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ProcessBuilder -> LabKeyProcessBuilder #427

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ProcessBuilder -> LabKeyProcessBuilder #427

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315425f
Migrate from ProcessBuilder to LabKeyProcessBuilder
labkey-jeckels May 29, 2026
b5f8ce4
Migrate from ProcessBuilder to LabKeyProcessBuilder
labkey-jeckels May 29, 2026
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13 changes: 7 additions & 6 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 @@ -17,12 +17,13 @@

import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Level;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.pipeline.PipelineJobException;
import org.labkey.api.pipeline.PipelineJobService;
import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
import org.labkey.api.util.LabKeyProcessBuilder;
import org.labkey.api.util.StringUtilsLabKey;

import java.io.BufferedReader;
Expand All @@ -43,7 +44,7 @@ abstract public class AbstractCommandWrapper implements CommandWrapper
{
private File _outputDir = null;
private File _workingDir = null;
private Logger _log;
private final Logger _log;
private boolean _logPath = false;
private Level _logLevel = Level.DEBUG;
private boolean _warnNonZeroExits = true;
Expand Down Expand Up @@ -105,9 +106,9 @@ public void execute(List<String> params, ProcessBuilder.Redirect redirect) throw
execute(params, redirect, null);
}

public ProcessBuilder getProcessBuilder(List<String> params)
public LabKeyProcessBuilder getProcessBuilder(List<String> params)
{
ProcessBuilder pb = new ProcessBuilder(params);
LabKeyProcessBuilder pb = new LabKeyProcessBuilder(params);
setPath(pb);

if (!_environment.isEmpty())
Expand All @@ -134,7 +135,7 @@ private void execute(List<String> params, ProcessBuilder.Redirect redirect, @Nul
getLogger().info("\t" + StringUtils.join(params, " "));
_commandsExecuted.add(StringUtils.join(params, " "));

ProcessBuilder pb = getProcessBuilder(params);
LabKeyProcessBuilder pb = getProcessBuilder(params);
pb.redirectErrorStream(false);
if (redirect != null)
{
Expand Down Expand Up @@ -197,7 +198,7 @@ public Integer getLastReturnCode()
return _lastReturnCode;
}

private void setPath(ProcessBuilder pb)
private void setPath(LabKeyProcessBuilder pb)
{
// Update PATH environment variable to make sure all files in the tools
// directory and the directory of the executable or on the path.
Expand Down
3 changes: 2 additions & 1 deletion SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceRemoteIntegrationTests.java
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Expand Up @@ -16,6 +16,7 @@
import org.labkey.api.pipeline.WorkDirectory;
import org.labkey.api.reader.Readers;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.LabKeyProcessBuilder;
import org.labkey.api.writer.PrintWriters;
import org.labkey.sequenceanalysis.pipeline.AlignmentInitTask;
import org.labkey.sequenceanalysis.pipeline.PrepareAlignerIndexesTask;
Expand Down Expand Up @@ -212,7 +213,7 @@ protected void executeJobRemote(File workDir, @Nullable File jobJson) throws IOE
args.add(jobJson.toURI().toString());
}

ProcessBuilder pb = new ProcessBuilder(args);
LabKeyProcessBuilder pb = new LabKeyProcessBuilder(args);
pb.directory(workDir);

_log.info("Executing job in '{}': {}", pb.directory().getAbsolutePath(), String.join(" ", pb.command()));
Expand Down
3 changes: 2 additions & 1 deletion SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TrimmomaticWrapper.java
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Expand Up @@ -21,6 +21,7 @@
import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.JobRunner;
import org.labkey.api.util.LabKeyProcessBuilder;
import org.labkey.api.util.Pair;
import org.labkey.api.util.StringUtilsLabKey;
import org.labkey.sequenceanalysis.model.AdapterModel;
Expand Down Expand Up @@ -272,7 +273,7 @@ else if (FileUtils.sizeOf(files.get(2)) == 0)

public void doTrim(List<String> params) throws PipelineJobException
{
ProcessBuilder pb = getProcessBuilder(params);
LabKeyProcessBuilder pb = getProcessBuilder(params);
getLogger().info(StringUtils.join(params, " "));
pb.redirectErrorStream(false);
Process p = null;
Expand Down
3 changes: 2 additions & 1 deletion SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java
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Expand Up @@ -33,6 +33,7 @@
import org.labkey.api.util.Compress;
import org.labkey.api.util.FileType;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.LabKeyProcessBuilder;
import org.labkey.api.util.Path;
import org.labkey.api.util.StringUtilsLabKey;
import org.labkey.sequenceanalysis.SequenceAnalysisModule;
Expand Down Expand Up @@ -139,7 +140,7 @@ private void runForFile(File f)

_logger.info("running fastqc:");
_logger.info(StringUtils.join(params, " "));
ProcessBuilder pb = new ProcessBuilder(params);
LabKeyProcessBuilder pb = new LabKeyProcessBuilder(params);
pb.redirectErrorStream(true);
pb.directory(f.getParentFile());

Expand Down