+
+ chash = {}
+ collections.each do |c|
+ c.reload()
+ chash[c.uuid] = c
+ end
+
+ combined = ""
+ files.each do |m|
+ mt = chash[m[1]+m[2]].manifest_text
+ if m[4]
+ IO.popen(['arv-normalize', '--extract', m[4][1..-1]], 'w+b') do |io|
+ io.write mt
+ io.close_write
+ while buf = io.read(2**20)
+ combined += buf
+ end
+ end
+ else
+ combined += chash[m[1]+m[2]].manifest_text
+ end
+ end
+
+ normalized = ''
+ IO.popen(['arv-normalize'], 'w+b') do |io|
+ io.write combined
+ io.close_write
+ while buf = io.read(2**20)
+ normalized += buf
+ end
+ end
+
+ require 'digest/md5'
+
+ d = Digest::MD5.new()
+ d << normalized
+ newuuid = "#{d.hexdigest}+#{normalized.length}"
+
+ env = Hash[ENV].
+ merge({
+ 'ARVADOS_API_HOST' =>
+ $arvados_api_client.arvados_v1_base.
+ sub(/\/arvados\/v1/, '').
+ sub(/^https?:\/\//, ''),
+ 'ARVADOS_API_TOKEN' => Thread.current[:arvados_api_token],
+ 'ARVADOS_API_HOST_INSECURE' =>
+ Rails.configuration.arvados_insecure_https ? 'true' : 'false'
+ })
+
+ IO.popen([env, 'arv-put', '--raw'], 'w+b') do |io|
+ io.write normalized
+ io.close_write
+ while buf = io.read(2**20)
+
+ end
+ end
+
+ newc = Collection.new({:uuid => newuuid, :manifest_text => normalized})
+ newc.save!
+
+ chash.each do |k,v|
+ l = Link.new({
+ tail_kind: "arvados#collection",
+ tail_uuid: k,
+ head_kind: "arvados#collection",
+ head_uuid: newuuid,
+ link_class: "provenance",
+ name: "provided"
+ })
+ l.save!