X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=bc11d2f7de7c66d6b6d8ccec8e6d0d6dd8925633;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=57cbd50d0c7d2c2a9adcd6dcde0f223fcd78744e;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 57cbd50..bc11d2f 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 2.8.2b1) - * 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 +20,62 @@ */ package jalview.ws.jabaws; -import static org.junit.Assert.*; +import java.util.Locale; -import java.awt.Component; -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 javax.swing.JMenu; -import javax.swing.JMenuItem; - -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.Jalview2XML; +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.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; +/* + * 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; @@ -65,17 +85,24 @@ public class RNAStructExportImport public static jalview.gui.AlignFrame af = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - - jalview.bin.Cache.initLogger(); + 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()) { - if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws")) + if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT) + .contains("rnaalifoldws")) { rnaalifoldws = svc; } @@ -84,28 +111,52 @@ 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); - af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE); + af = fl.LoadFileWaitTillLoaded(testseqs, + jalview.io.DataSourceType.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 - public void testRNAStructExport() + @Test(groups = { "Network" }) + public void testRNAAliFoldValidStructure() { alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null); @@ -120,68 +171,95 @@ public class RNAStructExportImport } 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 = { "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()); - testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig); + 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 { // what format would be appropriate for RNAalifold annotations? - String aligfileout = new FormatAdapter().formatSequences("PFAM", - al.getSequencesArray()); - - String anfileout = new AnnotationFile().printAnnotations( - al.getAlignmentAnnotation(), al.getGroups(), - al.getProperties()); - assertTrue( - "Test " - + testname - + "\nAlignment annotation file was not regenerated. Null string", - anfileout != null); - assertTrue( - "Test " - + testname - + "\nAlignment annotation file was not regenerated. Empty string", + 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); + assertTrue("Test " + testname + + "\nAlignment annotation file was not regenerated. Empty string", anfileout.length() > "JALVIEW_ANNOTATION".length()); - System.out.println("Output annotation file:\n" + anfileout - + "\n< 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 +268,7 @@ 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); @@ -214,20 +292,20 @@ 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); + 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()); + AutoCalcSetting acs = af.getViewport() + .getCalcIdSettingsFor(alifoldClient.getCalcId()); assertTrue("Calc ID settings not recovered from viewport stash", acs.equals(oldacs)); assertTrue( @@ -261,8 +339,8 @@ public class RNAStructExportImport } ; } - AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor( - alifoldClient.getCalcId()); + AutoCalcSetting acs2 = af.getViewport() + .getCalcIdSettingsFor(alifoldClient.getCalcId()); assertTrue( "Calc ID settings after recalculation has not been recovered.", acs2.getWsParamFile().equals(oldsettings));