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Debug JBrowseTest failures #373

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

Debug JBrowseTest failures #373

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ab6c4bd
Expose method to setLogLevel
bbimber Jul 29, 2025
bae59c2
Debug test failure
bbimber Jul 29, 2025
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2 changes: 1 addition & 1 deletion 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 @@ -275,7 +275,7 @@ public Logger getLogger()
return _log;
}

protected void setLogLevel(Level logLevel)
public void setLogLevel(Level logLevel)
{
_logLevel = logLevel;
}
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13 changes: 13 additions & 0 deletions jbrowse/src/org/labkey/jbrowse/JBrowseManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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"));
Expand All @@ -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());
}

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