Update Seurat/subset step

Author: bbimber

singlecell/resources/chunks/SubsetSeurat.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- seuratObjects[[datasetId]]
     seuratObjects[[datasetId]] <- NULL
 
-    seuratObj <- CellMembrane::SubsetSeurat(seuratObj, expressionStrings = expressionStrings)
+    seuratObj <- subset(seuratObj, subset = <EXPRESSION>)
 
     newSeuratObjects[[datasetId]] <- seuratObj
 

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

@@ -1,12 +1,20 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
+import org.apache.commons.lang3.StringUtils;
 import org.json.JSONObject;
+import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
 import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
 import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 public class SubsetSeurat extends AbstractCellMembraneStep
 {
@@ -19,13 +27,13 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("SubsetSeurat", "Subset", "CellMembrane/Seurat", "The seurat object will be subset based on the expressions below, one per line, which are passed directly to Seurat's subset(subset = X).", Arrays.asList(
-                    SeuratToolParameter.create("expressionStrings", "Expressions", "Enter one expression per line", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+            super("SubsetSeurat", "Subset", "CellMembrane/Seurat", "The seurat object will be subset based on the expression below, which is passed directly to Seurat's subset(subset = X).", Arrays.asList(
+                    SeuratToolParameter.create("expression", "Expression", "Filter Expression", "textarea", new JSONObject(){{
                         put("allowBlank", false);
                         put("height", 150);
                         put("delimiter", ",");
                     }}, null)
-            ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+            ), null, null);
         }
 
 
@@ -36,6 +44,34 @@ public SubsetSeurat create(PipelineContext ctx)
         }
     }
 
+    @Override
+    public Collection<String> getRLibraries()
+    {
+        Set<String> ret = new HashSet<>();
+        ret.add("Seurat");
+        ret.addAll(super.getRLibraries());
+
+        return ret;
+    }
+
+    final static String EXPRESSION = "<EXPRESSION>";
+
+    @Override
+    protected List<String> loadChunkFromFile() throws PipelineJobException
+    {
+        ToolParameterDescriptor pd = getProvider().getParameterByName("expression");
+        final String val = StringUtils.trimToNull(pd.extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx()));
+
+        return super.loadChunkFromFile().stream().map(x -> {
+            if (x.contains(EXPRESSION))
+            {
+                x = x.replaceAll(EXPRESSION, val);
+            }
+
+            return x;
+        }).collect(Collectors.toList());
+    }
+
     @Override
     public String getFileSuffix()
     {