class CollectionsController < ApplicationController
- skip_before_filter :find_object_by_uuid, :only => [:graph]
+ skip_around_filter :thread_with_mandatory_api_token, only: [:show_file]
+ skip_before_filter :find_object_by_uuid, only: [:provenance, :show_file]
+ skip_before_filter :check_user_agreements, only: [:show_file]
- def graph
- index
+ def show_pane_list
+ %w(Files Attributes Metadata Provenance_graph Used_by JSON API)
+ end
+
+ def set_persistent
+ case params[:value]
+ when 'persistent', 'cache'
+ persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
+ ['link_class', '=', 'resources'],
+ ['name', '=', 'wants'],
+ ['tail_uuid', '=', current_user.uuid],
+ ['head_uuid', '=', @object.uuid]])
+ logger.debug persist_links.inspect
+ else
+ return unprocessable "Invalid value #{value.inspect}"
+ end
+ if params[:value] == 'persistent'
+ if not persist_links.any?
+ Link.create(link_class: 'resources',
+ name: 'wants',
+ tail_uuid: current_user.uuid,
+ head_uuid: @object.uuid)
+ end
+ else
+ persist_links.each do |link|
+ link.destroy || raise
+ end
+ end
+
+ respond_to do |f|
+ f.json { render json: @object }
+ end
end
def index
- @links = Link.eager.limit(100).where(head_kind: 'arvados#collection') |
- Link.eager.limit(100).where(tail_kind: 'arvados#collection')
- @collections = Collection.limit(100).to_hash
- @collections.merge!(Collection.
- limit(100).
- where(uuid: @links.select{|x|x.head_kind=='arvados#collection'}.collect(&:head_uuid) |
- @links.select{|x|x.tail_kind=='arvados#collection'}.collect(&:tail_uuid)).
- to_hash)
- @collection_info = {}
- @collections.each do |uuid, c|
- ci = (@collection_info[uuid] ||= {uuid: uuid})
- ci[:created_at] = c.created_at
- end
- @links.each do |l|
- if l.head_kind == 'arvados#collection'
- c = (@collection_info[l.head_uuid] ||= {uuid: l.head_uuid})
- if l.link_class == 'resources' and l.name == 'wants'
- if l.head.respond_to? :created_at
- c[:created_at] = l.head.created_at
- end
- c[:wanted] = true
- if l.owner == current_user.uuid
- c[:wanted_by_me] = true
- end
- end
+ if params[:search].andand.length.andand > 0
+ tags = Link.where(any: ['contains', params[:search]])
+ @collections = (Collection.where(uuid: tags.collect(&:head_uuid)) |
+ Collection.where(any: ['contains', params[:search]])).
+ uniq { |c| c.uuid }
+ else
+ if params[:limit]
+ limit = params[:limit].to_i
+ else
+ limit = 100
end
- if l.tail_kind == 'arvados#collection'
- c = (@collection_info[l.tail_uuid] ||= {uuid: l.tail_uuid})
- if l.link_class == 'group' and l.name == 'member_of'
- c[:groups] ||= {}
- c[:groups][l.tail_uuid] = true
- end
- if l.link_class == 'data_origin'
- c[:origin] = l
- end
+
+ if params[:offset]
+ offset = params[:offset].to_i
+ else
+ offset = 0
+ end
+
+ @collections = Collection.limit(limit).offset(offset)
+ end
+ @links = Link.limit(1000).
+ where(head_uuid: @collections.collect(&:uuid))
+ @collection_info = {}
+ @collections.each do |c|
+ @collection_info[c.uuid] = {
+ tag_links: [],
+ wanted: false,
+ wanted_by_me: false,
+ provenance: [],
+ links: []
+ }
+ end
+ @links.each do |link|
+ @collection_info[link.head_uuid] ||= {}
+ info = @collection_info[link.head_uuid]
+ case link.link_class
+ when 'tag'
+ info[:tag_links] << link
+ when 'resources'
+ info[:wanted] = true
+ info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
+ when 'provenance'
+ info[:provenance] << link.name
end
+ info[:links] << link
+ end
+ @request_url = request.url
+ end
+
+ def show_file
+ # We pipe from arv-get to send the file to the user. Before we start it,
+ # we ask the API server if the file actually exists. This serves two
+ # purposes: it lets us return a useful status code for common errors, and
+ # helps us figure out which token to provide to arv-get.
+ coll = nil
+ usable_token = find_usable_token do
+ coll = Collection.find(params[:uuid])
+ end
+ if usable_token.nil?
+ return # Response already rendered.
