X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/468a80200c8ef3e4a56700714e9af537d87a20bc..b6f73f7acffa9b2f37c78826ff6cee89987a7edc:/apps/workbench/app/controllers/collections_controller.rb diff --git a/apps/workbench/app/controllers/collections_controller.rb b/apps/workbench/app/controllers/collections_controller.rb index 064acc689b..f4aa0395f3 100644 --- a/apps/workbench/app/controllers/collections_controller.rb +++ b/apps/workbench/app/controllers/collections_controller.rb @@ -1,13 +1,22 @@ +require "arvados/keep" + class CollectionsController < ApplicationController - skip_around_filter(:thread_with_mandatory_api_token, + 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 Attributes Metadata Provenance_graph Used_by JSON API) + panes = %w(Files Upload Provenance_graph Used_by Advanced) + panes = panes - %w(Upload) unless (@object.editable? rescue false) + panes end def set_persistent @@ -41,10 +50,14 @@ class CollectionsController < ApplicationController 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]])). + @objects = (base_search.where(uuid: tags.collect(&:head_uuid)) | + base_search.where(any: ['contains', params[:search]])). uniq { |c| c.uuid } else if params[:limit] @@ -59,12 +72,11 @@ class CollectionsController < ApplicationController offset = 0 end - @collections = Collection.limit(limit).offset(offset) + @objects = base_search.limit(limit).offset(offset) end - @links = Link.limit(1000). - where(head_uuid: @collections.collect(&:uuid)) + @links = Link.where(head_uuid: @objects.collect(&:uuid)) @collection_info = {} - @collections.each do |c| + @objects.each do |c| @collection_info[c.uuid] = { tag_links: [], wanted: false, @@ -94,7 +106,7 @@ class CollectionsController < ApplicationController def show_file_links Thread.current[:reader_tokens] = [params[:reader_token]] - find_object_by_uuid + return if false.equal?(find_object_by_uuid) render layout: false end @@ -108,18 +120,44 @@ class CollectionsController < ApplicationController usable_token = find_usable_token(tokens) do coll = Collection.find(params[:uuid]) end + + file_name = params[:file].andand.sub(/^(\.\/|\/|)/, './') if usable_token.nil? return # Response already rendered. - elsif params[:file].nil? or not file_in_collection?(coll, params[:file]) + elsif file_name.nil? or not coll.manifest.has_file?(file_name) 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 = file_enumerator opts + begin + file_enumerator(opts).each do |bytes| + response.stream.write bytes + end + ensure + response.stream.close + end end def sharing_scopes @@ -134,70 +172,88 @@ class CollectionsController < ApplicationController end end + def find_object_by_uuid + if not Keep::Locator.parse params[:id] + super + end + end + def show return super if !@object if current_user - jobs_with = lambda do |conds| - Job.limit(RELATION_LIMIT).where(conds) - .results.sort_by { |j| j.finished_at || j.created_at } + if Keep::Locator.parse params["uuid"] + @same_pdh = Collection.filter([["portable_data_hash", "=", @object.portable_data_hash]]) + 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 + 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.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 + + @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 + + 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 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 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 - super end def sharing_popup @search_sharing = search_scopes - respond_to do |format| - format.html - format.js - end + render("sharing_popup.js", content_type: "text/javascript") end helper_method :download_link def download_link - collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}" + collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}/" end def share - a = ApiClientAuthorization.create(scopes: sharing_scopes) - @search_sharing = search_scopes - render 'sharing_popup' + ApiClientAuthorization.create(scopes: sharing_scopes) + sharing_popup end def unshare - @search_sharing = search_scopes - @search_sharing.each do |s| + search_scopes.each do |s| s.destroy end - @search_sharing = search_scopes - render 'sharing_popup' + sharing_popup end protected @@ -210,18 +266,16 @@ class CollectionsController < ApplicationController # error we encounter, and return nil. most_specific_error = [401] token_list.each do |api_token| - using_specific_api_token(api_token) do - begin + begin + # We can't load the corresponding user, because the token may not + # be scoped for that. + using_specific_api_token(api_token, load_user: false) do 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] + rescue ArvadosApiClient::ApiError => error + if error.api_status >= most_specific_error.first + most_specific_error = [error.api_status, error] end end end @@ -234,14 +288,6 @@ class CollectionsController < ApplicationController return nil end - def file_in_collection?(collection, filename) - target = CollectionsHelper.file_path(File.split(filename)) - collection.files.each do |file_spec| - return true if (CollectionsHelper.file_path(file_spec) == target) - end - false - end - def file_enumerator(opts) FileStreamer.new opts end @@ -262,12 +308,19 @@ class CollectionsController < ApplicationController 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**16) - yield buf + 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