hyrax 5.0.1 → 5.0.3

data/app/controllers/hyrax/downloads_controller.rb

@@ -11,15 +11,38 @@ module Hyrax
       :original_file
     end
 
+    # We want to alias the show method for a later use with #show_active_fedora;
+    # because we're adding quite a bit of logic and need a good alias.  Why the
+    # alias?  Because we were using `super' for the show method and that just
+    # doesn't quite work with all of the antics we're performing.
+    alias hydra_show_active_fedora_file show
+
     # Render the 404 page if the file doesn't exist.
     # Otherwise renders the file.
     def show
+      # We will use the thumbnail from our file system first, if one exists
+      # Otherwise we will fallback to Valkyrie, then the default implementations
+      use = params.fetch(:file, :original_file).to_sym
+      if use == :thumbnail
+        thumbnail = Hyrax::DerivativePath.derivative_path_for_reference(params[:id], 'thumbnail')
+        if thumbnail.present? && File.exist?(thumbnail)
+          @file = thumbnail
+          return send_local_content
+        end
+      end
+
       return show_valkyrie if Hyrax.config.use_valkyrie?
 
+      show_active_fedora
+    end
+
+    private
+
+    def show_active_fedora
       case file
       when ActiveFedora::File
         # For original files that are stored in fedora
-        super
+        hydra_show_active_fedora_file
       when String
         # For derivatives stored on the local file system
         send_local_content
@@ -28,8 +51,6 @@ module Hyrax
       end
     end
 
-    private
-
     # Override the Hydra::Controller::DownloadBehavior#content_options so that
     # we have an attachement rather than 'inline'
     def content_options

data/app/controllers/hyrax/file_sets_controller.rb

@@ -8,7 +8,7 @@ module Hyrax
     include Hyrax::Breadcrumbs
 
     before_action :authenticate_user!, except: [:show, :citation, :stats]
-    load_and_authorize_resource class: ::FileSet, except: :show
+    load_and_authorize_resource class: Hyrax.config.file_set_class
     before_action :build_breadcrumbs, only: [:show, :edit, :stats]
     before_action do
       blacklight_config.track_search_session = false
@@ -94,7 +94,7 @@ module Hyrax
     # @api public
     def delete(file_set:)
       case file_set
-      when Valkyrie::Resource
+      when Hyrax::Resource
         transactions['file_set.destroy']
           .with_step_args('file_set.remove_from_work' => { user: current_user },
                           'file_set.delete' => { user: current_user })
@@ -123,20 +123,46 @@ module Hyrax
     def valkyrie_update_metadata
       change_set = Hyrax::Forms::ResourceForm.for(resource: file_set)
 
+      attributes = coerce_valkyrie_params
+
+      # TODO: We are not performing any error checks.  So that's something to
+      # correct.
       result =
         change_set.validate(attributes) &&
         transactions['change_set.update_file_set']
         .with_step_args(
-          'file_set.save_acl' => { permissions_params: change_set.input_params["permissions"] }
-        )
+            'file_set.save_acl' => { permissions_params: change_set.input_params["permissions"] }
+          )
         .call(change_set).value_or { false }
       @file_set = result if result
     end
 
+    def coerce_valkyrie_params
+      attrs = attributes
+      # The HTML form might not submit the required data structure for reform;
+      # namely instead of a hash with positional arguments for nested attributes
+      # of a collection, it is an array.  So we conditionally coerce that Array
+      # to a Hash.
+
+      # TODO: Do we need to concern ourself with embargo_attributes and
+      # lease_attributes?  My suspicion is that since these are singular (for
+      # now), we don't.  But it's a quick add.
+      [:permissions].each do |name|
+        next unless attrs["#{name}_attributes"].is_a?(Array)
+        new_perm_attrs = {}
+        attrs["#{name}_attributes"].each_with_index do |el, i|
+          new_perm_attrs[i] = el
+        end
+
+        attrs["#{name}_attributes"] = new_perm_attrs
+      end
+      attrs
+    end
+
     def parent(file_set: curation_concern)
       @parent ||=
         case file_set
-        when Hyrax::FileSet
+        when Hyrax::Resource
           # TODO: Add Hyrax::FileSet#parent method
           Hyrax.query_service.find_parents(resource: file_set).first
         else
@@ -145,7 +171,7 @@ module Hyrax
     end
 
