X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=0a9cb19472d648b19ef1a742e47f2bd85305190c;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=06c803f8396fb83aac2218d83fa76ede11c94006;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 06c803f..0a9cb19 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -20,21 +20,25 @@
  */
 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.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.jabaws2.Jws2Instance;
 import jalview.ws.params.AutoCalcSetting;
@@ -55,6 +59,11 @@ 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
 {
 
@@ -73,7 +82,7 @@ public class RNAStructExportImport
 
   public static Jws2Instance rnaalifoldws;
 
-  jalview.ws.jws2.RNAalifoldClient alifoldClient;
+  SeqAnnotationServiceCalcWorker alifoldClient;
 
   public static jalview.gui.AlignFrame af = null;
 
@@ -81,15 +90,22 @@ public class RNAStructExportImport
   public static void setUpBeforeClass() throws Exception
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
-    Cache.initLogger();
+    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);
+    }
+
+    for (ServiceWithParameters svc : disc.getServices())
     {
 
-      if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+      if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
+              .contains("rnaalifoldws"))
       {
-        rnaalifoldws = svc;
+        rnaalifoldws = (Jws2Instance) svc;
       }
     }
 
@@ -102,12 +118,13 @@ public class RNAStructExportImport
 
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
 
-    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.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())
     {
@@ -139,11 +156,12 @@ public class RNAStructExportImport
     }
   }
 
-  @Test(groups = { "Functional" })
+  @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);
 
@@ -172,11 +190,12 @@ public class RNAStructExportImport
     }
   }
 
-  @Test(groups = { "Functional" })
+  @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);
 
@@ -191,61 +210,57 @@ public class RNAStructExportImport
     } 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 = FileFormat.Pfam.getAlignmentFile().print(
-              al.getSequencesArray(), true);
+      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",
+      assertNotNull("Test " + testname
+              + "\nAlignment annotation file was not regenerated. Null string",
               anfileout);
-      assertTrue(
-              "Test "
-                      + testname
-                      + "\nAlignment annotation file was not regenerated. Empty string",
+      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,
               DataSourceType.PASTE, FileFormat.Pfam);
-      assertTrue(
-              "Test "
-                      + testname
-                      + "\nregenerated annotation file did not annotate alignment.",
+      assertTrue("Test " + testname
+              + "\nregenerated annotation file did not annotate alignment.",
               new AnnotationFile().readAnnotationFile(al_new, anfileout,
                       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<Argument> opts = new ArrayList<Argument>();
+    List<Argument> opts = new ArrayList<>();
     for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
             .getArguments())
     {
@@ -266,7 +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);
 
@@ -280,20 +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, JAR_FILE_NAME,
-                    "trial parameter writeout"));
-    assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
-            false).loadJalviewAlign(JAR_FILE_NAME)) != 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(
@@ -327,8 +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));