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November 17, 2009 15:38
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| #!/usr/bin/env ruby -wKU | |
| # Author:: Sébastien Briois (mailto:[email protected]) | |
| 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 | |
| ## | |
| ## Scenario 1: search and update an allele | |
| ## | |
| allele = { | |
| :pipeline_id => 1, | |
| :mgi_accession_id => 'MGI:123456', | |
| :project_design_id => 1, | |
| :cassette => 'L1L2_gt2', | |
| :backbone => 'L3L4_pZero_kan', | |
| :assembly => 'NCBIM37', | |
| :chromosome => '11', | |
| :strand => '+', | |
| :design_type => 'Knock Out', | |
| :design_subtype => 'Frameshift', | |
| :homology_arm_start => 10, | |
| :homology_arm_end => 10000, | |
| :cassette_start => 50, | |
| :cassette_end => 500, | |
| :loxp_start => 1000, | |
| :loxp_end => 1500 | |
| } | |
| # Let's search for this allele using discriminating attributes | |
| search_params = "mgi_accession_id=#{allele['mgi_accession_id']}" | |
| search_params += "&project_design_id=#{allele['project_design_id']}" | |
| # etc. | |
| response = request( 'GET', "alleles.json?#{search_params}" ) | |
| alleles_found = JSON.parse( response ) # Returns a list of matches | |
| # NOTE: | |
| # The alleles_found might hold more than one allele in which case the | |
| # search (above) could be run again with more details. | |
| if alleles_found | |
| # We now want to update our allele. | |
| allele_found = alleles_found[0] | |
| allele_json = JSON.generate( {:molecular_structure => allele} ) | |
| request( 'PUT', "alleles/#{allele_found['id']}", allele_json ) | |
| else | |
| # No allele has been found, let's create our allele from the Hash we've made | |
| allele_json = JSON.generate( {:molecular_structure => allele} ) | |
| response = request( 'POST', 'alleles', allele_json ) | |
| allele = JSON.parse( response ) | |
| # In this example we'll DELETE the created allele | |
| request( 'DELETE', "alleles/#{allele['id']}") | |
| end | |
| ## | |
| ## Scenario 2: Create an allele and all its products in a single request | |
| ## /!\ This trick will not work for an UPDATE. | |
| ## | |
| allele_and_products = { | |
| :pipeline_id => 1, | |
| :mgi_accession_id => "MGI:456789", | |
| :project_design_id => 2, | |
| :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 => 1000, | |
| :loxp_end => 1500, | |
| :targeting_vectors => [ | |
| { | |
| :name => 'PRPGD001', | |
| :intermediate_vector => 'PGS001', | |
| :ikmc_project_id => 1, | |
| :es_cells => [ | |
| { :name => 'EPD001' }, | |
| { :name => 'EPD002' }, | |
| { :name => 'EPD003' }, | |
| ] | |
| }, | |
| { | |
| :name => 'PRPGD002', | |
| :intermediate_vector => 'PGS001', | |
| :ikmc_project_id => 1, | |
| :es_cells => [ | |
| { :name => 'EPD004' }, | |
| { :name => 'EPD005' }, | |
| { :name => 'EPD006' }, | |
| ] | |
| } | |
| ], | |
| :genbank_file => { | |
| :escell_clone => "A GENBANK FILE IN PLAIN TEXT", | |
| :targeting_vector => "A GENBANK FILE IN PLAIN TEXT" | |
| } | |
| } | |
| allele_json = JSON.generate( {:molecular_structure => allele_and_products} ) | |
| response = request( 'POST', 'alleles.json', allele_json ) | |
| allele = JSON.parse( response ) | |
| # DELETE everything | |
| allele['es_cells'].each do |es_cell| | |
| request( 'DELETE', "es_cells/#{es_cell['id']}" ) | |
| end | |
| allele['targeting_vectors'].each do |targ_vec| | |
| request( 'DELETE', "targeting_vectors/#{targ_vec['id']}" ) | |
| end | |
| request( 'DELETE', "alleles/#{allele['id']}" ) |
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