     def attempt_update
-      return attempt_update_valkyrie if ::FileSet < Hyrax::Resource
+      return attempt_update_valkyrie if curation_concern.is_a?(Hyrax::Resource)
       if wants_to_revert?
         actor.revert_content(params[:revision])
       elsif params.key?(:file_set)

data/app/controllers/hyrax/my/works_controller.rb

@@ -24,6 +24,7 @@ module Hyrax
         add_breadcrumb t(:'hyrax.admin.sidebar.works'), hyrax.my_works_path
         managed_works_count
         @create_work_presenter = create_work_presenter_class.new(current_user)
+        @admin_sets_for_select = admin_sets_for_select
         super
       end
 
@@ -47,6 +48,25 @@ module Hyrax
       def managed_works_count
         @managed_works_count = Hyrax::Works::ManagedWorksService.managed_works_count(scope: self)
       end
+
+      def admin_sets_for_select
+        source_ids = Hyrax::Collections::PermissionsService.source_ids_for_deposit(ability: current_ability, source_type: 'admin_set')
+
+        admin_sets_list = Hyrax.query_service.find_many_by_ids(ids: source_ids).map do |source|
+          [source.title.first, source.id]
+        end
+
+        # Sorts the default admin set to be first, then the rest by title.
+        admin_sets_list.sort do |a, b|
+          if Hyrax::AdminSetCreateService.default_admin_set?(id: a[1])
+            -1
+          elsif Hyrax::AdminSetCreateService.default_admin_set?(id: b[1])
+            1
+          else
+            a[0] <=> b[0]
+          end
+        end
+      end
     end
   end
 end

data/app/controllers/hyrax/stats_controller.rb

@@ -27,7 +27,7 @@ module Hyrax
       when 'file'
         add_breadcrumb I18n.t("hyrax.file_set.browse_view"), main_app.hyrax_file_set_path(params["id"])
       when 'work'
-        add_breadcrumb @work.to_s, main_app.polymorphic_path(@work)
+        add_breadcrumb @work.title.first, main_app.polymorphic_path(@work)
       end
     end
   end

data/app/controllers/hyrax/uploads_controller.rb

@@ -4,8 +4,12 @@ module Hyrax
     load_and_authorize_resource class: Hyrax::UploadedFile
 
     def create
-      @upload.attributes = { file: params[:files].first,
-                             user: current_user }
+      if params[:id].blank?
+        @upload.attributes = { file: params[:files].first,
+                               user: current_user }
+      else
+        upload_with_chunking
+      end
       @upload.save!
     end
 
@@ -13,5 +17,27 @@ module Hyrax
       @upload.destroy
       head :no_content
     end
+
+    private
+
+    def upload_with_chunking
+      @upload = Hyrax::UploadedFile.find(params[:id])
+      unpersisted_upload = Hyrax::UploadedFile.new(file: params[:files].first, user: current_user)
+
+      # Check if CONTENT-RANGE header is present
+      content_range = request.headers['CONTENT-RANGE']
+      return @upload.file = unpersisted_upload.file if content_range.nil?
+
+      # deal with chunks
+      current_size = @upload.file.size
+      begin_of_chunk = content_range[/\ (.*?)-/, 1].to_i # "bytes 100-999999/1973660678" will return '100'
+
+      # Add the following chunk to the incomplete upload
+      if @upload.file.present? && begin_of_chunk == current_size
+        File.open(@upload.file.path, "ab") { |f| f.write(params[:files].first.read) }
+      else
+        @upload.file = unpersisted_upload.file
+      end
+    end
   end
 end

data/app/forms/hyrax/forms/admin/appearance.rb

@@ -47,7 +47,7 @@ module Hyrax
 
         # The color links
         def link_color
-          block_for('link_color', '#2e74b2')
+          block_for('link_color', '#104C75')
         end
 
