class CollectionsController < ApplicationController
- skip_before_filter :find_object_by_uuid, :only => [:graph]
+ skip_before_filter :find_object_by_uuid, :only => [:provenance]
+ 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 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)
+ 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
+ @collections = Collection.limit(100)
+ end
+ @links = Link.limit(1000).
+ where(head_uuid: @collections.collect(&:uuid))
@collection_info = {}
- @collections.each do |uuid, c|
- ci = (@collection_info[uuid] ||= {uuid: uuid})
- ci[:created_at] = c.created_at
+ @collections.each do |c|
+ @collection_info[c.uuid] = {
+ tag_links: [],
+ wanted: false,
+ wanted_by_me: false,
+ provenance: [],
+ links: []
+ }
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
- 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
+ @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
+ opts = params.merge(arvados_api_token: Thread.current[:arvados_api_token])
+ if r = params[:file].match(/(\.\w+)/)
+ ext = r[1]
end
+ 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 = FileStreamer.new opts
end
+
def show
return super if !@object
@provenance = []
@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
@sourcedata[collection.uuid][:collection] = collection
end
end
+
+ Collection.where(uuid: @object.uuid).each do |u|
+ puts request
+ @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
+ 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
projects / arvados.git / blobdiff