Refactor sequence pipeline generics

Author: bbimber

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

@@ -140,8 +140,7 @@ public JSONObject toJSON()
     @Override
     public Class<StepType> getStepClass()
     {
-        ParameterizedType parameterizedType = (ParameterizedType) getClass().getGenericSuperclass();
-        return (Class) parameterizedType.getActualTypeArguments()[0];
+        return (Class<StepType>) SequencePipelineService.get().findSuperClassParameterType(getClass());
     }
 
     @Override

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

@@ -146,4 +146,6 @@ static public void setInstance(SequencePipelineService instance)
     abstract public TaskFileManager getTaskFileManager();
 
     abstract public Set<JobResourceSettings> getResourceSettings();
+
+    abstract public Class<?> findSuperClassParameterType(Object instance);
 }

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequencePipelineServiceImpl.java

@@ -119,8 +119,14 @@ public <StepType extends PipelineStep> Set<PipelineStepProvider<StepType>> getPr
         return ret;
     }
 
+    @Override
+    public Class<?> findSuperClassParameterType(Object instance)
+    {
+        return findSuperClassParameterType(instance, 0);
+    }
+
     // Based on: https://www.javacodegeeks.com/2013/12/advanced-java-generics-retreiving-generic-type-arguments.html
-    private static Class<?> findSuperClassParameterType(Object instance, int parameterIndex) {
+    public static Class<?> findSuperClassParameterType(Object instance, int parameterIndex) {
         Class<?> clazz = instance.getClass();
         while (clazz != clazz.getSuperclass()) {
             if (clazz.getGenericSuperclass() instanceof ParameterizedType pt)