class CollectionsController < ApplicationController
- 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]
+ skip_around_filter(:thread_with_mandatory_api_token,
+ only: [:show_file, :show_file_links])
+ skip_before_filter(:find_object_by_uuid,
+ only: [:provenance, :show_file, :show_file_links])
+
+ RELATION_LIMIT = 5
def show_pane_list
%w(Files Attributes Metadata Provenance_graph Used_by JSON API)
@request_url = request.url
end
+ def show_file_links
+ Thread.current[:reader_tokens] = [params[:reader_token]]
+ find_object_by_uuid
+ render layout: false
+ 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
+ tokens = [Thread.current[:arvados_api_token], params[:reader_token]].compact
+ usable_token = find_usable_token(tokens) do
coll = Collection.find(params[:uuid])
end
if usable_token.nil?
self.response_body = file_enumerator opts
end
+ def sharing_scopes
+ ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/keep_services"]
+ end
+
def search_scopes
- ApiClientAuthorization.where(filters: [['scopes', '=', ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/"]]])
+ ApiClientAuthorization.where(filters: [['scopes', '=', sharing_scopes]])
end
def show
return super if !@object
- @provenance = []
- @output2job = {}
- @output2colorindex = {}
- @sourcedata = {params[:uuid] => {uuid: params[:uuid]}}
- @protected = {}
- @search_sharing = search_scopes.select { |s| s.scopes != ['all'] }
-
- colorindex = -1
- 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
- end
- 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
+ if current_user
+ jobs_with = lambda do |conds|
+ Job.limit(RELATION_LIMIT).where(conds)
+ .results.sort_by { |j| j.finished_at || j.created_at }
end
+ @output_of = jobs_with.call(output: @object.uuid)
+ @log_of = jobs_with.call(log: @object.uuid)
+ folder_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
+ .where(head_uuid: @object.uuid, link_class: 'name').results
+ folder_hash = Group.where(uuid: folder_links.map(&:tail_uuid)).to_hash
+ @folders = folder_links.map { |link| folder_hash[link.tail_uuid] }
+ @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
+ .where(head_uuid: @object.uuid, link_class: 'permission',
+ name: 'can_read').results
+ @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
+ .where(object_uuid: @object.uuid).results
+ @is_persistent = Link.limit(1)
+ .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
+ link_class: 'resources', name: 'wants')
+ .results.any?
+ @search_sharing = search_scopes.select { |s| s.scopes != ['all'] }
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_uuid]
- end
- end
- Collection.where(uuid: @sourcedata.keys).each do |collection|
- if @sourcedata[collection.uuid]
- @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
+ @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
+ {:request => request,
+ :direction => :bottom_up,
+ :combine_jobs => :script_only}) rescue nil
+ @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
+ {:request => request,
+ :direction => :top_down,
+ :combine_jobs => :script_only,
+ :pdata_only => true}) rescue nil
end
def sharing_popup
end
def share
- a = ApiClientAuthorization.create(scopes: ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/"])
+ a = ApiClientAuthorization.create(scopes: sharing_scopes)
@search_sharing = search_scopes.select { |s| s.scopes != ['all'] }
render 'sharing_popup'
end
protected
- def find_usable_token
- # Iterate over every token available to make it the current token and
+ def find_usable_token(token_list)
+ # Iterate over every given token 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|
+ token_list.each do |api_token|
using_specific_api_token(api_token) do
begin
yield
end
def file_in_collection?(collection, filename)
- def normalized_path(part_list)
- File.join(part_list).sub(%r{^\./}, '')
- end
- target = normalized_path([filename])
+ target = CollectionsHelper.file_path(File.split(filename))
collection.files.each do |file_spec|
- return true if (normalized_path(file_spec[0, 2]) == target)
+ return true if (CollectionsHelper.file_path(file_spec) == target)
end
false
end
end
class FileStreamer
+ include ArvadosApiClientHelper
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'
- })
+
+ env = Hash[ENV].dup
+
+ require 'uri'
+ u = URI.parse(arvados_api_client.arvados_v1_base)
+ env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
+ env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
+ env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
+
IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
'rb') do |io|
- while buf = io.read(2**20)
+ while buf = io.read(2**16)
yield buf
end
end
projects / arvados.git / blobdiff