         # The color for links in the footer

data/app/forms/hyrax/forms/admin/collection_type_form.rb

@@ -10,7 +10,7 @@ module Hyrax
         delegate :title, :description, :brandable, :discoverable, :nestable, :sharable, :share_applies_to_new_works,
                  :require_membership, :allow_multiple_membership, :assigns_workflow,
                  :assigns_visibility, :id, :collection_type_participants, :persisted?,
-                 :admin_set?, :user_collection?, :badge_color, to: :collection_type
+                 :admin_set?, :user_collection?, :badge_color, :collections?, to: :collection_type
 
         ##
         # @return [Boolean]
@@ -23,12 +23,6 @@ module Hyrax
         def share_options_disabled?
           all_settings_disabled? || !sharable
         end
-
-        ##
-        # @return [Boolean]
-        def collections?
-          collection_type.collections.any?
-        end
       end
     end
   end

data/app/forms/hyrax/forms/pcdm_collection_form.rb

@@ -81,6 +81,15 @@ module Hyrax
         secondary_terms.any?
       end
 
+      ##
+      # This feature is not supported in Valkyrie collections and should be removed as part of #5764
+      # However, the depreciated method is still needed for some specs
+      # @return [] always empty.
+      def select_files
+        Deprecation.warn "`Hyrax::PcdmCollection` does not currently support thumbnail_id. Collection thumbnails need to be redesigned as part of issue #5764"
+        []
+      end
+
       private
 
       def _form_field_definitions

data/app/forms/hyrax/forms/work_embargo_form.rb

@@ -31,6 +31,12 @@ module Hyrax
       def model_name
         model.to_model.model_name
       end
+
+      ##
+      # @return [String]
+      def to_s
+        [*model.title].join(' ')
+      end
     end
   end
 end

data/app/forms/hyrax/forms/work_lease_form.rb

@@ -31,6 +31,12 @@ module Hyrax
       def model_name
         model.to_model.model_name
       end
+
+      ##
+      # @return [String]
+      def to_s
+        [*model.title].join(' ')
+      end
     end
   end
 end

data/app/indexers/concerns/hyrax/location_indexer.rb

@@ -6,7 +6,7 @@ module Hyrax
   module LocationIndexer
     def to_solr
       super.tap do |index_document|
-        index_document[:based_near_label_tesim] = based_near_label_lookup(resource.based_near) if resource.respond_to? :based_near
+        index_document[:based_near_label_tesim] = index_document[:based_near_label_sim] = based_near_label_lookup(resource.based_near) if resource.respond_to? :based_near
       end
     end
 
@@ -14,7 +14,7 @@ module Hyrax
 
     def based_near_label_lookup(locations)
       locations.map do |loc|
-        location_service.full_label(loc)
+        location_service.full_label(loc) if loc.present?
       end
     end
 

data/app/indexers/hyrax/indexers/file_set_indexer.rb

@@ -101,6 +101,10 @@ module Hyrax
 
           # attributes set by fits for video
           solr_doc['aspect_ratio_tesim']      = file_metadata.aspect_ratio if file_metadata.aspect_ratio.present?
+
+          # support for derivatives download
+          derivatives = resource.extensions_and_mime_types
+          solr_doc['extensions_and_mime_types_ssm'] = derivatives.to_json if derivatives.present?
         end
       end
 

data/app/indexers/hyrax/indexers/resource_indexer.rb

@@ -47,6 +47,7 @@ module Hyrax
           "system_modified_dtsi": resource.updated_at,
           "has_model_ssim": resource.to_rdf_representation,
           "human_readable_type_tesim": resource.human_readable_type,
+          "human_readable_type_sim": resource.human_readable_type,
           "alternate_ids_sim": resource.alternate_ids.map(&:to_s)
         }.with_indifferent_access
       end

