Debug test failure

Author: bbimber

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

@@ -117,7 +117,7 @@ public ProcessBuilder getProcessBuilder(List<String> params)
 
         if (getWorkingDir() != null)
         {
-            getLogger().debug("using working directory: " + getWorkingDir().getPath());
+            getLogger().log(_logLevel, "using working directory: " + getWorkingDir().getPath());
             pb.directory(getWorkingDir());
         }
 
@@ -208,8 +208,8 @@ private void setPath(ProcessBuilder pb)
 
             if (_logPath)
             {
-                getLogger().debug("Existing PATH: " + path);
-                getLogger().debug("toolDir: " + toolDir);
+                getLogger().log(_logLevel, "Existing PATH: " + path);
+                getLogger().log(_logLevel, "toolDir: " + toolDir);
             }
 
             if (path == null)
@@ -234,7 +234,7 @@ private void setPath(ProcessBuilder pb)
 
             if (_logPath)
             {
-                getLogger().debug("using path: " + path);
+                getLogger().log(_logLevel, "using path: " + path);
             }
             pb.environment().put("PATH", path);
         }

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

@@ -253,6 +253,7 @@ public void testJBrowseCli() throws Exception
                 // Repeat without output going direct to the server log:
                 try
                 {
+                    _log.info("Retrying without all output direct to the system log:");
                     wrapper.execute(Arrays.asList(exe.getPath(), "help"));
                 }
                 catch (Exception e)
@@ -277,11 +278,6 @@ public File getBaseDir(Container c, boolean doCreate)
             return null;
         }
 
-        if (fileRoot == null || !fileRoot.exists())
-        {
-            return null;
-        }
-
         File jbrowseDir = new File(fileRoot, ".jbrowse");
         if (!jbrowseDir.exists())
         {