X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=e66f016f2bfdb452719d0396f9905d52bfe0e8dd;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=510b913e31c27e16c669a0928a9c2b24a82d1e5a;hpb=24c4dce749cbfccc4435e442090d04013e3e1b99;p=jalview.git diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 510b913..e66f016 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -1,31 +1,81 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.jabaws; -import static org.junit.Assert.*; +import java.util.Locale; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Vector; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertTrue; -import jalview.api.AlignCalcManagerI; +import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.datamodel.Annotation; +import jalview.gui.JvOptionPane; import jalview.io.AnnotationFile; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; import jalview.io.FormatAdapter; import jalview.io.StockholmFileTest; -import jalview.ws.jws2.AADisorderClient; +import jalview.project.Jalview2XML; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.RNAalifoldClient; +import jalview.ws.jws2.SequenceAnnotationWSClient; import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.params.AutoCalcSetting; + +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.junit.AfterClass; -import org.junit.BeforeClass; -import org.junit.Test; +import org.testng.Assert; +import org.testng.annotations.AfterClass; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; -public class RNAStructExportImport +import compbio.metadata.Argument; +import compbio.metadata.WrongParameterException; + +/* + * All methods in this class are set to the Network group because setUpBeforeClass will fail + * if there is no network. + */ +@Test(singleThreaded = true) +public class RNAStructExportImport { - public static String testseqs = "examples/unfolded_RF00031.aln"; + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + private static final String JAR_FILE_NAME = "testRnalifold_param.jar"; + + public static String testseqs = "examples/RF00031_folded.stk"; public static Jws2Discoverer disc; @@ -35,72 +85,82 @@ public class RNAStructExportImport public static jalview.gui.AlignFrame af = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - - - System.out.println("test1"); - - jalview.bin.Cache.initLogger(); - disc = JalviewJabawsTestUtils.getJabawsDiscoverer(); - - System.out.println("test2"); - + Cache.loadProperties("test/jalview/io/testProps.jvprops"); + Console.initLogger(); + disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false); + + while (disc.isRunning()) + { + // don't get services until discoverer has finished + Thread.sleep(100); + } + for (Jws2Instance svc : disc.getServices()) { - - System.out.println("Service type: " + svc.serviceType); - - if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws")) + + if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("rnaalifoldws")) { rnaalifoldws = svc; } } - + System.out.println("State of rnaalifoldws: " + rnaalifoldws); - - if (rnaalifoldws == null) System.exit(0); - - System.out.println("test3"); - + + if (rnaalifoldws == null) + { + Assert.fail("no web service"); + } + jalview.io.FileLoader fl = new jalview.io.FileLoader(false); - - // Following this method a long way we find some (probably important!) - // code that I have just commented out! - af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE); - + + af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE); + assertNotNull("Couldn't load test data ('" + testseqs + "')", af); - - System.out.println("test5"); - + + // 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 for patches to JAL-1294 - */ - @Test - public void testRNAStructExport() + @Test(groups = { "Network" }) + public void testRNAAliFoldValidStructure() { + alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null); - - System.out.println("Service action text:\n" + alifoldClient.getServiceActionText()); - - - System.out.println("START FOLDING"); + af.getViewport().getCalcManager().startWorker(alifoldClient); - - + do { try @@ -109,62 +169,64 @@ public class RNAStructExportImport } catch (InterruptedException x) { } - ; } while (af.getViewport().getCalcManager().isWorking()); - - System.out.println("END FOLDING"); - - // ALL FOR TESTING - AlignCalcManagerI test = af.getViewport().getCalcManager(); - RNAalifoldClient testWorker = ((RNAalifoldClient)test.getRegisteredWorkersOfClass(RNAalifoldClient.class).get(0)); - testWorker.updateResultAnnotation(true); - System.out.println("Annotation from RNAalifoldclient"); - for (Annotation ann : testWorker.ourAnnots.get(0).annotations) { - System.out.print(ann.toString()+"|"); - } - System.out.println(); - - - // Why are the AlignViewport.alignment and the RNAalifoldClient alignment - // Annotations different + AlignmentI orig_alig = af.getViewport().getAlignment(); - - System.out.println("orig_alig has class: " + orig_alig.getClass()); - - // some time before here but after the RNAalifoldClient Update method - // the alignment annotation is replaced.... - - System.out.println("orig_alig annotation:\n"); - for (AlignmentAnnotation an : orig_alig.getAlignmentAnnotation()) { - for (Annotation ann : an.annotations) { - System.out.print(ann.toString()+"|"); - } - System.out.println(); + for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation()) + { + if (alifoldClient.involves(aa)) + { + if (aa.isRNA()) + { + assertTrue( + "Did not create valid structure from RNAALiFold prediction", + aa.isValidStruc()); + } + } } - - - testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig); + } + + @Test(groups = { "Network" }) + public void testRNAStructExport() + { + + 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(); + // JBPNote: this assert fails (2.10.2) because the 'Reference Positions' + // annotation is mistakenly recognised as an RNA annotation row when read in + // as an annotation file. + verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig); } - public static void testAnnotationFileIO(String testname, AlignmentI al) + static void verifyAnnotationFileIO(String testname, AlignmentI al) { try { - String aligfileout = new FormatAdapter().formatSequences("CLUSTAL", - al.getSequencesArray()); - - // test -// System.out.println("aligfileout:\n" + aligfileout); - - String anfileout = new AnnotationFile().printAnnotations( - al.getAlignmentAnnotation(), al.getGroups(), - al.getProperties()); - assertTrue( + // what format would be appropriate for RNAalifold annotations? + String aligfileout = FileFormat.Pfam.getWriter(null).print( + al.getSequencesArray(), true); + + String anfileout = new AnnotationFile() + .printAnnotationsForAlignment(al); + assertNotNull( "Test " + testname + "\nAlignment annotation file was not regenerated. Null string", - anfileout != null); + anfileout); assertTrue( "Test " + testname @@ -174,25 +236,119 @@ public class RNAStructExportImport System.out.println("Output annotation file:\n" + anfileout + "\n< opts = new ArrayList<>(); + for (Argument rg : (List) rnaalifoldws.getRunnerConfig() + .getArguments()) + { + if (rg.getDescription().contains("emperature")) + { + try + { + rg.setValue("292"); + } catch (WrongParameterException q) + { + Assert.fail("Couldn't set the temperature parameter " + + q.getStackTrace()); + } + opts.add(rg); + } + if (rg.getDescription().contains("max")) + { + opts.add(rg); + } + } + alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts); + + af.getViewport().getCalcManager().startWorker(alifoldClient); + + do + { + try + { + Thread.sleep(50); + } catch (InterruptedException x) + { + } + ; + } while (af.getViewport().getCalcManager().isWorking()); + 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, 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()) + { + if (itm instanceof JMenuItem) + { + JMenuItem i = (JMenuItem) itm; + if (i.getText().equals( + rnaalifoldws.getAlignAnalysisUI().getAAconToggle())) + { + i.doClick(); + break; + } + } + } + while (af.getViewport().isCalcInProgress()) + { + 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)); + } + } }