sufia 6.0.0.rc4 → 6.0.0

data/spec/views/users/show.html.erb_spec.rb

@@ -31,7 +31,7 @@ describe 'users/show.html.erb', :type => :view do
 
   context "with trophy" do
 
-    let(:generic_file) { GenericFile.new(title: ["Fake object"], id: "abc123") }
+    let(:generic_file) { stub_model(GenericFile, title: ["Fake object"], id: "abc123") }
     before do
       allow(view).to receive(:search_session).and_return({})
       allow(view).to receive(:blacklight_config).and_return(CatalogController.blacklight_config)

data/sufia-models/app/actors/sufia/generic_file/actor.rb

@@ -31,7 +31,7 @@ module Sufia::GenericFile
     def create_content(file, file_name, path, mime_type)
       generic_file.add_file(file, path: path, original_name: file_name, mime_type: mime_type)
       generic_file.label ||= file_name
-      generic_file.title = [file_name] if generic_file.title.blank?
+      generic_file.title = [generic_file.label] if generic_file.title.blank?
       save_characterize_and_record_committer do
         if Sufia.config.respond_to?(:after_create_content)
           Sufia.config.after_create_content.call(generic_file, user)

data/sufia-models/app/jobs/active_fedora_id_based_job.rb

@@ -0,0 +1,22 @@
+class ActiveFedoraIdBasedJob
+  def queue_name
+    :id_based
+  end
+
+  attr_accessor :id
+
+  def initialize(id)
+    self.id = id
+  end
+
+  def object
+    @object ||= ActiveFedora::Base.find(id)
+  end
+
+  alias_method :generic_file, :object
+  alias_method :generic_file_id, :id
+
+  def run
+    raise RuntimeError, "Define #run in a subclass"
+  end
+end

data/sufia-models/app/jobs/active_fedora_pid_based_job.rb

@@ -1,22 +1,7 @@
-class ActiveFedoraPidBasedJob
-  def queue_name
-    :pid_based
-  end
-
-  attr_accessor :pid
-
-  def initialize(pid)
-    self.pid = pid
-  end
-
-  def object
-    @object ||= ActiveFedora::Base.find(pid)
-  end
-
-  alias_method :generic_file, :object
-  alias_method :generic_file_id, :pid
-
-  def run
-    raise RuntimeError, "Define #run in a subclass"
+class ActiveFedoraPidBasedJob < ActiveFedoraIdBasedJob
+  extend Deprecation
+  def self.extended(document)
+    Deprecation.warn ActiveFedoraPidBasedJob, "ActiveFedoraPidBasedJob is deprecated; use ActiveFedoraIdBasedJob instead."
   end
 end
+

data/sufia-models/app/jobs/audit_job.rb

@@ -1,4 +1,4 @@
-class AuditJob < ActiveFedoraPidBasedJob
+class AuditJob < ActiveFedoraIdBasedJob
   def queue_name
     :audit
   end
@@ -6,7 +6,7 @@ class AuditJob < ActiveFedoraPidBasedJob
   PASS = 'Passing Audit Run'
   FAIL = 'Failing Audit Run'
 
-  attr_accessor :uri, :pid, :path
+  attr_accessor :uri, :id, :path
 
   # URI of the resource to audit.
   # This URI could include the actual resource (e.g. content) and the version to audit:
@@ -14,8 +14,7 @@ class AuditJob < ActiveFedoraPidBasedJob
   # but it could also just be:
   #     http://localhost:8983/fedora/rest/test/a/b/c/abcxyz/content
   def initialize(id, path, uri)
-    super(uri)
-    self.pid = id
+    super(id)
     self.path = path
     self.uri = uri
   end
@@ -49,12 +48,12 @@ class AuditJob < ActiveFedoraPidBasedJob
 
       if fixity_ok
         passing = 1
-        ChecksumAuditLog.prune_history(pid, path)
+        ChecksumAuditLog.prune_history(id, path)
       else
         logger.warn "***AUDIT*** Audit failed for #{uri} #{error_msg}"
         passing = 0
       end
-      ChecksumAuditLog.create!(pass: passing, pid: pid, version: uri, dsid: path)
+      ChecksumAuditLog.create!(pass: passing, generic_file_id: id, version: uri, dsid: path)
     end
 
