X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=0a9cb19472d648b19ef1a742e47f2bd85305190c;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=9398c55f80c74c797ac2bb38c97b68e77b8bc669;hpb=420357044cf67b53c45aa7274dc29b8e0077c8a7;p=jalview.git diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 9398c55..0a9cb19 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -20,59 +20,92 @@ */ package jalview.ws.jabaws; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; +import java.util.Locale; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertTrue; + +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +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.project.Jalview2XML; +import jalview.ws.api.ServiceWithParameters; +import jalview.ws.jws2.JabaParamStore; +import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.jws2.SeqAnnotationServiceCalcWorker; +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; +import compbio.metadata.Argument; import compbio.metadata.WrongParameterException; -import jalview.datamodel.AlignmentI; -import jalview.gui.Jalview2XML; -import jalview.io.AnnotationFile; -import jalview.io.FormatAdapter; -import jalview.io.StockholmFileTest; -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; - +/* + * 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; public static Jws2Instance rnaalifoldws; - jalview.ws.jws2.RNAalifoldClient alifoldClient; + SeqAnnotationServiceCalcWorker alifoldClient; 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); - for (Jws2Instance svc : disc.getServices()) + while (disc.isRunning()) { + // don't get services until discoverer has finished + Thread.sleep(100); + } - if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws")) + for (ServiceWithParameters svc : disc.getServices()) + { + + if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT) + .contains("rnaalifoldws")) { - rnaalifoldws = svc; + rnaalifoldws = (Jws2Instance) svc; } } @@ -80,32 +113,55 @@ public class RNAStructExportImport if (rnaalifoldws == null) { - fail("no web service"); + 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 + @Test(groups = { "Network" }) public void testRNAAliFoldValidStructure() { - alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null); + alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null, + null); af.getViewport().getCalcManager().startWorker(alifoldClient); @@ -117,27 +173,29 @@ public class RNAStructExportImport } catch (InterruptedException x) { } - ; } while (af.getViewport().getCalcManager().isWorking()); AlignmentI orig_alig = af.getViewport().getAlignment(); - for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation()) + for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation()) { if (alifoldClient.involves(aa)) { if (aa.isRNA()) { - Assert.assertTrue("Did not create valid structure from RNAALiFold prediction", aa.isValidStruc()); + assertTrue( + "Did not create valid structure from RNAALiFold prediction", + aa.isValidStruc()); } } } } - @Test + @Test(groups = { "Network" }) public void testRNAStructExport() { - alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null); + alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null, + null); af.getViewport().getCalcManager().startWorker(alifoldClient); @@ -149,67 +207,62 @@ public class RNAStructExportImport } catch (InterruptedException x) { } - ; } while (af.getViewport().getCalcManager().isWorking()); AlignmentI orig_alig = af.getViewport().getAlignment(); - - testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig); + // 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. bug is JAL-3122 + 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() .printAnnotationsForAlignment(al); - assertTrue( - "Test " - + testname - + "\nAlignment annotation file was not regenerated. Null string", - anfileout != null); - assertTrue( - "Test " - + testname - + "\nAlignment annotation file was not regenerated. Empty string", + 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")) { @@ -218,7 +271,7 @@ 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); @@ -228,7 +281,8 @@ public class RNAStructExportImport opts.add(rg); } } - alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts); + alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null, + JabaParamStore.getJwsArgsfromJaba(opts)); af.getViewport().getCalcManager().startWorker(alifoldClient); @@ -242,20 +296,20 @@ 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( @@ -289,8 +343,8 @@ 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));