Without a controller/service script you'll not be able to meet single responsibility principle in fact. Here's a high level design I'd implement if I were you.
FileRepository
Should expose a method to get a file. Let's name it GetFileById.
MongoDBRepository Methods for CRUD operations. Such as SelectById, SelectByQuery, Update, Create, Delete.
Object creation logic
If your createNewObj logic is simple it would be enough to move it to your object contructor so that your code looks like that: var newObj = new MyObj(json[i]);
But if it's relatively complex maybe because you use some third party frameforks for validation or whatever you'd better create a factory. Then you could would look this way: var newObj = MyObjFactory.Create(json[i]);
Service/controller
Finally you'll need to implement controller/service object. Let's name it WorkService with a method DoWork which should handle all interactions between the repositories and other objects discribed above. Here's approximately DoWork should look like:
function DoWork(fileId){
var json = fileRepository.SelectById(fileId);
for(var i=0;i<json.length;i++){
var newObj = new MyObj(json[i]); // or calling factory method
var dbRecord = MongoDBRepository.SelectByQuery(newObj.name, newObj.date);
if(dbRecord){
MongoDBRepository.Update(newObj);
}
else{
MongoDBRepository.Create(newObj);
}
}
}
Please note it's just a javascript syntax pseudo-code. Your actual code might look absolutley different but it gives your a feeling of what kind of design your should have. Also I exmplicitly didn't create a repository objects inside DoWork method, think of the way to inject them so you meet Dependency inversion principle.
Hope it helps!