Merge pull request #373 from BimberLab/fb_debugtest

Debug JBrowseTest failures

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java

@@ -275,7 +275,7 @@ public Logger getLogger()
         return _log;
     }
 
-    protected void setLogLevel(Level logLevel)
+    public void setLogLevel(Level logLevel)
     {
         _logLevel = logLevel;
     }

jbrowse/src/org/labkey/jbrowse/JBrowseManager.java

@@ -17,6 +17,7 @@
 package org.labkey.jbrowse;
 
 import org.apache.commons.lang3.SystemUtils;
+import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
@@ -237,6 +238,8 @@ public void testJBrowseCli() throws Exception
         {
             File exe = JBrowseManager.get().getJbrowseCli();
             SimpleScriptWrapper wrapper = new SimpleScriptWrapper(_log);
+            wrapper.setLogLevel(Level.INFO);
+            wrapper.setLogPath(true);
             wrapper.setThrowNonZeroExits(false);
 
             String output = wrapper.executeWithOutput(Arrays.asList(exe.getPath(), "help"));
@@ -247,6 +250,16 @@ public void testJBrowseCli() throws Exception
                 _log.error("output: ");
                 _log.error(output);
 
+                // Repeat without output going direct to the server log:
+                try
+                {
+                    wrapper.execute(Arrays.asList(exe.getPath(), "help"));
+                }
+                catch (Exception e)
+                {
+                    // Ignore
+                }
+
                 throw new RuntimeException("Non-zero exit running testJBrowseCli: " + wrapper.getLastReturnCode());
             }