Separate docker and process environments

Author: bbimber

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

@@ -48,7 +48,7 @@ abstract public class AbstractCommandWrapper implements CommandWrapper
     private boolean _warnNonZeroExits = true;
     private boolean _throwNonZeroExits = true;
     private Integer _lastReturnCode = null;
-    protected final Map<String, String> _environment = new HashMap<>();
+    private final Map<String, String> _environment = new HashMap<>();
     private final List<String> _commandsExecuted = new ArrayList<>();
 
     public AbstractCommandWrapper(@Nullable Logger logger)

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

@@ -15,8 +15,10 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 
@@ -28,14 +30,13 @@ public class DockerWrapper extends AbstractCommandWrapper
     private String _entryPoint = null;
     private boolean _runPrune = true;
     private String _alternateUserHome = null;
+    private final Map<String, String> _dockerEnvironment = new HashMap<>();
 
     public DockerWrapper(String containerName, Logger log, PipelineContext ctx)
     {
         super(log);
         _containerName = containerName;
         _ctx = ctx;
-
-        _environment.clear();
     }
 
     public void setAlternateUserHome(String alternateUserHome)
@@ -75,7 +76,7 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
         {
             writer.println("#!/bin/bash");
             writer.println("set -x");
-            writer.println("WD=`pwd`");
+            writer.println("set -e");
 
             writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
             writer.println("$DOCKER pull " + _containerName);
@@ -100,12 +101,12 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
                     _ctx.getLogger().debug("homeDir already present in docker volumes, will not re-add");
                 }
 
-                _environment.put("USER_HOME", homeDir.getPath());
+                _dockerEnvironment.put("USER_HOME", homeDir.getPath());
             }
 
             if (_alternateUserHome != null)
             {
-                _environment.put("HOME", _alternateUserHome);
+                _dockerEnvironment.put("HOME", _alternateUserHome);
             }
 
             _ctx.getDockerVolumes().forEach(v -> writer.println("\t-v '" + v + "':'" + v + "' \\"));
@@ -126,7 +127,7 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
                     _ctx.getLogger().debug("tmpDir already present in docker volumes, omitting");
                 }
 
-                addToEnvironment("TMPDIR", _tmpDir.getPath());
+                addToDockerEnvironment("TMPDIR", _tmpDir.getPath());
             }
 
             if (_entryPoint != null)
@@ -135,7 +136,7 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
             }
 
             writer.println("\t-w " + workDir.getPath() + " \\");
-            addToEnvironment("WORK_DIR", workDir.getPath());
+            addToDockerEnvironment("WORK_DIR", workDir.getPath());
 
             Integer maxRam = SequencePipelineService.get().getMaxRam();
             if (maxRam != null)
@@ -144,9 +145,9 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
                 writer.println("\t--memory='" + maxRam + "g' \\");
             }
 
-            for (String key : _environment.keySet())
+            for (String key : _dockerEnvironment.keySet())
             {
-                writer.println("\t-e " + key + "='" + _environment.get(key) + "' \\");
+                writer.println("\t-e " + key + "='" + _dockerEnvironment.get(key) + "' \\");
             }
             writer.println("\t" + _containerName + " \\");
             writer.println("\t/bin/bash " + dockerBashScript.getPath());
@@ -171,6 +172,11 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
         execute(Arrays.asList("/bin/bash", localBashScript.getPath()));
     }
 
+    public void addToDockerEnvironment(String key, String value)
+    {
+        _dockerEnvironment.put(key, value);
+    }
+
     private Collection<File> inspectInputFiles(Collection<File> inputFiles)
     {
         Set<File> toAdd = inputFiles.stream().map(f -> f.isDirectory() ? f : f.getParentFile()).filter(x -> _ctx.getDockerVolumes().stream().noneMatch(x.getPath()::startsWith)).collect(Collectors.toSet());

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -326,7 +326,7 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
                 seuratThreads = maxThreads;
             }
 
-            wrapper.addToEnvironment("SEURAT_MAX_THREADS", seuratThreads.toString());
+            wrapper.addToDockerEnvironment("SEURAT_MAX_THREADS", seuratThreads.toString());
         }
 
         File tmpDir = new File(SequencePipelineService.get().getJavaTempDir());

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -1253,7 +1253,7 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
         }
 
         DockerWrapper wrapper = new DockerWrapper("ghcr.io/bimberlab/cellhashr:latest", ctx.getLogger(), ctx);
-        wrapper.addToEnvironment("CELLHASHR_DEBUG", "1");
+        wrapper.addToDockerEnvironment("CELLHASHR_DEBUG", "1");
 
         PipelineStepOutput output = new DefaultPipelineStepOutput();
         wrapper.executeWithDocker(Arrays.asList("Rscript", "--vanilla", localRScript.getPath()), ctx.getWorkingDirectory(), output, inputFiles);

singlecell/src/org/labkey/singlecell/run/NimbleHelper.java

@@ -573,7 +573,7 @@ private static boolean runUsingDocker(List<String> nimbleArgs, PipelineStepOutpu
 
         wrapper.setTmpDir(null);
 
-        wrapper.addToEnvironment("RUST_BACKTRACE", "1");
+        wrapper.addToDockerEnvironment("RUST_BACKTRACE", "1");
 
         File doneFile = null;
         if (resumeString != null)