X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a59152e34814f453a7380e68a55534e2f8922d57..949c388c5ec3bc4f8cc6b3d503c11dcd20e5bbd4:/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 4ca9212959..7ef85a5cfc 100644
--- a/apps/workbench/app/controllers/collections_controller.rb
+++ b/apps/workbench/app/controllers/collections_controller.rb
@@ -1,49 +1,113 @@
 class CollectionsController < ApplicationController
-  before_filter :ensure_current_user_is_admin
-  skip_before_filter :find_object_by_uuid, :only => [:graph]
+  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 graph
-    index
+  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
-    @links = Link.eager.limit(100).where(head_kind: 'orvos#collection') |
-      Link.eager.limit(100).where(tail_kind: 'orvos#collection')
-    @collections = Collection.limit(100).to_hash
-    @collections.merge!(Collection.
-                        limit(100).
-                        where(uuid: @links.select{|x|x.head_kind=='orvos#collection'}.collect(&:head_uuid) |
-                              @links.select{|x|x.tail_kind=='orvos#collection'}.collect(&:tail_uuid)).
-                        to_hash)
-    @collection_info = {}
-    @collections.each do |uuid, c|
-      ci = (@collection_info[uuid] ||= {uuid: uuid})
-      ci[:created_at] = c.created_at
-    end
-    @links.each do |l|
-      if l.head_kind == 'orvos#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
+    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
+      if params[:limit]
+        limit = params[:limit].to_i
+      else
+        limit = 100
       end
-      if l.tail_kind == 'orvos#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
+
+      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] = {
+        tag_links: [],
+        wanted: false,
+        wanted_by_me: false,
+        provenance: [],
+        links: []
+      }
+    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
+    # 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 = file_enumerator opts
   end
 
   def show
@@ -53,34 +117,39 @@ class CollectionsController < ApplicationController
     @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
+        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|
@@ -88,5 +157,97 @@ class CollectionsController < ApplicationController
         @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
+  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 =~ /\[API: (\d+)\]$/) ? $1.to_i : nil
+          raise unless [401, 403, 404].include?(status)
+        end
+        if status >= most_specific_error.first
+          most_specific_error = [status, error]
+        end
+      end
+    end
+    case most_specific_error.shift
+    when 401, 403
+      redirect_to_login
+    when 404
+      render_not_found(*most_specific_error)
+    end
+    return nil
+  end
+
+  def file_in_collection?(collection, filename)
+    def normalized_path(part_list)
+      File.join(part_list).sub(%r{^\./}, '')
+    end
+    target = normalized_path([filename])
+    collection.files.each do |file_spec|
+      return true if (normalized_path(file_spec[0, 2]) == target)
+    end
+    false
+  end
+
+  def file_enumerator(opts)
+    FileStreamer.new opts
+  end
+
+  class FileStreamer
+    def initialize(opts={})
+      @opts = opts
+    end
+    def each
+      return unless @opts[:uuid] && @opts[:file]
+      env = Hash[ENV].
+        merge({
+                'ARVADOS_API_HOST' =>
+                arvados_api_client.arvados_v1_base.
+                sub(/\/arvados\/v1/, '').
+                sub(/^https?:\/\//, ''),
+                'ARVADOS_API_TOKEN' =>
+                @opts[:arvados_api_token],
+                'ARVADOS_API_HOST_INSECURE' =>
+                Rails.configuration.arvados_insecure_https ? 'true' : 'false'
+              })
+      IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
+               'rb') do |io|
+        while buf = io.read(2**20)
+          yield buf
+        end
+      end
+      Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
+    end
   end
 end