From ab6c4bdb18c50e8857e405952d2cccaf7103b5bf Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Jul 2025 08:46:38 -0700 Subject: [PATCH 1/2] Expose method to setLogLevel --- .../labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java index 27152ed45..cf76f157a 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java +++ b/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; } From bae59c22ec71c9983e34bbda4ec1b6633164f883 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Jul 2025 08:48:37 -0700 Subject: [PATCH 2/2] Debug test failure --- jbrowse/src/org/labkey/jbrowse/JBrowseManager.java | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java b/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java index c1039d844..888abd0c7 100644 --- a/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java +++ b/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()); }