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JAL-4196 structure view cli tests wait using new jalview.Desktop.instance.operationsA...
[jalview.git] / test / jalview / bin / CommandsTest2.java
diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java
index 12e61e4..d6b6f3c 100644 (file)
--- a/test/jalview/bin/CommandsTest2.java
+++ b/test/jalview/bin/CommandsTest2.java
@@ -51,20 +51,33 @@ public class CommandsTest2
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    if (Desktop.instance != null)
-      Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.closeDesktop();
   }
 
   @Test(
     groups =
-    { "Functional" },
-    dataProvider = "structureOpeningArgsParams")
+    { "Functional", "testTask1" },
+    dataProvider = "structureOpeningArgsParams",
+    singleThreaded = true)
   public void structureOpeningArgsTest(String cmdLine, int seqNum,
           int annNum, int viewerNum)
   {
     String[] args = cmdLine.split("\\s+");
 
-    Jalview.main(args);
+    CommandsTest.callJalviewMain(args);
+    while (Desktop.instance!=null && Desktop.instance.operationsAreInProgress())
+    {
+      try
+      {
+        // sleep for slow build server to open annotations and viewer windows
+        Thread.sleep(viewerNum * 50);
+      } catch (InterruptedException e)
+      {
+        e.printStackTrace();
+      }
+    }
+    ;
+
     AlignFrame[] afs = Desktop.getAlignFrames();
     Assert.assertNotNull(afs);
     Assert.assertTrue(afs.length > 0);
@@ -88,6 +101,7 @@ public class CommandsTest2
 
     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
     int visibleAnn = 0;
+    int dcount = 0;
     for (AlignmentAnnotation aa : aas)
     {
       if (aa.visible)
@@ -99,18 +113,16 @@ public class CommandsTest2
 
     if (viewerNum > -1)
     {
-      try
-      {
-        // sleep for slow build server to open viewer window
-        Thread.sleep(2000);
-      } catch (InterruptedException e)
-      {
-        e.printStackTrace();
-      }
       List<StructureViewerBase> openViewers = Desktop.instance
               .getStructureViewers(ap, null);
       Assert.assertNotNull(openViewers);
-      Assert.assertEquals(openViewers.size(), viewerNum,
+      int count = 0;
+      for (StructureViewerBase svb : openViewers)
+      {
+        if (svb.isVisible())
+          count++;
+      }
+      Assert.assertEquals(count, viewerNum,
               "Wrong number of structure viewers opened");
     }
   }
@@ -122,55 +134,78 @@ public class CommandsTest2
       String cmdLine,
       int seqNum,
       int annNum,
-      int viewerNum,
-      String propsFile
+      int structureViewerNum,
      */
     return new Object[][] {
         //
         /*
          */
-        { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+        { "--gui --nonews --nosplash --debug "
+                + "--append=examples/uniref50.fa "
+                + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 7, 1 },
-        { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+        { "--gui --nonews --nosplash --debug "
+                + "--append=examples/uniref50.fa "
+                + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
             15, 4, 1 },
-        { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+        { "--gui --nonews --nosplash --debug "
+                + "--append=examples/uniref50.fa "
+                + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
-                + "--nossannotations "
+                + "--noshowssannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 4, 1 },
-        { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+        { "--gui --nonews --nosplash --debug "
+                + "--append=examples/uniref50.fa "
+                + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
-                + "--noannotations "
+                + "--noshowannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 3, 1 },
-        { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+        { "--gui --nonews --nosplash --debug "
+                + "--append=examples/uniref50.fa "
+                + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
-                + "--noannotations " + "--nossannotations "
+                + "--noshowannotations " + "--noshowssannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 0, 1 },
-        { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+        { "--gui --nonews --nosplash --debug "
+                + "--append=examples/uniref50.fa "
+                + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
-                + "--noannotations " + "--nossannotations "
+                + "--noshowannotations " + "--noshowssannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 0, 1 },
-        { "--argfile=test/jalview/bin/commandsTest2.argfile1 ", 16, 19, 3 },
-        { "--argfile=test/jalview/bin/commandsTest2.argfile2 ", 16, 0, 2 },
+        { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
+            16, 19, 3 },
+        { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
+            16, 0, 2 },
+        { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
+                + "--allstructures "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+                + "--structureviewer=none "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
+            16, 10, 0 },
+        { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
+                + "--allstructures "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+                + "--noallstructures " + "--structureviewer=none "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
+            16, 10, 2 },
+        /*
+         */
         //
     };
   }