Consolidate Rdiscvr markdown code

Author: bbimber

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

@@ -1,11 +1,14 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
+import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
 import org.labkey.api.singlecell.pipeline.AbstractSingleCellPipelineStep;
 import org.labkey.api.util.PageFlowUtil;
 
 import java.util.Collection;
+import java.util.List;
 
 abstract public class AbstractRDiscvrStep extends AbstractSingleCellPipelineStep
 {
@@ -27,4 +30,15 @@ public String getDockerContainerName()
     {
         return CONTAINER_NAME;
     }
+
+    @Override
+    protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException
+    {
+        Chunk ret = super.createParamChunk(ctx, inputObjects, outputPrefix);
+
+        ret.bodyLines.add("serverBaseUrl <- '" + getPipelineCtx().getJob().getParameters().get("serverBaseUrl") + "'");
+        ret.bodyLines.add("defaultLabKeyFolder <- '" + getPipelineCtx().getJob().getParameters().get("labkeyFolderPath") + "'");
+
+        return ret;
+    }
 }

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

@@ -1,13 +1,10 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
-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.SequenceOutputHandler;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
 import java.util.Arrays;
-import java.util.List;
 
 public class AppendMetadata extends AbstractRDiscvrStep
 {
@@ -38,16 +35,5 @@ public String getFileSuffix()
     {
         return "metadata";
     }
-
-    @Override
-    protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException
-    {
-        Chunk ret = super.createParamChunk(ctx, inputObjects, outputPrefix);
-
-        ret.bodyLines.add("serverBaseUrl <- '" + getPipelineCtx().getJob().getParameters().get("serverBaseUrl") + "'");
-        ret.bodyLines.add("defaultLabKeyFolder <- '" + getPipelineCtx().getJob().getParameters().get("labkeyFolderPath") + "'");
-
-        return ret;
-    }
 }
 

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

@@ -56,9 +56,6 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
     {
         Chunk ret = super.createParamChunk(ctx, inputObjects, outputPrefix);
 
-        ret.bodyLines.add("serverBaseUrl <- '" + getPipelineCtx().getJob().getParameters().get("serverBaseUrl") + "'");
-        ret.bodyLines.add("defaultLabKeyFolder <- '" + getPipelineCtx().getJob().getParameters().get("labkeyFolderPath") + "'");
-
         ret.bodyLines.add("nimbleGenomes <- list(");
         String genomeStr = getProvider().getParameterByName("nimbleGenomes").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class);
         JSONArray json = new JSONArray(genomeStr);

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

@@ -1,15 +1,12 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
 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.SequenceOutputHandler;
 import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
 import java.util.Arrays;
-import java.util.List;
 
 public class AppendTcr extends AbstractRDiscvrStep
 {
@@ -42,16 +39,5 @@ public String getFileSuffix()
     {
         return "tcr";
     }
-
-    @Override
-    protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException
-    {
-        Chunk ret = super.createParamChunk(ctx, inputObjects, outputPrefix);
-
-        ret.bodyLines.add("serverBaseUrl <- '" + getPipelineCtx().getJob().getParameters().get("serverBaseUrl") + "'");
-        ret.bodyLines.add("defaultLabKeyFolder <- '" + getPipelineCtx().getJob().getParameters().get("labkeyFolderPath") + "'");
-
-        return ret;
-    }
 }
 

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

@@ -63,6 +63,5 @@ public Collection<String> getRLibraries()
 
         return ret;
     }
-
 }