X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=7bb6bddc78163e70fc4235b4ba2733493d4c4b09;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=519a94601ae33d5dfc0f3db5cbc373d2eafcea62;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 519a946..7bb6bdd 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,42 +20,44 @@ */ package jalview.ws.jabaws; -import static org.junit.Assert.*; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertTrue; -import java.awt.Component; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Vector; - -import javax.swing.JMenu; -import javax.swing.JMenuItem; - -import jalview.api.AlignCalcManagerI; +import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.datamodel.Annotation; import jalview.gui.Jalview2XML; import jalview.io.AnnotationFile; +import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.StockholmFileTest; -import jalview.ws.jws2.AADisorderClient; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.RNAalifoldClient; import jalview.ws.jws2.SequenceAnnotationWSClient; -import jalview.ws.jws2.dm.JabaOption; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.AutoCalcSetting; -import org.junit.AfterClass; -import org.junit.BeforeClass; -import org.junit.Test; +import java.awt.Component; +import java.io.File; +import java.util.ArrayList; +import java.util.List; + +import javax.swing.JMenu; +import javax.swing.JMenuItem; + +import org.testng.Assert; +import org.testng.annotations.AfterClass; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; +import compbio.metadata.Argument; import compbio.metadata.WrongParameterException; public class RNAStructExportImport { - public static String testseqs = "examples/unfolded_RF00031.aln"; + private static final String JAR_FILE_NAME = "testRnalifold_param.jar"; + + public static String testseqs = "examples/RF00031_folded.stk"; public static Jws2Discoverer disc; @@ -65,12 +67,12 @@ public class RNAStructExportImport public static jalview.gui.AlignFrame af = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - - jalview.bin.Cache.initLogger(); - disc = JalviewJabawsTestUtils.getJabawsDiscoverer(); + Cache.loadProperties("test/jalview/io/testProps.jvprops"); + Cache.initLogger(); + disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false); for (Jws2Instance svc : disc.getServices()) { @@ -84,27 +86,83 @@ public class RNAStructExportImport System.out.println("State of rnaalifoldws: " + rnaalifoldws); if (rnaalifoldws == null) - System.exit(0); + { + Assert.fail("no web service"); + } - jalview.io.FileLoader fl = new jalview.io.FileLoader(false); + FileLoader fl = new FileLoader(false); - af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE); + af = fl.LoadFileWaitTillLoaded(testseqs, FormatAdapter.FILE); assertNotNull("Couldn't load test data ('" + testseqs + "')", af); + // remove any existing annotation + List aal = new ArrayList(); + for (AlignmentAnnotation rna : af.getViewport().getAlignment() + .getAlignmentAnnotation()) + { + if (rna.isRNA()) + { + aal.add(rna); + } + } + for (AlignmentAnnotation rna : aal) + { + af.getViewport().getAlignment().deleteAnnotation(rna); + } + af.getViewport().alignmentChanged(af.alignPanel); // why is af.alignPanel + // public? } - @AfterClass + @AfterClass(alwaysRun = true) public static void tearDownAfterClass() throws Exception { if (af != null) { af.setVisible(false); af.dispose(); + File f = new File(JAR_FILE_NAME); + if (f.exists()) + { + f.delete(); + } } } - @Test + @Test(groups = { "Functional" }) + public void testRNAAliFoldValidStructure() + { + + alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null); + + af.getViewport().getCalcManager().startWorker(alifoldClient); + + do + { + try + { + Thread.sleep(50); + } catch (InterruptedException x) + { + } + } while (af.getViewport().getCalcManager().isWorking()); + + AlignmentI orig_alig = af.getViewport().getAlignment(); + for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation()) + { + if (alifoldClient.involves(aa)) + { + if (aa.isRNA()) + { + assertTrue( + "Did not create valid structure from RNAALiFold prediction", + aa.isValidStruc()); + } + } + } + } + + @Test(groups = { "Functional" }) public void testRNAStructExport() { @@ -120,7 +178,6 @@ public class RNAStructExportImport } catch (InterruptedException x) { } - ; } while (af.getViewport().getCalcManager().isWorking()); AlignmentI orig_alig = af.getViewport().getAlignment(); @@ -137,14 +194,13 @@ public class RNAStructExportImport String aligfileout = new FormatAdapter().formatSequences("PFAM", al.getSequencesArray()); - String