     def logger

data/sufia-models/app/jobs/characterize_job.rb

@@ -1,4 +1,4 @@
-class CharacterizeJob < ActiveFedoraPidBasedJob
+class CharacterizeJob < ActiveFedoraIdBasedJob
   def queue_name
     :characterize
   end

data/sufia-models/app/jobs/create_derivatives_job.rb

@@ -1,4 +1,4 @@
-class CreateDerivativesJob < ActiveFedoraPidBasedJob
+class CreateDerivativesJob < ActiveFedoraIdBasedJob
   def queue_name
     :derivatives
   end

data/sufia-models/app/jobs/import_url_job.rb

@@ -2,7 +2,7 @@ require 'net/https'
 require 'uri'
 require 'tempfile'
 
-class ImportUrlJob < ActiveFedoraPidBasedJob
+class ImportUrlJob < ActiveFedoraIdBasedJob
 
   def queue_name
     :import_url
@@ -11,7 +11,7 @@ class ImportUrlJob < ActiveFedoraPidBasedJob
   def run
     user = User.find_by_user_key(generic_file.depositor)
 
-    Tempfile.open(pid.gsub('/', '_')) do |f|
+    Tempfile.open(id.gsub('/', '_')) do |f|
       path, mime_type = copy_remote_file(generic_file.import_url, f)
       # attach downloaded file to generic file stubbed out
       if Sufia::GenericFile::Actor.new(generic_file, user).create_content(f, path, 'content', mime_type)

data/sufia-models/app/models/batch.rb

@@ -10,13 +10,27 @@ class Batch < ActiveFedora::Base
   property :status, predicate: ::RDF::DC.type
 
   def self.find_or_create(id)
-    # FIXME potential race condition in this method. Consider that `find' may raise
-    # ObjectNotFound in multiple processes. However, Fedora should raise an error
-    # if we try to create two objects with the same id.
     begin
       Batch.find(id)
     rescue ActiveFedora::ObjectNotFoundError
-      Batch.create(id: id)
+      safe_create(id)
     end
   end
+
+  private
+
+    # This method handles most race conditions gracefully. 
+    # If a batch with the same ID is created by another thread
+    # we fetch the batch that was created (rather than throwing
+    # an error) and continute.
+    def self.safe_create(id)
+      begin      
+        Batch.create(id: id)
+      rescue ActiveFedora::IllegalOperation => ex
+        # This is the exception thrown by LDP when we attempt to 
+        # create a duplicate object. If we can find the object
+        # then we are good to go.
+        Batch.find(id)
+      end
+    end
 end

data/sufia-models/app/models/checksum_audit_log.rb

@@ -1,7 +1,7 @@
 class ChecksumAuditLog < ActiveRecord::Base
 
   def self.get_audit_log(id, path, version_uri)
-    ChecksumAuditLog.find_or_create_by(pid: id, dsid: path, version: version_uri)
+    ChecksumAuditLog.find_or_create_by(generic_file_id: id, dsid: path, version: version_uri)
   end
 
   # Check to see if there are previous passing logs that we can delete
@@ -16,6 +16,6 @@ class ChecksumAuditLog < ActiveRecord::Base
   end
 
   def self.logs_for(id, path)
-    ChecksumAuditLog.where(pid: id, dsid: path).order('created_at desc, id desc')
+    ChecksumAuditLog.where(generic_file_id: id, dsid: path).order('created_at desc, id desc')
   end
 end