data/app/indexers/hyrax/valkyrie_indexer.rb

@@ -9,11 +9,9 @@ module Hyrax
       super
     end
 
-    class << self
-      def for(*args, **kwargs)
-        Deprecation.warn "`Hyrax::ValkyrieIndexer.for` is deprecated. Use `Hyrax::Indexers::ResourceIndexer.for` instead."
-        Hyrax::Indexers::ResourceIndexer.for(*args, **kwargs)
-      end
+    def self.for(*args, **kwargs)
+      Deprecation.warn "`Hyrax::ValkyrieIndexer.for` is deprecated. Use `Hyrax::Indexers::ResourceIndexer.for` instead."
+      Hyrax::Indexers::ResourceIndexer.for(*args, **kwargs)
     end
   end
 end

data/app/jobs/migrate_files_to_valkyrie_job.rb

@@ -0,0 +1,109 @@
+##
+# Responsible for conditionally enqueuing the file and thumbnail migration
+# logic of an ActiveFedora object.
+class MigrateFilesToValkyrieJob < Hyrax::ApplicationJob
+  ##
+  #
+  # @param resource [Hyrax::FileSet]
+  def perform(resource)
+    migrate_derivatives!(resource:)
+    # need to reload file_set to get the derivative ids
+    resource = Hyrax.query_service.find_by(id: resource.id)
+    migrate_files!(resource: resource)
+  end
+
+  def attribute_mapping
+    return @attribute_mapping if @attribute_mapping
+    @attribute_mapping = %w[
+      aspect_ratio bit_depth bit_rate byte_order capture_device channels character_count character_set
+      checksum color_map color_space compression creator data_format duration exif_version file_title
+      fits_version format_label frame_rate gps_timestamp graphics_count height image_producer language
+      latitude line_count longitude markup_basis markup_language offset orientation page_count
+      paragraph_count profile_name profile_version recorded_size sample_rate scanning_software
+      table_count well_formed width word_count ].inject({}) { |j, i| j[i] = i; j}
+    @attribute_mapping['recorded_size'] = 'file_size'
+    @attribute_mapping['channels'] = 'alpha_channels'
+    @attribute_mapping['checksum'] = 'original_checksum'
+    @attribute_mapping
+  end
+
+  private
+
+  def migrate_derivatives!(resource:)
+    # @todo should we trigger a job if the member is a child work?
+    paths = Hyrax::DerivativePath.derivatives_for_reference(resource)
+    paths.each do |path|
+      container = container_for(path)
+      mime_type = Marcel::MimeType.for(extension: File.extname(path))
+      directives = { url: path, container: container, mime_type: mime_type }
+      File.open(path, 'rb') do |content|
+        Hyrax::ValkyriePersistDerivatives.call(content, directives)
+      end
+    end
+  end
+
+  ##
+  # Move the ActiveFedora files out of ActiveFedora's domain and into the
+  # configured {Hyrax.storage_adapter}'s domain.
+  def migrate_files!(resource:)
+    return unless resource.respond_to?(:file_ids)
+
+    files = Hyrax.custom_queries.find_many_file_metadata_by_ids(ids: resource.file_ids)
+    files.each do |file|
+      # If it doesn't start with fedora, we've likely already migrated it.
+      next unless /^fedora:/.match?(file.file_identifier.to_s)
+      resource.file_ids.delete(file.id)
+
+      Tempfile.create do |tempfile|
+        tempfile.binmode
+        tempfile.write(URI.open(file.file_identifier.to_s.gsub("fedora:", "http:")).read)
+        tempfile.rewind
+
+        # valkyrie_file = Hyrax.storage_adapter.upload(resource: resource, file: tempfile, original_filename: file.original_filename)
+        valkyrie_file = Hyrax::ValkyrieUpload.file(
+          filename: resource.label,
+          file_set: resource,
+          io: tempfile,
+          use: file.pcdm_use.select {|use| Hyrax::FileMetadata::Use.use_list.include?(use)},
+          user: User.find_or_initialize_by(User.user_key_field => resource.depositor),
+          mime_type: file.mime_type,
+          skip_derivatives: true
+        )
+        valkyrie_file = copy_attributes(valkyrie_file:, original_file: file)
+        Hyrax.persister.save(resource: valkyrie_file)
+      end
+    end
+    # reindex the file set after migrating files to include characterization info
+    Hyrax.index_adapter.save(resource: resource)
+  end
+
+  def copy_attributes(valkyrie_file:, original_file:)
+    attribute_mapping.each do |k, v|
+      valkyrie_file.set_value(k, original_file.send(v))
+    end
+    # Special case as this property isn't in the characterization proxy
+    valkyrie_file.set_value('alternate_ids', original_file.alternate_ids)
+    valkyrie_file
+  end
+
+  ##
+  # Map from the file name used for the derivative to a valid option for
+  # container that ValkyriePersistDerivatives can convert into a
+  # Hyrax::Metadata::Use
+  #
+  # @param filename [String] the name of the derivative file: i.e. 'x-thumbnail.jpg'
+  # @return [String]
+  def container_for(filename)
+    # we want the portion between the '-' and the '.'
+    file_blob = File.basename(filename, '.*').split('-').last
+
+    case file_blob
+    when 'thumbnail'
+      'thumbnail_image'
+    when 'txt', 'json', 'xml'
+      'extracted_text'
+    else
+      'service_file'
+    end
+  end
+end

