class CollectionsController < ApplicationController
- skip_before_filter :find_object_by_uuid, :only => [:provenance]
- skip_before_filter :check_user_agreements, :only => [:show_file]
+ include ActionController::Live
+
+ skip_around_filter(:require_thread_api_token,
+ only: [:show_file, :show_file_links])
+ skip_before_filter(:find_object_by_uuid,
+ only: [:provenance, :show_file, :show_file_links])
+ # We depend on show_file to display the user agreement:
+ skip_before_filter :check_user_agreements, only: :show_file
+ skip_before_filter :check_user_profile, only: :show_file
+
+ RELATION_LIMIT = 5
+
+ def show_pane_list
+ %w(Files Provenance_graph Used_by Advanced)
+ 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 choose
+ # Find collections using default find_objects logic, then search for name
+ # links, and preload any other links connected to the collections that are
+ # found.
+ # Name links will be obsolete when issue #3036 is merged,
+ # at which point this entire custom #choose function can probably be
+ # eliminated.
+
+ params[:limit] ||= 40
+
+ find_objects_for_index
+ @collections = @objects
+
+ @filters += [['link_class','=','name'],
+ ['head_uuid','is_a','arvados#collection']]
+
+ @objects = Link
+ find_objects_for_index
+
+ @name_links = @objects
+
+ @objects = Collection.
+ filter([['uuid','in',@name_links.collect(&:head_uuid)]])
+
+ preload_links_for_objects (@collections.to_a + @objects.to_a)
+ super
+ end
def index
+ # API server index doesn't return manifest_text by default, but our
+ # callers want it unless otherwise specified.
+ @select ||= Collection.columns.map(&:name)
+ base_search = Collection.select(@select)
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]])).
+ @collections = (base_search.where(uuid: tags.collect(&:head_uuid)) |
+ base_search.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 = base_search.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
info[:links] << link
end
@request_url = request.url
+
+ render_index
+ end
+
+ def show_file_links
+ Thread.current[:reader_tokens] = [params[:reader_token]]
+ return if false.equal?(find_object_by_uuid)
+ render layout: false
end
def show_file
- opts = params.merge(arvados_api_token: Thread.current[:arvados_api_token])
- if r = params[:file].match(/(\.\w+)/)
- ext = r[1]
+ # 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
+ 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?
+ return # Response already rendered.
+ elsif params[:file].nil? or not coll.manifest.has_file?(params[:file])
+ return render_not_found
end
+
+ opts = params.merge(arvados_api_token: usable_token)
+
+ # Handle Range requests. Currently we support only 'bytes=0-....'
+ if request.headers.include? 'HTTP_RANGE'
+ if m = /^bytes=0-(\d+)/.match(request.headers['HTTP_RANGE'])
+ opts[:maxbytes] = m[1]
+ size = params[:size] || '*'
+ self.response.status = 206
+ self.response.headers['Content-Range'] = "bytes 0-#{m[1]}/#{size}"
+ end
+ end
+
+ 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]
+ if params[:size]
+ size = params[:size].to_i
+ if opts[:maxbytes]
+ size = [size, opts[:maxbytes].to_i].min
+ end
+ self.response.headers['Content-Length'] = size.to_s
+ end
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
- ""
+ begin
+ file_enumerator(opts).each do |bytes|
+ response.stream.write bytes
+ end
+ ensure
+ response.stream.close
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}\"];"
+ def sharing_scopes
+ ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
end
- def job_uuid(job)
- "#{job.script}\\n#{job.script_version}"
+ def search_scopes
+ begin
+ ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
+ rescue ArvadosApiClient::AccessForbiddenException
+ nil
+ end
end
- def collection_uuid(uuid)
- m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid)
- if m
- m[1]
- else
- nil
+ def find_object_by_uuid
+ if not Keep::Locator.parse params[:id]
+ super
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)
+ def show
+ return super if !@object
+ if current_user
+ if Keep::Locator.parse params["uuid"]
+ @same_pdh = Collection.filter([["portable_data_hash", "=", @object.portable_data_hash]]).limit(1000)