data/sufia-models/app/models/concerns/sufia/ability.rb

@@ -8,6 +8,7 @@ module Sufia
 
     def sufia_abilities
       generic_file_abilities
+      user_abilities
       featured_work_abilities
       editor_abilities
       stats_abilities
@@ -23,7 +24,10 @@ module Sufia
       can :reject, ProxyDepositRequest, receiving_user_id: current_user.id, status: 'pending'
       # a user who sent a proxy deposit request can cancel it if it's pending.
       can :destroy, ProxyDepositRequest, sending_user_id: current_user.id, status: 'pending'
-      can :edit, ::User, id: current_user.id
+    end
+
+    def user_abilities
+      can [:edit, :update, :toggle_trophy], ::User, id: current_user.id
     end
 
     def featured_work_abilities
@@ -31,6 +35,7 @@ module Sufia
     end
 
     def generic_file_abilities
+      can :view_share_work, [GenericFile]
       can :create, [GenericFile, Collection] if user_groups.include? 'registered'
     end
 
@@ -51,5 +56,6 @@ module Sufia
     def depositor_for_document(document_id)
       ::GenericFile.load_instance_from_solr(document_id).depositor
     end
+
   end
 end

data/sufia-models/app/models/concerns/sufia/collection_behavior.rb

@@ -18,7 +18,7 @@ module Sufia
     # Compute the sum of each file in the collection
     # Return an integer of the result
     def bytes
-      members.reduce(0) { |sum, gf| sum + gf.file_size.first.to_i }
+      members.reduce(0) { |sum, gf| sum + gf.content.size.to_i }
     end
   end
 end

data/sufia-models/app/models/concerns/sufia/generic_file/full_text_indexing.rb

@@ -14,21 +14,30 @@ module Sufia
 
       private
 
-        def extract_content
-          url = Blacklight.solr_config[:url] ? Blacklight.solr_config[:url] : Blacklight.solr_config["url"] ? Blacklight.solr_config["url"] : Blacklight.solr_config[:fulltext] ? Blacklight.solr_config[:fulltext]["url"] : Blacklight.solr_config[:default]["url"]
-          uri = URI("#{url}/update/extract?extractOnly=true&wt=json&extractFormat=text")
-          req = Net::HTTP.new(uri.host, uri.port)
-          resp = req.post(uri.to_s, self.content.content, {
-              'Content-type' => "#{self.mime_type};charset=utf-8",
-              'Content-Length' => self.content.content.size.to_s
-            })
-          raise "URL '#{uri}' returned code #{resp.code}" unless resp.code == "200"
-          self.content.content.rewind if self.content.content.respond_to?(:rewind)
-          extracted_text = JSON.parse(resp.body)[''].rstrip
-          full_text.content = extracted_text if extracted_text.present?
-        rescue => e
-          logger.error("Error extracting content from #{self.id}: #{e.inspect}")
+      def extract_content
+        uri = URI("#{connection_url}/update/extract?extractOnly=true&wt=json&extractFormat=text")
+        req = Net::HTTP.new(uri.host, uri.port)
+        resp = req.post(uri.to_s, self.content.content, {
+            'Content-type' => "#{self.mime_type};charset=utf-8",
+            'Content-Length' => self.content.content.size.to_s
+          })
+        raise "URL '#{uri}' returned code #{resp.code}" unless resp.code == "200"
+        self.content.content.rewind if self.content.content.respond_to?(:rewind)
+        extracted_text = JSON.parse(resp.body)[''].rstrip
+        full_text.content = extracted_text if extracted_text.present?
+      rescue => e
+        logger.error("Error extracting content from #{self.id}: #{e.inspect}")
+      end
+
+      def connection_url
+        case
+          when Blacklight.connection_config[:url] then Blacklight.connection_config[:url]
+          when Blacklight.connection_config["url"] then Blacklight.connection_config["url"]
+          when Blacklight.connection_config[:fulltext] then Blacklight.connection_config[:fulltext]["url"]
+          else Blacklight.connection_config[:default]["url"]
         end
+      end
+
     end
   end
 end

data/sufia-models/app/models/concerns/sufia/generic_file/proxy_deposit.rb

@@ -24,7 +24,7 @@ module Sufia
       def request_transfer_to(target)
         raise ArgumentError, "Must provide a target" unless target
         deposit_user = ::User.find_by_user_key(depositor)
-        ProxyDepositRequest.create!(pid: id, receiving_user: target, sending_user: deposit_user)
+        ProxyDepositRequest.create!(generic_file_id: id, receiving_user: target, sending_user: deposit_user)
       end
     end
   end

