I've found a working code:

JSONParser parser = new JSONParser();
Object obj  = parser.parse(content);
JSONArray array = new JSONArray();
array.add(obj);

If you don't need the array (like the author), you can simply use

JSONParser parser = new JSONParser();
Object obj  = parser.parse(content);

The first element of the sites array is an array, as you can see indenting the JSON:

{"units":[{"id":42,               
    ...
    "sites":
    [
      [
        {
          "id":316,
          "article":42,
          "clip":133904
        }
      ],
      {"length":5}
    ]
    ...
}

Therefore you need to treat its value accordingly; probably you could do something like:

JSONObject site = (JSONObject)(((JSONArray)jsonSites.get(i)).get(0));

this worked:

System.out.println("resultList.toString() " + resultList);
            org.json.JSONObject obj = new JSONObject(resultList);
            org.json.JSONArray jsonArray = obj.getJSONArray(someField);

            for(int i=0;i<jsonArray.length();i++){
                System.out.println("array is " + jsonArray.get(i));

            }

JSONObject site=jsonSites.getJSONObject(i) should work out

JSONObject obj=(JSONObject)JSONValue.parse(content); 
JSONArray arr=(JSONArray)obj.get("units"); 
System.out.println(arr.get(1));  //this will print {"id":42,...sities ..}

@cyberz is right but explain it reverse

You can first read the whole content of file into a String.

FileInputStream fileInputStream = null;
String data="";
StringBuffer stringBuffer = new StringBuffer("");
try{
    fileInputStream=new FileInputStream(filename);
    int i;
    while((i=fileInputStream.read())!=-1)
    {
        stringBuffer.append((char)i);
    }
    data = stringBuffer.toString();
}
catch(Exception e){
        LoggerUtil.printStackTrace(e);
}
finally{
    if(fileInputStream!=null){  
        fileInputStream.close();
    }
}

Now You will have the whole content into String ( data variable ).

JSONParser parser = new JSONParser();
org.json.simple.JSONArray jsonArray= (org.json.simple.JSONArray) parser.parse(data);

After that you can use jsonArray as you want.

If you want to re-filter the json data you can use following method. Given example is getting all document data from couchdb.

{
    Gson gson = new Gson();
    String resultJson = restTemplate.getForObject(url+"_all_docs?include_docs=true", String.class);
    JSONObject object =  (JSONObject) new JSONParser().parse(resultJson);
    JSONArray rowdata = (JSONArray) object.get("rows");   
    List<Object>list=new ArrayList<Object>();   
    for(int i=0;i<rowdata.size();i++) {
        JSONObject index = (JSONObject) rowdata.get(i);
        JSONObject data = (JSONObject) index.get("doc");
        list.add(data);      
    }
    // convert your list to json
    String devicelist = gson.toJson(list);
    return devicelist;
}

JSONObject site = (JSONObject)jsonSites.get(i); // Exception happens here.

The return type of jsonSites.get(i) is JSONArray not JSONObject. Because sites have two '[', two means there are two arrays here.

use your jsonsimpleobject direclty like below

JSONObject unitsObj = parser.parse(new FileReader("file.json");

JSONObject baseReq
LinkedHashMap insert = (LinkedHashMap) baseReq.get("insert");
LinkedHashMap delete = (LinkedHashMap) baseReq.get("delete");