From 7ce2e1f63202ad3707219707ff4264fe7b47e40d Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 3 Oct 2019 17:53:46 +0100
Subject: [PATCH 1/1] JAL-3070 test jabaws and slivka AACon service
 functionality

---
 .../jalview/ws/jabaws/AAConAnnotAndSettingsIO.java |  118 ++++++++++----------
 1 file changed, 58 insertions(+), 60 deletions(-)

diff --git a/test/jalview/ws/jabaws/AAConAnnotAndSettingsIO.java b/test/jalview/ws/jabaws/AAConAnnotAndSettingsIO.java
index fae8b21..02d0d82 100644
--- a/test/jalview/ws/jabaws/AAConAnnotAndSettingsIO.java
+++ b/test/jalview/ws/jabaws/AAConAnnotAndSettingsIO.java
@@ -28,21 +28,17 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.AlignFrame;
 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.api.ServiceWithParameters;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
+import jalview.ws.slivkaws.SlivkaWSDiscoverer;
 
 import java.util.ArrayList;
 import java.util.List;
 
-import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 /*
@@ -50,7 +46,7 @@ import org.testng.annotations.Test;
  * if there is no network.
  */
 @Test(singleThreaded = true)
-public class DisorderAnnotExportImport
+public class AAConAnnotAndSettingsIO
 {
 
   @BeforeClass(alwaysRun = true)
@@ -64,7 +60,7 @@ public class DisorderAnnotExportImport
 
   public static Jws2Discoverer disc;
 
-  public static List<ServiceWithParameters> aacon;
+  public static List<ServiceWithParameters[]> aacon;
 
   jalview.ws.jws2.SeqAnnotationServiceCalcWorker aaconClient;
 
@@ -83,19 +79,25 @@ public class DisorderAnnotExportImport
       Thread.sleep(100);
     }
 
+
     aacon = new ArrayList<>();
     for (ServiceWithParameters svc : disc.getServices())
     {
       if (svc.getNameURI().toLowerCase().contains("aacon"))
       {
-        aacon.add(svc);
+        aacon.add(new ServiceWithParameters[] { svc });
+      }
+    }
+
+    for (ServiceWithParameters svc : SlivkaWSDiscoverer.getServices())
+    {
+      if (svc.getNameURI().toLowerCase().contains("aacon"))
+      {
+        aacon.add(new ServiceWithParameters[] { svc });
       }
     }
     assertTrue("Couldn't discover any AACon services to use to test.",
             aacon.size() > 0);
-    jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
-    assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
   }
 
   @AfterClass(alwaysRun = true)
@@ -109,21 +111,58 @@ public class DisorderAnnotExportImport
     }
   }
 
+  @DataProvider(name = "aacons")
+  public Object[][] getAaconArray()
+  {
+
+    Object[][] rtn = new Object[aacon.size()][1];
+    int i = 0;
+    for (ServiceWithParameters[] aa : aacon)
+    {
+      rtn[i++] = aa;
+    }
+    return rtn;
+  }
   /**
    * Run AACon on an alignment with defaults and verify Just Shenkin annotation
    * appears
    */
-  @Test(groups = { "External", "Network" })
-  public void testAAConAnnotAndRecovery()
+  @Test(groups = { "External", "Network" }, dataProvider = "aacons")
+  public void testAAConAnnotAndRecovery(ServiceWithParameters service)
   {
-    testAAConClient(af, aacon.get(0));
+    jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+    AlignFrame _af = fl.LoadFileWaitTillLoaded(testseqs,
+            jalview.io.DataSourceType.FILE);
+    assertNotNull("Couldn't load test data ('" + testseqs + "')", _af);
+    af = _af;
+    try
+    {
+    testAAConClient(_af, service);
+    } finally
+    {
+      af = null;
+      _af.setVisible(false);
+      _af.dispose();
+      _af = null;
+
+    }
   }
 
+  /**
+   * triggers the given aacon worker on the alignment, waits for 5s and gives up
+   * or verifies SHENKIN annotation is produced.
+   * 
+   * @param af
+   *          - test data in an alignment frame
+   * @param aacon
+   *          - the service to test
+   */
   static void testAAConClient(AlignFrame af, ServiceWithParameters aacon)
   {
     SeqAnnotationServiceCalcWorker aaconClient = new SeqAnnotationServiceCalcWorker(
             aacon, af, null,
             null);
+    long current = System.currentTimeMillis(), limit = 5;
     af.getViewport().getCalcManager().startWorker(aaconClient);
     do
     {
@@ -134,6 +173,10 @@ public class DisorderAnnotExportImport
       {
       }
       ;
+      assertTrue(
+              "Waited " + limit + "s for " + aacon.getHostURL()
+                      + " - giving up.",
+              (System.currentTimeMillis() - current) < limit * 1000);
     } while (af.getViewport().getCalcManager().isWorking());
     AlignmentI orig_alig = af.getViewport().getAlignment();
     boolean foundShenkin = false;
@@ -150,49 +193,4 @@ public class DisorderAnnotExportImport
     }
     assertTrue("Failed to locate 'SHENKIN' annotation row.", foundShenkin);
   }
-
-  static void checkAnnotationFileIO(String testname, AlignmentI al)
-  {
-    try
-    {
-      String aligfileout = FileFormat.Pfam.getWriter(al).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",
-              anfileout.length() > "JALVIEW_ANNOTATION".length());
-
-      System.out.println("Output annotation file:\n" + anfileout
-              + "\n<<EOF\n");
-
-      AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
-              DataSourceType.PASTE, FileFormat.Pfam);
-      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, true, false,
-              false);
-      return;
-    } catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-    Assert.fail("Test "
-            + testname
-            + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
-  }
-
 }
-- 
1.7.10.2