Merge pull request #375 from BimberLab/fb_debugtest

Debug JBrowseTest

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

@@ -43,6 +43,7 @@
 import org.labkey.api.security.permissions.InsertPermission;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
+import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
 import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.FileUtil;
@@ -247,12 +248,26 @@ public void testJBrowseCli() throws Exception
             {
                 _log.error("Non-zero exit from testJBrowseCli: " + wrapper.getLastReturnCode());
                 wrapper.getCommandsExecuted().forEach(_log::error);
+                _log.error("NODE_PATH: " + System.getenv("NODE_PATH"));
+
+                File node = AbstractCommandWrapper.resolveFileInPath("node", null, false);
+                if (node == null)
+                {
+                    _log.info("Unable to find node in PATH, trying node.exe");
+                    node = AbstractCommandWrapper.resolveFileInPath("node.exe", null, false);
+                    if (node == null)
+                    {
+                        _log.info("Unable to find node.exe in PATH");
+                    }
+                }
+
                 _log.error("output: ");
                 _log.error(output);
 
                 // 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 +292,6 @@ 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())
         {