data/sufia-models/app/models/datastreams/fits_datastream.rb

@@ -144,42 +144,7 @@ class FitsDatastream < ActiveFedora::OmDatastream
     http://hul.harvard.edu/ois/xml/xsd/fits/fits_output.xsd",
                version: "0.6.0",
                timestamp: "1/25/12 11:04 AM") {
-        xml.identification {
-          xml.identity(format: '', mimetype: '',
-                       toolname: 'FITS', toolversion: '') {
-            xml.tool(toolname: '', toolversion: '')
-            xml.version(toolname: '', toolversion: '')
-            xml.externalIdentifier(toolname: '', toolversion: '')
-          }
-        }
-        xml.fileinfo {
-          xml.size(toolname: '', toolversion: '')
-          xml.creatingApplicatioName(toolname: '', toolversion: '',
-                                     status: '')
-          xml.lastmodified(toolname: '', toolversion: '', status: '')
-          xml.filepath(toolname: '', toolversion: '', status: '')
-          xml.filename(toolname: '', toolversion: '', status: '')
-          xml.md5checksum(toolname: '', toolversion: '', status: '')
-          xml.fslastmodified(toolname: '', toolversion: '', status: '')
-        }
-        xml.filestatus {
-          xml.tag! "well-formed", toolname: '', toolversion: '', status: ''
-          xml.valid(toolname: '', toolversion: '', status: '')
-        }
-        xml.metadata {
-          xml.document {
-            xml.title(toolname: '', toolversion: '', status: '')
-            xml.author(toolname: '', toolversion: '', status: '')
-            xml.pageCount(toolname: '', toolversion: '')
-            xml.isTagged(toolname: '', toolversion: '')
-            xml.hasOutline(toolname: '', toolversion: '')
-            xml.hasAnnotations(toolname: '', toolversion: '')
-            xml.isRightsManaged(toolname: '', toolversion: '',
-                                status: '')
-            xml.isProtected(toolname: '', toolversion: '')
-            xml.hasForms(toolname: '', toolversion: '', status: '')
-          }
-        }
+        xml.identification { xml.identity(toolname: 'FITS') }
       }
     end
     builder.doc

data/sufia-models/app/models/proxy_deposit_request.rb

@@ -1,11 +1,11 @@
 class ProxyDepositRequest < ActiveRecord::Base
-  include Blacklight::SolrHelper
+  include Blacklight::SearchHelper
   include ActionView::Helpers::UrlHelper
 
   belongs_to :receiving_user, class_name: 'User'
   belongs_to :sending_user, class_name: 'User'
 
-  validates :sending_user, :pid, presence: true
+  validates :sending_user, :generic_file_id, presence: true
   validate :transfer_to_should_be_a_valid_username
   validate :sending_user_should_not_be_receiving_user
   validate :should_not_be_already_part_of_a_transfer
@@ -28,7 +28,7 @@ class ProxyDepositRequest < ActiveRecord::Base
   end
 
   def should_not_be_already_part_of_a_transfer
-    transfers = ProxyDepositRequest.where(pid: pid)
+    transfers = ProxyDepositRequest.where(generic_file_id: generic_file_id, status: 'pending')
     errors.add(:open_transfer, 'must close open transfer on the file before creating a new one') unless transfers.blank? || ( transfers.count == 1 && transfers[0].id == self.id)
   end
 
