Allow single cell handlers to use default value in the case that no value for the parameter is provided at all in JSON

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ToolParameterDescriptor.java

@@ -187,6 +187,22 @@ public <ParamType> ParamType extractValue(PipelineJob job, PipelineStepProvider<
         return this.extractValue(job, provider, stepIdx, clazz, null);
     }
 
+    public boolean hasValueInJson(PipelineJob job, PipelineStepProvider<?> provider, int stepIdx)
+    {
+        String key = getJsonParamName(provider, stepIdx);
+        JSONObject jobParams;
+        if (job instanceof HasJobParams)
+        {
+            jobParams = ((HasJobParams)job).getParameterJson();
+        }
+        else
+        {
+            jobParams = new JSONObject(job.getParameters());
+        }
+
+        return jobParams.has(key);
+    }
+
     public <ParamType> ParamType extractValue(PipelineJob job, PipelineStepProvider<?> provider, int stepIdx, Class<ParamType> clazz, @Nullable ParamType defaultValue)
     {
         String key = getJsonParamName(provider, stepIdx);

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

@@ -383,6 +383,13 @@ public String getDockerHomeDir()
     protected void addParameterVariables(SeuratToolParameter pd, List<String> body)
     {
         String val = StringUtils.trimToNull(pd.extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx()));
+
+        // Note: use this only if there is no value provided at all in JSON
+        if (pd.getDefaultValue() != null && !pd.hasValueInJson(getPipelineCtx().getJob(), getProvider(), getStepIdx()))
+        {
+            val = String.valueOf(pd.getDefaultValue());
+        }
+
         if (val == null)
         {
             body.add((pd.getVariableName() + " <- NULL"));