anfileout = new AnnotationFile().printAnnotations( - al.getAlignmentAnnotation(), al.getGroups(), - al.getProperties()); - assertTrue( + String anfileout = new AnnotationFile() + .printAnnotationsForAlignment(al); + assertNotNull( "Test " + testname + "\nAlignment annotation file was not regenerated. Null string", - anfileout != null); + anfileout); assertTrue( "Test " + testname @@ -165,23 +221,23 @@ public class RNAStructExportImport FormatAdapter.PASTE)); // test for consistency in io - StockholmFileTest.testAlignmentEquivalence(al, al_new); + StockholmFileTest.testAlignmentEquivalence(al, al_new, false); return; } catch (Exception e) { e.printStackTrace(); } - fail("Test " + Assert.fail("Test " + testname + "\nCouldn't complete Annotation file roundtrip input/output/input test."); } - @Test + @Test(groups = { "Functional" }) public void testRnaalifoldSettingsRecovery() { - List opts = new ArrayList(); - for (compbio.metadata.Argument rg : (List) rnaalifoldws - .getRunnerConfig().getArguments()) + List opts = new ArrayList(); + for (Argument rg : (List) rnaalifoldws.getRunnerConfig() + .getArguments()) { if (rg.getDescription().contains("emperature")) { @@ -190,7 +246,7 @@ public class RNAStructExportImport rg.setValue("292"); } catch (WrongParameterException q) { - fail("Couldn't set the temperature parameter " + Assert.fail("Couldn't set the temperature parameter " + q.getStackTrace()); } opts.add(rg); @@ -201,9 +257,9 @@ public class RNAStructExportImport } } alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts); - + af.getViewport().getCalcManager().startWorker(alifoldClient); - + do { try @@ -214,39 +270,58 @@ public class RNAStructExportImport } ; } while (af.getViewport().getCalcManager().isWorking()); - AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId()); + AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor( + alifoldClient.getCalcId()); String oldsettings = oldacs.getWsParamFile(); // write out parameters - jalview.gui.AlignFrame nalf=null; - assertTrue("Couldn't write out the Jar file",new Jalview2XML(false).SaveAlignment(af, "testRnalifold_param.jar","trial parameter writeout")); - assertTrue("Couldn't read back the Jar file",(nalf = new Jalview2XML(false).LoadJalviewAlign("testRnalifold_param.jar"))!=null); - if (nalf!=null) + jalview.gui.AlignFrame nalf = null; + assertTrue("Couldn't write out the Jar file", + new Jalview2XML(false).saveAlignment(af, JAR_FILE_NAME, + "trial parameter writeout")); + assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML( + false).loadJalviewAlign(JAR_FILE_NAME)) != null); + if (nalf != null) { - AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId()); - assertTrue("Calc ID settings not recovered from viewport stash", acs.equals(oldacs)); - assertTrue("Serialised Calc ID settings not identical to those recovered from viewport stash", acs.getWsParamFile().equals(oldsettings)); - JMenu nmenu=new JMenu(); - new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu, rnaalifoldws, af); - assertTrue("Couldn't get menu entry for service",nmenu.getItemCount()>0); - for (Component itm: nmenu.getMenuComponents()) + AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor( + alifoldClient.getCalcId()); + assertTrue("Calc ID settings not recovered from viewport stash", + acs.equals(oldacs)); + assertTrue( + "Serialised Calc ID settings not identical to those recovered from viewport stash", + acs.getWsParamFile().equals(oldsettings)); + JMenu nmenu = new JMenu(); + new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu, + rnaalifoldws, af); + assertTrue("Couldn't get menu entry for service", + nmenu.getItemCount() > 0); + for (Component itm : nmenu.getMenuComponents()) { if (itm instanceof JMenuItem) { JMenuItem i = (JMenuItem) itm; - if (i.getText().equals(rnaalifoldws.getAlignAnalysisUI().getAAconToggle())) - { + if (i.getText().equals( + rnaalifoldws.getAlignAnalysisUI().getAAconToggle())) + { i.doClick(); break; - } + } } } while (af.getViewport().isCalcInProgress()) { - try { Thread.sleep(200); - } catch (Exception x) {}; + try + { + Thread.sleep(200); + } catch (Exception x) + { + } + ; } - AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId()); - assertTrue("Calc ID settings after recalculation has not been recovered.", acs2.getWsParamFile().equals(oldsettings)); + AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor( + alifoldClient.getCalcId()); + assertTrue( + "Calc ID settings after recalculation has not been recovered.", + acs2.getWsParamFile().equals(oldsettings)); } } }