X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=cc9aba0444651201e63740388e93d03989dc4b7d;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=e74ebe7082adc6d27b532b855653e9e62f07fbb4;hpb=c4ec878c9cb59fc40a88ed8ecdf5fda46f3de111;p=jalview.git diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index e74ebe7..cc9aba0 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 +20,61 @@ */ 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 javax.swing.JMenu; -import javax.swing.JMenuItem; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertTrue; -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.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 +84,23 @@ 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"); + Cache.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 +109,51 @@ 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); @@ -120,31 +168,64 @@ 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()); + } + } + } + } - 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 { // what format would be appropriate for RNAalifold annotations? - String aligfileout = new FormatAdapter().formatSequences("PFAM", - al.getSequencesArray()); + String aligfileout = FileFormat.Pfam.getWriter(null).print( + al.getSequencesArray(), true); - 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 @@ -156,32 +237,33 @@ public class RNAStructExportImport // again what format would be appropriate? AlignmentI al_new = new FormatAdapter().readFile(aligfileout, - FormatAdapter.PASTE, "PFAM"); + DataSourceType.PASTE, FileFormat.Pfam); assertTrue( "Test " + testname + "\nregenerated annotation file did not annotate alignment.", new AnnotationFile().readAnnotationFile(al_new, anfileout, - FormatAdapter.PASTE)); + DataSourceType.PASTE)); // test for consistency in io - StockholmFileTest.testAlignmentEquivalence(al, al_new); + StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false, + 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 = { "Network" }) 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 +272,7 @@ 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); @@ -220,10 +302,10 @@ public class RNAStructExportImport // 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")); + new Jalview2XML(false).saveAlignment(af, JAR_FILE_NAME, + "trial parameter writeout")); assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML( - false).loadJalviewAlign("testRnalifold_param.jar")) != null); + false).loadJalviewAlign(JAR_FILE_NAME)) != null); if (nalf != null) { AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(