Quick and dirty querying of the ensembl REST api with Groovy

ensembl.groovy

@Grab( 'org.codehaus.groovy.modules.http-builder:http-builder:0.5.2' )
import groovyx.net.http.RESTClient

// A connection to ensembl
def ensembl = new RESTClient( 'http://beta.rest.ensembl.org/' )

// Get a list of species
def spec = ensembl.get( path:'info/species', 
                        query:[ 'content-type':'application/json' ] )

// Find the species with "baker's yeast" as an alias
String species = spec.data.species.findResult { "baker's yeast" in it.aliases ? it.name : null }

// Get all the assemblies for this species
def assembly = ensembl.get( path:"assembly/info/$species", 
                            query:[ 'content-type':'application/json' ] )
List assemblies = assembly.data.top_level_seq_region_names

// For each assembly, try and get the assembly info for it
// (Currently the API fails for non-chromosomal assemblies)
List chromosomes = assemblies.findAll {
  // Need to limit to 3 requests per second (max)
  Thread.sleep( 400 )
  print '.'
  try {
    ensembl.get( path:"assembly/info/$species/$it", query:[ 'content-type':'application/json' ] )
  } catch( e ) { false }
}

println "\n$species has chromosomes $chromosomes"