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Debug JBrowseTest #375

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Merged
bbimber merged 2 commits into from
Jul 29, 2025
Merged

Debug JBrowseTest #375

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5cc0962
Debug test failure
bbimber Jul 29, 2025
f23d798
Debug test failure
bbimber Jul 29, 2025
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8 changes: 4 additions & 4 deletions SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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());
}

Expand Down Expand Up @@ -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)
Expand All @@ -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);
}
Expand Down
20 changes: 15 additions & 5 deletions jbrowse/src/org/labkey/jbrowse/JBrowseManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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)
Expand All @@ -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())
{
Expand Down