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bbimber wants to merge 7 commits into from
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Debug JBrowseTest failures #374

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75000d0
Expose method to setLogLevel
bbimber Jul 29, 2025
fff9eab
Debug test failure
bbimber Jul 29, 2025
cc85268
Debug test failure
bbimber Jul 29, 2025
47806fd
Debug test failure
bbimber Jul 29, 2025
5206a0a
Debug test failure
bbimber Jul 30, 2025
fc33ba0
More debugging efforts
bbimber Jul 30, 2025
34019e6
Add --publicto debug pkg
bbimber Aug 5, 2025
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10 changes: 5 additions & 5 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 Expand Up @@ -275,7 +275,7 @@ public Logger getLogger()
return _log;
}

protected void setLogLevel(Level logLevel)
public void setLogLevel(Level logLevel)
{
_logLevel = logLevel;
}
Expand Down
43 changes: 30 additions & 13 deletions jbrowse/package-lock.json
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4 changes: 2 additions & 2 deletions jbrowse/package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
"build-prod": "npm run clean && cross-env NODE_ENV=production PROD_SOURCE_MAP=source-map webpack --config ./config/prod.config.js --progress --profile",
"clean": "rimraf resources/web/gen && rimraf resources/web/jbrowse/gen && rimraf resources/views/gen",
"prepareCli": "rimraf ./buildCli && rimraf ./resources/external/jb-cli && npm install @jbrowse/cli@1.7.4 --prefix ./buildCli",
"jb-pkg": "npm run prepareCli && npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli"
"jb-pkg": "npm run prepareCli && npx pkg --public --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli"
},
"dependencies": {
"@gmod/vcf": "^6.0.9",
Expand All @@ -24,7 +24,7 @@
"@labkey/api": "^1.39.0",
"@labkey/components": "^6.32.2",
"@mui/x-data-grid": "^7.28.1",
"@yao-pkg/pkg": "^6.3.2",
"@yao-pkg/pkg": "^6.6.0",
"assert": "^2.1.0",
"browserify-zlib": "^0.2.0",
"buffer": "^6.0.3",
Expand Down
36 changes: 31 additions & 5 deletions jbrowse/src/org/labkey/jbrowse/JBrowseManager.java
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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 All @@ -42,6 +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 @@ -237,16 +239,45 @@ 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);

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.info("node executable location: " + node);

String output = wrapper.executeWithOutput(Arrays.asList(exe.getPath(), "help"));
if (wrapper.getLastReturnCode() != 0)
{
_log.error("Non-zero exit from testJBrowseCli: " + wrapper.getLastReturnCode());
wrapper.getCommandsExecuted().forEach(_log::error);
_log.error("NODE_PATH: " + System.getenv("NODE_PATH"));

_log.error("output: ");
_log.error(output);

// Repeat without output going direct to the server log:
try
{
// NOTE: this is only useful if "npx pkg --debug" is used when building the executables
_log.info("Retrying without all output direct to the system log and DEBUG_PKG=1:");
wrapper.addToEnvironment("DEBUG_PKG", "1");
wrapper.execute(Arrays.asList(exe.getPath(), "help"));
}
catch (Exception e)
{
// Ignore
}

throw new RuntimeException("Non-zero exit running testJBrowseCli: " + wrapper.getLastReturnCode());
}

Expand All @@ -264,11 +295,6 @@ 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