1
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To catch errors, I have written if-else blocks in every function which looks bad. Please suggest a better way to handle errors in async node.

   async.waterfall([

            function(callback){

                fnOne.GetOne(req, res,function(err,result) {  

                  if(err){
                    console.error("Controller : fnOne",err);
                    callback(err,null);
                  }
                  else{

                    var fnOne = result; 

                   callback(null, fnOne);
                  }
                })            
            },

            function(fnOne, callback){

               fnTwo.two(fnOne,function(err,result) {
                  if(err) {
                    console.error(err);
                    callback(err,null);
                  }
                  else{

                    callback(null, context);
                  }
               })            
            }
        ], function (err, result) {     

           if(err){
              console.error("Controller waterfall Error" , err);
              res.send("Error in serving request.");
           }
        });
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2
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Check out promises. They are not (yet) available natively in Node.js, but you can use Q library.

Promises allow you to make your control flow explicit with methods like catch and finally instead of hiding it in callbacks.

Also you won't need async with promises.

Q provides a convenience method to “convert” a function that accepts a callback to a promise-returning function.

I don't understand what fnOne or fnTwo is your code (seemingly objects and not functions), so I can't really translate your example, but it would look similar to this:

var Q = require('q');

// Convert our functions to promise-returning functions
var getOne = Q.nbind(fnOne.GetOne, fnOne),
    getTwo = Q.nbind(fnTwo.two, fnTwo) ;

getOne(req, res)
  .then(function (result) {
    return getTwo(result);
  })
  .then(function (result) {
    // do something useful with final result
  })
  .catch(function (err) {
    console.error("Three was an error", err);    
    res.send("Error in serving request.");
  })
  .done();
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