S2 Mapper

S2 Mapper is a wrapper for an S2 LIMS (Laboritory Information Management System) compatible API.

S2 is a backend LIMS server sending and receiving JSON.

Installation

S2Mapper is a Bower module. It hasn't yet been registered with the central Bower repository but can be installed with:-

bower install git@github.com:sanger/S2Mapper.git

Resources

A plain S2 resouce typically has the following structure:-

{
  resourceType: 'tube',
  read:     function(){...},  // a function to reread the resource using an AJAX
                              // request.

  create:   function() {...},
  update:   function() {...},
  delete:   function() {...},
  rawJson:  {...},            // holds the JSON as sent back by the S2API.
  batch:    function(){ },    // returns a Batch Promise
}

Searching for Resources

Searching is carried out asynchronusly and returns a jQuery promise object.

var s2root = S2Root.load();
s2root.tubes.findByEan13Barcode('0123456789123');
// => Resource Promise

The resource can then be extracted with a callback. E.g.

var s2root = S2Root.load();
var tube;

s2root.tubes.findByEan13Barcode('0123456789123').done(function(returnedResource){
  tube = returnedResource;
});

Order and Batch

An order represents a request for work to be carried out on a number of items (tubes, plates, spin columns, etc.)

An order may span several laboritory pipelines. For example, from Sample reception through library preparation and into cluster formation (sequencing).

A project investigator will be created an Order ahead of sample reception.

To allow individual pipelines the flexibility to decide how work processed items from 1 or more Orders can be processed in batches.

Batch is used as the unit of work for items in S2.

The S2Mapper allows you to retrieve the batch for an item through the batch function.

tube.batch(); 
// => Batch Promise

Both Order and Batch are S2 Resources but with some specialiation.

##Services ###Printing

S2Mapper also includes a service to print barcodes. Currently this is bound to one printer, and only tube labels.

To use the printing service, include 'services/prints.js' and call

print (barcode, desc, name, prefix, project, suffix) // => Promise