Migrate to non-deprecated methods (getNewJsonObject() -> getJsonObject()) (#222)

Author: labkey-adam

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

@@ -1952,23 +1952,23 @@ public enum TYPE
 
         public String getJobName()
         {
-            return getNewJsonObject().optString("jobName");
+            return getJsonObject().optString("jobName");
         }
 
         public String getDescription()
         {
-            return getNewJsonObject().optString("description");
+            return getJsonObject().optString("description");
         }
 
         public TYPE getType()
         {
-            return !getNewJsonObject().has("type") ? null : TYPE.valueOf(getNewJsonObject().getString("type"));
+            return !getJsonObject().has("type") ? null : TYPE.valueOf(getJsonObject().getString("type"));
         }
 
         public JSONObject getJobParameters()
         {
-            // Return clone so we dont mutate it:
-            return new JSONObject(getNewJsonObject().optJSONObject("jobParameters").toMap());
+            // Return clone so we don't mutate it:
+            return new JSONObject(getJsonObject().optJSONObject("jobParameters").toMap());
         }
 
         public JSONArray getReadsetIds()

jbrowse/src/org/labkey/jbrowse/JBrowseController.java

@@ -414,14 +414,14 @@ public static class ModifyAttributesAction extends MutatingApiAction<SimpleApiJs
         @Override
         public ApiResponse execute(SimpleApiJsonForm form, BindException errors)
         {
-            JSONArray jsonFiles = form.getNewJsonObject().getJSONArray("jsonFiles");
+            JSONArray jsonFiles = form.getJsonObject().getJSONArray("jsonFiles");
             Set<String> objectIds = new HashSet<>();
             for (Object o : jsonFiles.toList())
             {
                 objectIds.add(o.toString());
             }
 
-            JSONObject attributes = form.getNewJsonObject().getJSONObject("attributes");
+            JSONObject attributes = form.getJsonObject().getJSONObject("attributes");
 
             final Map<Container, List<Map<String, Object>>> rows = new HashMap<>();
             TableSelector ts = new TableSelector(JBrowseSchema.getInstance().getTable(JBrowseSchema.TABLE_JSONFILES), PageFlowUtil.set("objectid", "container", "trackJson"), new SimpleFilter(FieldKey.fromString("objectid"), objectIds, CompareType.IN), null);

singlecell/src/org/labkey/singlecell/SingleCellController.java

@@ -346,12 +346,12 @@ private static void validateBarcodes(List<Map<String, Object>> readsetRows, Cont
 
     private static List<Map<String, Object>> parseRows(SimpleApiJsonForm form, String propName, Container container) throws ApiUsageException
     {
-        if (!form.getNewJsonObject().has(propName))
+        if (!form.getJsonObject().has(propName))
         {
             throw new ApiUsageException("Missing property: " + propName);
         }
 
-        JSONArray arr = form.getNewJsonObject().getJSONArray(propName);
+        JSONArray arr = form.getJsonObject().getJSONArray(propName);
 
         List<Map<String, Object>> ret = new ArrayList<>();
         JsonUtil.toJSONObjectList(arr).forEach(m -> {