/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
*/
package jalview.ws.jabaws;
+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.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.project.Jalview2XML;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Component;
+import java.io.File;
import java.util.ArrayList;
import java.util.List;
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
{
+
+ @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;
@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;
}
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<AlignmentAnnotation> aal = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> aal = new ArrayList<>();
for (AlignmentAnnotation rna : af.getViewport().getAlignment()
.getAlignmentAnnotation())
{
// 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(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testRNAAliFoldValidStructure()
{
} catch (InterruptedException x)
{
}
- ;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testRNAStructExport()
{
} 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.
+ 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<<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, "PFAM");
- 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, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ false);
return;
} catch (Exception e)
{
e.printStackTrace();
}
- Assert.fail("Test "
- + testname
+ Assert.fail("Test " + testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testRnaalifoldSettingsRecovery()
{
- List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
- for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) rnaalifoldws
- .getRunnerConfig().getArguments())
+ List<Argument> opts = new ArrayList<>();
+ for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
+ .getArguments())
{
if (rg.getDescription().contains("emperature"))
{
}
;
} 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(
}
;
}
- 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));
git://source.jalview.org / jalview.git / blobdiff