X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=0a9cb19472d648b19ef1a742e47f2bd85305190c;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=2753e64cae129de1b4058eb5545c740b600968bb;hpb=bc469bb898fd42c92d9b8b70660b4c94a93b3118;p=jalview.git

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 2753e64..0a9cb19 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -1,94 +1,167 @@
+/*
+ * 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 static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
 
-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 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.api.ServiceWithParameters;
+import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 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;
 
   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
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Console.initLogger();
+    disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
-    jalview.bin.Cache.initLogger();
-    disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+    while (disc.isRunning())
+    {
+      // don't get services until discoverer has finished
+      Thread.sleep(100);
+    }
 
-    for (Jws2Instance svc : disc.getServices())
+    for (ServiceWithParameters svc : disc.getServices())
     {
 
-      if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+      if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
+              .contains("rnaalifoldws"))
       {
-        rnaalifoldws = svc;
+        rnaalifoldws = (Jws2Instance) svc;
       }
     }
 
     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<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
-  public void testRNAStructExport()
+  @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);
 
@@ -100,68 +173,96 @@ 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 SeqAnnotationServiceCalcWorker(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. 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 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<<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);
+      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
+  @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"))
       {
@@ -170,7 +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);
@@ -180,10 +281,11 @@ 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);
-    
+
     do
     {
       try
@@ -194,39 +296,58 @@ 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);
-    if (nalf!=null)
+    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())
+      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()))
-                  {
+          if (i.getText().equals(
+                  rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
+          {
             i.doClick();
             break;
-                  }
+          }
         }
       }
       while (af.getViewport().isCalcInProgress())
       {
-        try { Thread.sleep(200);
-        } catch (Exception x) {};
+        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));
+      AutoCalcSetting acs2 = af.getViewport()
+              .getCalcIdSettingsFor(alifoldClient.getCalcId());
+      assertTrue(
+              "Calc ID settings after recalculation has not been recovered.",
+              acs2.getWsParamFile().equals(oldsettings));
     }
   }
 }