@@ -53,7 +53,7 @@ class ProxyDepositRequest < ActiveRecord::Base
 
   # @param [Boolean] reset (false) should the access controls be reset. This means revoking edit access from the depositor
   def transfer!(reset = false)
-    Sufia.queue.push(ContentDepositorChangeEventJob.new(pid, receiving_user.user_key, reset))
+    Sufia.queue.push(ContentDepositorChangeEventJob.new(generic_file_id, receiving_user.user_key, reset))
     self.status = 'accepted'
     self.fulfillment_date = Time.now
     save!
@@ -73,12 +73,12 @@ class ProxyDepositRequest < ActiveRecord::Base
   end
 
   def deleted_file?
-    !GenericFile.exists?(pid)
+    !GenericFile.exists?(generic_file_id)
   end
 
   def title
     return 'file not found' if deleted_file?
-    query = ActiveFedora::SolrQueryBuilder.construct_query_for_ids([pid])
+    query = ActiveFedora::SolrQueryBuilder.construct_query_for_ids([generic_file_id])
     solr_response = ActiveFedora::SolrService.query(query, raw: true)
     SolrDocument.new(solr_response['response']['docs'].first, solr_response).title
   end

data/sufia-models/app/services/sufia/generic_file_audit_service.rb

@@ -63,7 +63,7 @@ module Sufia
         latest_audit = ChecksumAuditLog.logs_for(generic_file.id, file).first
         return latest_audit unless needs_audit?(latest_audit)
         Sufia.queue.push(AuditJob.new(generic_file.id, file, uri))
-        latest_audit || ChecksumAuditLog.new(pass: NO_RUNS, pid: generic_file.id, dsid: file, version: label)
+        latest_audit || ChecksumAuditLog.new(pass: NO_RUNS, generic_file_id: generic_file.id, dsid: file, version: label)
       end
 
       def needs_audit?(latest_audit)

data/sufia-models/app/services/sufia/generic_file_indexing_service.rb

@@ -6,7 +6,6 @@ module Sufia
         solr_doc[Solrizer.solr_name('file_format')] = object.file_format
         solr_doc[Solrizer.solr_name('file_format', :facetable)] = object.file_format
         solr_doc['all_text_timv'] = object.full_text.content
-        solr_doc = object.index_collection_ids(solr_doc)
       end
     end
   end

data/sufia-models/app/services/sufia/id_service.rb

@@ -8,7 +8,6 @@ module Sufia
     end
 
     @minter = ::Noid::Minter.new(template: noid_template)
-    @pid = $$
     @semaphore = Mutex.new
     def self.valid?(identifier)
       # remove the fedora namespace since it's not part of the noid
@@ -18,8 +17,8 @@ module Sufia
     def self.mint
       @semaphore.synchronize do
         while true
-          pid = self.next_id
-          return pid unless ActiveFedora::Base.exists?(pid)
+          id = self.next_id
+          return id unless ActiveFedora::Base.exists?(id)
         end
       end
     end

data/sufia-models/app/services/sufia/noid.rb

@@ -2,7 +2,7 @@ module Sufia
   module Noid
     extend ActiveSupport::Concern
 
-    ## This overrides the default behavior, which is to ask Fedora for a pid
+    ## This overrides the default behavior, which is to ask Fedora for an id
     # @see ActiveFedora::Persistence.assign_id
     def assign_id
       Sufia::IdService.mint if Sufia.config.enable_noids

data/sufia-models/lib/generators/sufia/models/templates/config/sufia.rb

@@ -123,7 +123,7 @@ Sufia.config do |config|
   # NOTE: if you have always sent analytics to GA for downloads and page views leave this commented out
   # config.analytic_start_date = DateTime.new(2014,9,10)
   #
-  # Method of converting pids into URIs for storage in Fedora
+  # Method of converting ids into URIs for storage in Fedora
   # config.translate_uri_to_id = lambda { |uri| uri.to_s.split('/')[-1] }
   # config.translate_id_to_uri = lambda { |id|
   #      "#{ActiveFedora.fedora.host}#{ActiveFedora.fedora.base_path}/#{Sufia::Noid.treeify(id)}" }

data/sufia-models/lib/generators/sufia/models/templates/migrations/change_audit_log_pid_to_generic_file_id.rb

@@ -0,0 +1,5 @@
+class ChangeAuditLogPidToGenericFileId < ActiveRecord::Migration
+  def change
+    rename_column :checksum_audit_logs, :pid, :generic_file_id
+  end
+end