class CollectionsController < ApplicationController
- skip_before_filter :find_object_by_uuid, :only => [:provenance]
- skip_before_filter :check_user_agreements, :only => [:show_file]
+ 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 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
if params[:search].andand.length.andand > 0
Collection.where(any: ['contains', params[:search]])).
uniq { |c| c.uuid }
else
- @collections = Collection.limit(100)
+ if params[:limit]
+ limit = params[:limit].to_i
+ else
+ limit = 100
+ 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] = {
- tags: [],
+ tag_links: [],
wanted: false,
wanted_by_me: false,
provenance: [],
info = @collection_info[link.head_uuid]
case link.link_class
when 'tag'
- info[:tags] << link.name
+ info[:tag_links] << link
when 'resources'
info[:wanted] = true
info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
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
+ # 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 = FileStreamer.new opts
- end
-
- def describe_node(uuid)
- rsc = ArvadosBase::resource_class_for_uuid uuid
- if rsc
- "\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"#{url_for rsc}/#{uuid}\"];"
- else
- ""
- end
- end
-
- def describe_script(job)
- #"""\"#{job.script_version}\" [label=\"#{job.script}: #{job.script_version}\"];
- # \"#{job.uuid}\" -> \"#{job.script_version}\" [label=\"script\"];"""
- "\"#{job.uuid}\" [label=\"#{job.script}\\n#{job.script_version}\"];"
- end
-
- def job_uuid(job)
- "#{job.script}\\n#{job.script_version}"
- end
-
- def collection_uuid(uuid)
- m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid)
- if m
- m[1]
- else
- nil
- end
- end
-
- def script_param_edges(visited, job, prefix, sp)
- gr = ""
- if sp and not sp.empty?
- case sp
- when Hash
- sp.each do |k, v|
- if prefix.size > 0
- k = prefix + "::" + k.to_s
- end
- gr += script_param_edges(visited, job, k.to_s, v)
- end
- when Array
- sp.each do |v|
- gr += script_param_edges(visited, job, prefix, v)
- end
- else
- m = collection_uuid(sp)
- if m
- gr += "\"#{job_uuid(job)}\" -> \"#{m}\" [label=\" #{prefix}\"];"
- gr += generate_provenance_edges(visited, m)
- end
- end
- end
- gr
- end
-
- def generate_provenance_edges(visited, uuid)
- gr = ""
- m = collection_uuid(uuid)
-
- if not uuid or uuid.empty? or visited[uuid] or visited[m]
- return ""
- end
-
- #puts "visiting #{uuid}"
-
- if m
- # uuid is a collection
- uuid = m
- visited[uuid] = true
-
- gr += describe_node(uuid)
-
- Job.where(output: uuid).each do |job|
- #gr += describe_node(job_uuid(job))
- gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\" output\"];"
- gr += generate_provenance_edges(visited, job.uuid)
- end
-
- Job.where(log: uuid).each do |job|
- #gr += describe_node(job_uuid(job))
- gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\" log\"];"
- gr += generate_provenance_edges(visited, job.uuid)
- end
-
- else
- visited[uuid] = true
-
- # uuid is something else
- rsc = ArvadosBase::resource_class_for_uuid uuid
-
- if rsc == Job
- Job.where(uuid: uuid).each do |job|
- gr += script_param_edges(visited, job, "", job.script_parameters)
- #gr += describe_script(job)
- end
- else
- gr += describe_node(uuid)
- end
- end
-
- Link.where(head_uuid: uuid, link_class: "provenance").each do |link|
- gr += describe_node(link.tail_uuid)
- gr += "\"#{link.head_uuid}\" -> \"#{link.tail_uuid}\" [label=\" #{link.name}\", href=\"/links/#{link.uuid}\"];"
- gr += generate_provenance_edges(visited, link.tail_uuid)
- end
-
- #puts "finished #{uuid}"
-
- gr
- end
-
- def create_provenance_graph(uuid)
- require 'open3'
-
- gr = """strict digraph {
-//rankdir=LR;
-node [fontsize=8,shape=box];
-edge [dir=back,fontsize=8];"""
-
- visited = {}
- gr += generate_provenance_edges(visited, uuid)
-
- gr += "}"
- svg = ""
-
- Open3.popen2("dot", "-Tsvg") do |stdin, stdout, wait_thr|
- stdin.print(gr)
- stdin.close
- svg = stdout.read()
- wait_thr.value
- stdout.close()
- end
-
- svg = svg.sub(/<\?xml.*?\?>/m, "")
- svg = svg.sub(/<!DOCTYPE.*?>/m, "")
+ self.response_body = file_enumerator opts
end
def show
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|
end
end
- @prov_svg = create_provenance_graph(@object.uuid)
+ 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
env = Hash[ENV].
merge({
'ARVADOS_API_HOST' =>
- $arvados_api_client.arvados_v1_base.
+ arvados_api_client.arvados_v1_base.
sub(/\/arvados\/v1/, '').
sub(/^https?:\/\//, ''),
'ARVADOS_API_TOKEN' =>
projects / arvados.git / blobdiff