+ elsif params[:file].nil? or not file_in_collection?(coll, params[:file])
+ return render_not_found
end
+ opts = params.merge(arvados_api_token: usable_token)
+ ext = File.extname(params[:file])
+ self.response.headers['Content-Type'] =
+ Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
+ self.response.headers['Content-Length'] = params[:size] if params[:size]
+ self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
+ self.response_body = file_enumerator opts
end
def show
@output2colorindex = {}
@sourcedata = {params[:uuid] => {uuid: params[:uuid]}}
@protected = {}
- whence = `whence #{params[:uuid]}`
+
colorindex = -1
- whence.split("\n").each do |line|
- if line.match /^(\#\d+@\S+)$/
- job = Job.where(submit_id: line).first
- @provenance << {job: job, target: line}
- elsif (re = line.match /^ +output *= *(\S+)/)
- if !@provenance.empty?
- @provenance[-1][:output] = re[1]
- @output2job[re[1]] = @provenance[-1][:job]
- if !@output2colorindex[re[1]]
- @output2colorindex[re[1]] = (colorindex += 1) % 10
+ any_hope_left = true
+ while any_hope_left
+ any_hope_left = false
+ Job.where(output: @sourcedata.keys).sort_by { |a| a.finished_at || a.created_at }.reverse.each do |job|
+ if !@output2colorindex[job.output]
+ any_hope_left = true
+ @output2colorindex[job.output] = (colorindex += 1) % 10
+ @provenance << {job: job, output: job.output}
+ @sourcedata.delete job.output
+ @output2job[job.output] = job
+ job.dependencies.each do |new_source_data|
+ unless @output2colorindex[new_source_data]
+ @sourcedata[new_source_data] = {uuid: new_source_data}
+ end
end
- @sourcedata.delete re[1]
end
- elsif (re = line.match /^([0-9a-f]{32}\b)/)
- @sourcedata[re[1]] ||= {uuid: re[1]}
end
end
+
Link.where(head_uuid: @sourcedata.keys | @output2job.keys).each do |link|
if link.link_class == 'resources' and link.name == 'wants'
@protected[link.head_uuid] = true
+ if link.tail_uuid == current_user.uuid
+ @is_persistent = true
+ end
end
end
Link.where(tail_uuid: @sourcedata.keys).each do |link|
if link.link_class == 'data_origin'
@sourcedata[link.tail_uuid][:data_origins] ||= []
- @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_kind, link.head_uuid]
+ @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_uuid]
end
end
Collection.where(uuid: @sourcedata.keys).each do |collection|
@sourcedata[collection.uuid][:collection] = collection
end
end
+
+ Collection.where(uuid: @object.uuid).each do |u|
+ @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
+ {:request => request,
+ :direction => :bottom_up,
+ :combine_jobs => :script_only}) rescue nil
+ @used_by_svg = ProvenanceHelper::create_provenance_graph(u.used_by, "used_by_svg",
+ {:request => request,
+ :direction => :top_down,
+ :combine_jobs => :script_only,
+ :pdata_only => true}) rescue nil
+ end
+ end
+
+ protected
+
+ def find_usable_token
+ # Iterate over every token available to make it the current token and
+ # yield the given block.
+ # If the block succeeds, return the token it used.
+ # Otherwise, render an error response based on the most specific
+ # error we encounter, and return nil.
+ read_tokens = [Thread.current[:arvados_api_token]].compact
+ if params[:reader_tokens].is_a? Array
+ read_tokens += params[:reader_tokens]
+ end
+ most_specific_error = [401]
+ read_tokens.each do |api_token|
+ using_specific_api_token(api_token) do
+ begin
+ yield
+ return api_token
+ rescue ArvadosApiClient::NotLoggedInException => error
+ status = 401
+ rescue => error
+ status = (error.message =~ /\[API: (\d+)\]$/) ? $1.to_i : nil
+ raise unless [401, 403, 404].include?(status)
+ end
+ if status >= most_specific_error.first
+ most_specific_error = [status, error]
+ end
+ end
+ end
+ case most_specific_error.shift
+ when 401, 403
+ redirect_to_login
+ when 404
+ render_not_found(*most_specific_error)
+ end
+ return nil
+ end
+
+ def file_in_collection?(collection, filename)
+ def normalized_path(part_list)
+ File.join(part_list).sub(%r{^\./}, '')
+ end
+ target = normalized_path([filename])
+ collection.files.each do |file_spec|
+ return true if (normalized_path(file_spec[0, 2]) == target)
+ end
+ false
+ end
+
+ def file_enumerator(opts)
+ FileStreamer.new opts
+ end
+
+ class FileStreamer
+ def initialize(opts={})
+ @opts = opts
+ end
+ def each
+ return unless @opts[:uuid] && @opts[:file]
+ env = Hash[ENV].
+ merge({
+ 'ARVADOS_API_HOST' =>
+ arvados_api_client.arvados_v1_base.
+ sub(/\/arvados\/v1/, '').
+ sub(/^https?:\/\//, ''),
+ 'ARVADOS_API_TOKEN' =>
+ @opts[:arvados_api_token],
+ 'ARVADOS_API_HOST_INSECURE' =>
+ Rails.configuration.arvados_insecure_https ? 'true' : 'false'
+ })
+ IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
+ 'rb') do |io|
+ while buf = io.read(2**20)
+ yield buf
+ end
+ end
+ Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
+ end
end
end