data/app/jobs/migrate_resources_job.rb

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+# migrates models from AF to valkyrie
+class MigrateResourcesJob < ApplicationJob
+  attr_writer :errors
+  # input [Array>>String] Array of ActiveFedora model names to migrate to valkyrie objects
+  # defaults to AdminSet & Collection models if empty
+  def perform(ids: [], models: ['AdminSet', 'Collection'])
+    if ids.blank?
+      models.each do |model|
+        model.constantize.find_each do |item|
+          migrate(item.id)
+        end
+      end
+    else
+      ids.each do |id|
+        migrate(id)
+      end
+    end
+    raise errors.inspect if errors.present?
+  end
+
+  def errors
+    @errors ||= []
+  end
+
+  def migrate(id)
+    resource = Hyrax.query_service.find_by(id: id)
+    return unless resource.wings? # this resource has already been converted
+    result = MigrateResourceService.new(resource: resource).call
+    errors << result unless result.success?
+    result
+  end
+end

data/app/jobs/valkyrie_create_derivatives_job.rb

@@ -16,8 +16,9 @@ class ValkyrieCreateDerivativesJob < Hyrax::ApplicationJob
 
   def reindex_parent(file_set_id)
     file_set = Hyrax.query_service.find_by(id: file_set_id)
+    return unless file_set
     parent = Hyrax.custom_queries.find_parent_work(resource: file_set)
-    return unless parent.thumbnail_id == file_set.id
+    return unless parent&.thumbnail_id == file_set.id
     Hyrax.logger.debug { "Reindexing #{parent.id} due to creation of thumbnail derivatives." }
     Hyrax.index_adapter.save(resource: parent)
   end

data/app/models/admin_set.rb

@@ -17,6 +17,7 @@
 # @see Hyrax::DefaultAdminSetActor
 # @see Hyrax::ApplyPermissionTemplateActor
 class AdminSet < ActiveFedora::Base
+  include Hydra::PCDM::CollectionBehavior
   include Hydra::AccessControls::Permissions
   include Hyrax::Noid
   include Hyrax::HumanReadableType

