idcc_ruby_simple_example.rb

#! /usr/bin/env ruby -wKU

# Author::    Sébastien Briois (mailto:sebriois@gmail.com)

require "rubygems"
require "rest_client"
require "json"

IDCC_SITE = "http://user:password@localhost:3000"

# Generic helper method for handling the web calls to the repository.
def request(method, url, data = nil, datatype = "application/json", repository = IDCC_SITE)
  resource = RestClient::Resource.new( repository )
  
  response =
    case method.upcase
    when "GET"    then resource[url].get
    when "POST"   then resource[url].post data, :content_type => datatype
    when "PUT"    then resource[url].put  data, :content_type => datatype
    when "DELETE" then resource[url].delete
    else
      raise "Method #{method} unknown when requesting url #{url}"
    end
  
  puts "#{method} #{url} - #{response.code} #{RestClient::STATUSES[response.code]}"
  return response.body
end

##
##  Scenarios: 
##      - GET, CREATE, UPDATE some allele(s)
##      - CREATE a Targeting Vector
##      - CREATE a ES Cell
##      - DELETE created objects
##

# Get allele lists - first page
response = request( 'GET' , 'alleles.json?page=1' )
alleles = JSON.parse( response )
first_allele = alleles[0]

# Get first allele from this page - no need to keep track of the ids
# a search method is provided, see extended example.
request( 'GET', "alleles/#{first_allele['id']}.json" )

# Create an allele
data = {
  :pipeline_id        => 1,
  :mgi_accession_id   => "MGI:123456",
  :project_design_id  => 1,
  :cassette           => "L1L2_gt2",
  :backbone           => "L3L4_pZero_kan",
  :assembly           => "NCBIM37",
  :chromosome         => "1",
  :strand             => "+",
  :design_type        => "Knock Out",
  :design_subtype     => "Frameshift",
  :homology_arm_start => 10,
  :homology_arm_end   => 10000,
  :cassette_start     => 50,
  :cassette_end       => 500,
  :loxp_start         => 600,
  :loxp_end           => 700
}
allele_json     = JSON.generate( {:molecular_structure => data} )
response        = request( 'POST', 'alleles.json', allele_json )
created_allele  = JSON.parse( response )


# Update an allele (for example: the one created above)
data = { :subtype_description => "SOME NEW INFORMATION" }
allele_json     = JSON.generate( {:molecular_structure => data} )
response        = request( 'PUT', "alleles/#{created_allele['id']}.json", allele_json )
updated_allele  = JSON.parse( response )


# Create a targeting vector related to this allele
data = {
  :molecular_structure_id => created_allele['id'],
  :name                   => 'PGDGR001',
  :ikmc_project_id        => 1
}
targ_vec_json    = JSON.generate( {:targeting_vector => data} )
response         = request( 'POST', 'targeting_vectors.json', targ_vec_json )
created_targ_vec = JSON.parse( response )


# Create an ES Cell related to these targeting vector and allele
data = {
  :molecular_structure_id => created_allele['id'],
  :targeting_vector_id    => created_targ_vec['id'],
  :name                   => 'EPD001'
}
es_cell_json    = JSON.generate( {:es_cell => data} )
response        = request( 'POST', 'es_cells.json', es_cell_json )
created_es_cell = JSON.parse( response )


# Delete everything
request( 'DELETE', "es_cells/#{created_es_cell['id']}" )
request( 'DELETE', "targeting_vectors/#{created_targ_vec['id']}" )
request( 'DELETE', "alleles/#{created_allele['id']}" )