+ if @same_pdh.results.size == 1
+ redirect_to collection_path(@same_pdh[0]["uuid"])
+ return
end
+ owners = @same_pdh.map(&:owner_uuid).to_a.uniq
+ preload_objects_for_dataclass Group, owners
+ preload_objects_for_dataclass User, owners
+ render 'hash_matches'
+ return
else
- m = collection_uuid(sp)
- if m
- gr += "\"#{job_uuid(job)}\" -> \"#{m}\" [label=\" #{prefix}\"];"
- gr += generate_provenance_edges(visited, m)
+ jobs_with = lambda do |conds|
+ Job.limit(RELATION_LIMIT).where(conds)
+ .results.sort_by { |j| j.finished_at || j.created_at }
end
- end
- end
- gr
- end
-
- def generate_provenance_edges(visited, uuid)
- gr = ""
- m = collection_uuid(uuid)
+ @output_of = jobs_with.call(output: @object.portable_data_hash)
+ @log_of = jobs_with.call(log: @object.portable_data_hash)
+ @project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
+ .where(head_uuid: @object.uuid, link_class: 'name').results
+ project_hash = Group.where(uuid: @project_links.map(&:tail_uuid)).to_hash
+ @projects = project_hash.values
- 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
+ @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
- 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)
+ if params["tab_pane"] == "Provenance_graph"
+ @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
+ {:request => request,
+ :direction => :bottom_up,
+ :combine_jobs => :script_only}) rescue nil
+ end
+ if params["tab_pane"] == "Used_by"
+ @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
- else
- gr += describe_node(uuid)
end
end
+ super
+ 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)
+ def sharing_popup
+ @search_sharing = search_scopes
+ respond_to do |format|
+ format.html
+ format.js
end
+ end
- #puts "finished #{uuid}"
+ helper_method :download_link
- gr
+ def download_link
+ collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}/"
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, "")
+ def share
+ a = ApiClientAuthorization.create(scopes: sharing_scopes)
+ @search_sharing = search_scopes
+ render 'sharing_popup'
end
- def show
- return super if !@object
- @provenance = []
- @output2job = {}
- @output2colorindex = {}
- @sourcedata = {params[:uuid] => {uuid: params[:uuid]}}
- @protected = {}
-
- 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
+ def unshare
+ @search_sharing = search_scopes
+ @search_sharing.each do |s|
+ s.destroy
end
+ @search_sharing = search_scopes
+ render 'sharing_popup'
+ 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
- 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]
+ protected
+
+ 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.
+ most_specific_error = [401]
+ token_list.each do |api_token|
+ begin
+ using_specific_api_token(api_token) do
+ yield
+ return api_token
+ end
+ rescue ArvadosApiClient::ApiError => error
+ if error.api_status >= most_specific_error.first
+ most_specific_error = [error.api_status, error]
+ end
end
end
- Collection.where(uuid: @sourcedata.keys).each do |collection|
- if @sourcedata[collection.uuid]
- @sourcedata[collection.uuid][:collection] = collection
- end
+ case most_specific_error.shift
+ when 401, 403
+ redirect_to_login
+ when 404
+ render_not_found(*most_specific_error)
end
+ return nil
+ end
- @prov_svg = create_provenance_graph(@object.uuid)
+ def file_enumerator(opts)
+ FileStreamer.new opts
end
- protected
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'
- })
- IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
- 'rb') do |io|
- while buf = io.read(2**20)
- yield buf
+
+ 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
+
+ bytesleft = @opts[:maxbytes].andand.to_i || 2**16
+ io = IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"], 'rb')
+ while bytesleft > 0 && (buf = io.read([bytesleft, 2**16].min)) != nil
+ # shrink the bytesleft count, if we were given a maximum byte
+ # count to read
+ if @opts.include? :maxbytes
+ bytesleft = bytesleft - buf.length
end
+ yield buf
end
+ io.close
+ # "If ios is opened by IO.popen, close sets $?."
+ # http://www.ruby-doc.org/core-2.1.3/IO.html#method-i-close
Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
end
end
projects / arvados.git / blobdiff