Initial support for futures::plan and seurat steps

Author: bbimber

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

@@ -5,6 +5,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.math.NumberUtils;
 import org.jetbrains.annotations.Nullable;
+import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.reader.Readers;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
@@ -32,6 +33,8 @@
 
 abstract public class AbstractSingleCellPipelineStep extends AbstractPipelineStep implements SingleCellStep
 {
+    public static final String SEURAT_THREADS = "seuratMaxThreads";
+
     public AbstractSingleCellPipelineStep(PipelineStepProvider provider, PipelineContext ctx)
     {
         super(provider, ctx);
@@ -250,12 +253,25 @@ protected void executeR(SequenceOutputHandler.JobContext ctx, File rmd, String o
             errorFile.delete();
         }
 
-        executeR(ctx, getDockerContainerName(), outputPrefix, lines);
+        Integer seuratThreads = null;
+        if (getProvider().getParameterByName(SEURAT_THREADS) != null)
+        {
+            seuratThreads = getProvider().getParameterByName(SEURAT_THREADS).extractValue(ctx.getJob(), getProvider(), getStepIdx(), Integer.class, null);
+        }
+
+        executeR(ctx, getDockerContainerName(), outputPrefix, lines, seuratThreads);
 
         handlePossibleFailure(ctx, outputPrefix);
     }
 
-    public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerContainerName, String outputPrefix, List<String> lines) throws PipelineJobException
+    protected static SeuratToolParameter getSeuratThreadsParam()
+    {
+        return SeuratToolParameter.create(SEURAT_THREADS, "Max Threads", "If provided, the docker session will set future::plan(strategy='multisession', workers=XXX), which is supported by certain Seurat functions.", "ldk-integerfield", new JSONObject(){{
+            put("minValue", 0);
+        }}, null);
+    }
+
+    public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerContainerName, String outputPrefix, List<String> lines, @Nullable Integer seuratThreads) throws PipelineJobException
     {
         File localRScript = new File(ctx.getOutputDir(), FileUtil.makeLegalName(outputPrefix + ".R").replaceAll(" ", "_"));
         try (PrintWriter writer = PrintWriters.getPrintWriter(localRScript))
@@ -285,6 +301,11 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
                 writer.println("\t-e SEQUENCEANALYSIS_MAX_THREADS=" + maxThreads + " \\");
             }
 
+            if (seuratThreads != null)
+            {
+                writer.println("\t-e SEURAT_MAX_THREADS=" + seuratThreads + " \\");
+            }
+
             Integer maxRam = SequencePipelineService.get().getMaxRam();
             if (maxRam != null)
             {

singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java

@@ -503,7 +503,7 @@ else if (step.createsSeuratObjects())
             File finalHtml = new File(ctx.getOutputDir(), "finalHtml.html");
             List<String> lines = new ArrayList<>();
             lines.add("rmarkdown::render(output_file = '" + finalHtml.getName() + "', input = '" + finalMarkdownFile.getName() + "', intermediates_dir  = '/work')");
-            AbstractSingleCellPipelineStep.executeR(ctx, AbstractCellMembraneStep.CONTAINER_NAME, "pandoc", lines);
+            AbstractSingleCellPipelineStep.executeR(ctx, AbstractCellMembraneStep.CONTAINER_NAME, "pandoc", lines, null);
             _resumer.getFileManager().addIntermediateFile(finalMarkdownFile);
             _resumer.getFileManager().addIntermediateFiles(_resumer.getMarkdownsInOrder());
             _resumer.getFileManager().addIntermediateFiles(_resumer.getHtmlFilesInOrder());

singlecell/src/org/labkey/singlecell/pipeline/singlecell/FindMarkers.java

@@ -44,7 +44,8 @@ public Provider()
                     }}, 0.001),
                     SeuratToolParameter.create("foldChangeThreshold", "Log2 Fold-Change Threshold", "Only genes with log2-foldchange above this will be reported", "ldk-numberfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 0.25)
+                    }}, 0.25),
+                    getSeuratThreadsParam()
                 ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }
 

singlecell/src/org/labkey/singlecell/pipeline/singlecell/NormalizeAndScale.java

@@ -48,7 +48,8 @@ public Provider()
                     }}, false),
                     SeuratToolParameter.create("nVariableFeatures", "# Variable Features", "Controls the number of variable features that will be used. This only applies to the standard NormalizeData/ScaleData pipeline, not SCTransform", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, null)
+                    }}, null),
+                    getSeuratThreadsParam()
                     ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }