Fix issues with JSONObject migration

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/AlignmentMetricsHandler.java

@@ -83,7 +83,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             RecordedAction action = new RecordedAction(getName());
             action.setStartTime(new Date());
 
-            Integer windowSize = params.has("windowSize") && params.get("windowSize") != null ? Integer.valueOf(params.getInt("windowSize")) : null;
+            Integer windowSize = params.has("windowSize") && !params.isNull("windowSize") ? Integer.valueOf(params.getInt("windowSize")) : null;
             if (windowSize == null)
             {
                 job.error("No window size provided, aborting");

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/UnmappedSequenceBasedGenotypeHandler.java

@@ -232,7 +232,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                     }
 
                     int minAlignmentLength = 0;
-                    if (params.get("minAlignmentLength") != null)
+                    if (!params.isNull("minAlignmentLength"))
                     {
                         minAlignmentLength = params.getInt("minAlignmentLength");
                     }

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java

@@ -257,7 +257,7 @@ public Map<String, String> getParameters()
 
         for (String key : json.keySet())
         {
-            ret.put(key, json.opt(key) == null ? null : String.valueOf(json.get(key)));
+            ret.put(key, json.isNull(key) ? null : String.valueOf(json.get(key)));
         }
 
         return ret;