Migrate from ProcessBuilder to LabKeyProcessBuilder

Author: labkey-jeckels

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java

@@ -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;
@@ -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;
@@ -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())
@@ -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)
         {
@@ -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.

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TrimmomaticWrapper.java

@@ -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;
@@ -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;