JAL-1953 fix test and expected for canonical name for PFAM!

[jalview.git] / test / jalview / bin / CommandLineOperations.java

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 6bf1505..2d8ebce 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -54,10 +54,10 @@ public class CommandLineOperations
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  private static final int TEST_TIMEOUT = 10500; // Note longer timeout needed
-                                                // on
-                                                // full test run than on
-                                                // individual tests
+  private static final int TEST_TIMEOUT = 12500; // Note longer timeout needed
+                                                 // on
+                                                 // full test run than on
+                                                 // individual tests
 
   private static final int SETUP_TIMEOUT = 9000;
 
@@ -167,8 +167,8 @@ public class CommandLineOperations
     // not expanded by the shell
     String classpath = getClassPath();
     String _cmd = java_exe + " "
-            + (withAwt ? "-Djava.awt.headless=true" : "")
-            + " -classpath " + classpath
+            + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
+            + classpath
             + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
                     : "")
             + " jalview.bin.Jalview ";
@@ -246,18 +246,52 @@ public class CommandLineOperations
   public void setUpForCommandLineInputOperations() throws IOException
   {
     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
-    Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
-    String ln = null;
-    int count = 0;
-    while ((ln = worker.getErrorReader().readLine()) != null)
+    final Worker worker = getJalviewDesktopRunner(false, cmds,
+            SETUP_TIMEOUT);
+
+    // number of lines expected on STDERR when Jalview starts up normally
+    // may need to adjust this if Jalview is excessively noisy ?
+    final int STDERR_SETUPLINES = 30;
+
+    // thread monitors stderr - bails after SETUP_TIMEOUT or when
+    // STDERR_SETUPLINES have been read
+    Thread runner = new Thread(new Runnable()
     {
-      System.out.println(ln);
-      successfulCMDs.add(ln);
-      if (++count > 30)
+      public void run()
+      {
+        String ln = null;
+        int count = 0;
+        try
+        {
+          while ((ln = worker.getErrorReader().readLine()) != null)
+          {
+            System.out.println(ln);
+            successfulCMDs.add(ln);
+            if (++count > STDERR_SETUPLINES)
+            {
+              break;
+            }
+          }
+        } catch (Exception e)
+        {
+          System.err.println(
+                  "Unexpected Exception reading stderr from the Jalview process");
+          e.printStackTrace();
+        }
+      }
+    });
+    long t = System.currentTimeMillis() + SETUP_TIMEOUT;
+    runner.start();
+    while (!runner.isInterrupted() && System.currentTimeMillis() < t)
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (InterruptedException e)
       {
-        break;
       }
     }
+    runner.interrupt();
     if (worker != null && worker.exit == null)
     {
       worker.interrupt();
@@ -345,26 +379,26 @@ public class CommandLineOperations
         " -eps", workingDir + "test_uniref50_out.eps", true,
         MINFILESIZE_BIG, TEST_TIMEOUT },
         { "nodisplay -open examples/uniref50.fa", " -eps",
-            workingDir + "test_uniref50_out.eps", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
-            workingDir + "test_uniref50_out.eps", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -svg",
-            workingDir + "test_uniref50_out.svg", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -png",
             workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -html",
-            workingDir + "test_uniref50_out.html", true,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -fasta",
             workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },