+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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;
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");
+ 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);
-
+
+ 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);
-
+
+ // remove any existing annotation
+ List<AlignmentAnnotation> 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("START FOLDING");
+
af.getViewport().getCalcManager().startWorker(alifoldClient);
-
-
+
do
{
try
} 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(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Null string",
- anfileout != null);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Empty string",
+ // 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);
+ 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<<EOF\n");
+ System.out.println(
+ "Output annotation file:\n" + anfileout + "\n<<EOF\n");
+ // again what format would be appropriate?
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
- FormatAdapter.PASTE, "CLUSTAL");
- assertTrue(
- "Test "
- + testname
- + "\nregenerated annotation file did not annotate alignment.",
+ 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 "
- + testname
+ Assert.fail("Test " + testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
+ @Test(groups = { "Network" })
+ public void testRnaalifoldSettingsRecovery()
+ {
+ List<Argument> opts = new ArrayList<>();
+ for (Argument rg : (List<Argument>) 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));
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff