Migrate to new JSONObject/JSONArray library (#202)

Author: labkey-adam

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

@@ -2075,17 +2075,17 @@ public static enum TYPE
 
         public String getJobName()
         {
-            return getJsonObject().optString("jobName");
+            return getNewJsonObject().optString("jobName");
         }
 
         public String getDescription()
         {
-            return getJsonObject().optString("description");
+            return getNewJsonObject().optString("description");
         }
 
         public TYPE getType()
         {
-            return !getJsonObject().containsKey("type") ? null : TYPE.valueOf(getJsonObject().getString("type"));
+            return !getNewJsonObject().has("type") ? null : TYPE.valueOf(getNewJsonObject().getString("type"));
         }
 
         public JSONObject getJobParameters()

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

@@ -441,41 +441,36 @@ public ApiResponse execute(SimpleApiJsonForm form, BindException errors)
 
             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);
-            ts.forEachResults(new Selector.ForEachBlock<Results>()
-            {
-                @Override
-                public void exec(Results rs) throws SQLException, StopIteratingException
+            ts.forEachResults(rs -> {
+                Container c = ContainerManager.getForId(rs.getString(FieldKey.fromString("container")));
+                if (!c.hasPermission(getUser(), UpdatePermission.class))
                 {
-                    Container c = ContainerManager.getForId(rs.getString(FieldKey.fromString("container")));
-                    if (!c.hasPermission(getUser(), UpdatePermission.class))
-                    {
-                        throw new UnauthorizedException("User does not have permission to update records in the folder: " + c.getPath());
-                    }
+                    throw new UnauthorizedException("User does not have permission to update records in the folder: " + c.getPath());
+                }
 
-                    JSONObject json = rs.getString("trackJson") == null ? new JSONObject() : new JSONObject(rs.getString("trackJson"));
-                    for (String key : attributes.keySet())
+                JSONObject json = rs.getString("trackJson") == null ? new JSONObject() : new JSONObject(rs.getString("trackJson"));
+                for (String key : attributes.keySet())
+                {
+                    if (StringUtils.trimToNull(attributes.getString(key)) == null)
                     {
-                        if (StringUtils.trimToNull(attributes.getString(key)) == null)
-                        {
-                            json.remove(key);
-                        }
-                        else
-                        {
-                            json.put(key, attributes.get(key));
-                        }
+                        json.remove(key);
                     }
-
-                    if (!rows.containsKey(c))
+                    else
                     {
-                        rows.put(c, new ArrayList<>());
+                        json.put(key, attributes.get(key));
                     }
+                }
 
-                    Map<String, Object> row = new CaseInsensitiveHashMap<>();
-                    row.put("objectid", rs.getString("objectid"));
-                    row.put("trackJson", json.isEmpty() ? null : json.toString());
-
-                    rows.get(c).add(row);
+                if (!rows.containsKey(c))
+                {
+                    rows.put(c, new ArrayList<>());
                 }
+
+                Map<String, Object> row = new CaseInsensitiveHashMap<>();
+                row.put("objectid", rs.getString("objectid"));
+                row.put("trackJson", json.isEmpty() ? null : json.toString());
+
+                rows.get(c).add(row);
             });
 
             try (DbScope.Transaction transaction = DbScope.getLabKeyScope().ensureTransaction())

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

@@ -345,7 +345,7 @@ 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.getJsonObject().containsKey(propName))
+        if (!form.getNewJsonObject().has(propName))
         {
             throw new ApiUsageException("Missing property: " + propName);
         }