(), AllTestSuit.test_input);\r
- assertEquals(disembl.getError(), "errrr.txt");\r
- assertEquals(disembl.getOutput(), "outtt.txt");\r
+ IUPred iupred = new IUPred();\r
+ iupred.setError("errrr.txt").setInput(AllTestSuit.test_input);\r
+ assertEquals(iupred.getInput(), AllTestSuit.test_input);\r
+ assertEquals(iupred.getError(), "errrr.txt");\r
+\r
ConfiguredExecutable<IUPred> cIUPred = Configurator\r
- .configureExecutable(disembl, Executable.ExecProvider.Local);\r
+ .configureExecutable(iupred, Executable.ExecProvider.Local);\r
\r
SyncExecutor sexec = Configurator.getSyncEngine(cIUPred);\r
sexec.executeJob();\r
AllTestSuit.test_input);\r
assertEquals(resurrectedCIUPred.getExecutable().getError(),\r
"errrr.txt");\r
- assertEquals(resurrectedCIUPred.getExecutable().getOutput(),\r
- "outtt.txt");\r
+\r
// See in details whether executables are the same\r
- assertEquals(resurrectedCIUPred.getExecutable(), disembl);\r
+ assertEquals(resurrectedCIUPred.getExecutable(), iupred);\r
\r
ConfiguredExecutable<IUPred> resIUPred = Configurator\r
.configureExecutable(resurrectedCIUPred.getExecutable(),\r
@Test(groups = {AllTestSuit.test_group_runner})\r
public void testConfigurationLoading() {\r
try {\r
- RunnerConfig<IUPred> disemblConfig = ConfExecutable\r
+ RunnerConfig<IUPred> iupredConfig = ConfExecutable\r
.getRunnerOptions(IUPred.class);\r
- // There is no disembl parameters\r
- assertNull(disemblConfig);\r
\r
- // If there were a IUPredParameter.xml file and reference to it,\r
- // it would be like that\r
- // assertTrue(disemblConfig.getArguments().size() == 0);\r
+ assertNotNull(iupredConfig);\r
+\r
+ assertTrue(iupredConfig.getArguments().size() != 0);\r
\r
- PresetManager<IUPred> disemblPresets = ConfExecutable\r
+ PresetManager<IUPred> iupredPresets = ConfExecutable\r
.getRunnerPresets(IUPred.class);\r
- assertNull(disemblPresets); // there is no presets\r
+ assertNull(iupredPresets); // there is no presets\r
\r
- LimitsManager<IUPred> disemblLimits = ConfExecutable\r
+ LimitsManager<IUPred> iupredLimits = ConfExecutable\r
.getRunnerLimits(IUPred.class);\r
- assertNotNull(disemblLimits);\r
- assertTrue(disemblLimits.getLimits().size() > 0);\r
- disemblLimits.validate(disemblPresets);\r
+ assertNotNull(iupredLimits);\r
+ assertTrue(iupredLimits.getLimits().size() > 0);\r
+ iupredLimits.validate(iupredPresets);\r
\r
} catch (FileNotFoundException e) {\r
e.printStackTrace();\r
git://source.jalview.org / jabaws.git / blobdiff