data/app/models/concerns/hyrax/ar_resource.rb

@@ -0,0 +1,104 @@
+# frozen_string_literal: true
+module Hyrax
+  # An optional model to bring active record like accessors to your Valkyrie resources. This
+  # is simply for simplicity in the console and backward compatibility.
+  module ArResource
+    extend ActiveSupport::Concern
+
+    class_methods do
+      ##
+      # find a Valkyrie object by its primary identifyer.
+      #
+      # @param id [String]
+      # @return [Valkyrie::Resource]
+      def find(id, query_service: Hyrax.query_service)
+        query_service.find_by(id: id)
+      end
+
+      ##
+      # find and item by an arbitrary keyword arguements if and only if that property is supported
+      # by the current query_service. custom queries are often limited so be aware that this does
+      # support all properties of an object.
+      #
+      # @params query_service [Valkyrie::QueryService] (optional) the query service to use
+      # @param [Hash] opts the options to send to the query service. Can only be one argument.
+      #               this argument will be converted to the query in the form of find_by_#{opts.keys.first}
+      # @return [Valkyrie::Resource]
+      def find_by(query_service: Hyrax.query_service, **opts)
+        if opts.key?(:id)
+          find(opts[:id], query_service: query_service)
+        else
+          method_name = "find_by_#{opts.keys.first}"
+          value = opts[opts.values.first]
+          return query_service.send(method_name, value) if query_service.respond_to?(method_name)
+          query_service.custom_query.send(method_name, value)
+        end
+
+      rescue Valkyrie::Persistence::ObjectNotFoundError
+        nil
+      end
+    end
+
+    ##
+    # @param query_service [#find_parents]
+    #
+    # @return [NilClass] when this object does not have a parent.
+    # @return [Valkyrie::Resource] when this object has at least one parent.
+    def parent(query_service: Hyrax.query_service)
+      query_service.find_parents(resource: self).first
+    end
+
+    ##
+    # This will persist the object to the repository. Not a complete transaction set up, but will
+    # index and notify listeners of metadata update
+    #
+    # @param [Hyrax::Persister] Valkyrie persister (optional) will default to Hyrax.persister
+    # @param [Hyrax::IndexAdapter] Valkyrie index adapter (optional) will default to Hyrax.index_adapter
+    # @param [User] user the user to record the event for. Will not set depositor yet
+    # @return [Valkyrie::Resource]
+    def save(persister: Hyrax.persister, index_adapter: Hyrax.index_adapter, user: ::User.system_user)
+      is_new = new_record
+      result = persister.save(resource: self)
+      return nil unless result.persisted?
+      index_adapter.save(resource: result)
+      if result.collection?
+        Hyrax.publisher.publish('collection.metadata.updated', collection: result, user: user)
+      else
+        Hyrax.publisher.publish('object.deposited', object: result, user: user) if is_new
+        Hyrax.publisher.publish('object.metadata.updated', object: result, user: user)
+      end
+      # TODO: do we need to replace the properties here?
+      self.new_record = false
+      self.id = result.id
+
+      result
+    end
+    alias create save
+    alias update save
+
+    def save!(**opts)
+      raise Valkyrie::Persistence::ObjectNotFoundError unless save(**opts)
+    end
+    alias create! save!
+    alias update! save!
+
+    ##
+    # This will delete the resource and publish its delete event
+    #
+    # @param [Hyrax::Persister] Valkyrie persister (optional) will default to Hyrax.persister
+    # @param [Hyrax::IndexAdapter] Valkyrie index adapter (optional) will default to Hyrax.index_adapter
+    # @param [User] user the user to record the event for. Will not set depositor yet
+    # @return [Boolean]
+    def destroy(persister: Hyrax.persister, index_adapter: Hyrax.index_adapter, user: ::User.system_user)
+      return false unless persisted?
+      persister.delete(resource: self)
+      index_adapter.delete(resource: self)
+      Hyrax.publisher.publish('object.deleted', object: self, user: user)
+      true
+    end
+
+    def destroy!(**opts)
+      raise Valkyrie::Persistence::ObjectNotFoundError unless destroy(**opts)
+    end
+  end
+end

data/app/models/concerns/hyrax/solr_document/ordered_members.rb

@@ -26,7 +26,8 @@ module Hyrax
       #   only includes ids of ordered members.
       def ordered_member_ids
         return [] if id.blank?
-        @ordered_member_ids ||= query_for_ordered_ids
+        # Valkyrie members are always ordered
+        @ordered_member_ids ||= valkyrie? ? member_ids : query_for_ordered_ids
       end
 
       private

data/app/models/concerns/hyrax/solr_document_behavior.rb

@@ -74,10 +74,17 @@ module Hyrax
       Hyrax::ModelRegistry.work_classes.include?(hydra_model)
     end
 
+    ##
+    # @return [Boolean]
+    def valkyrie?
+      self['valkyrie_bsi']
+    end
+
     # Method to return the model
     def hydra_model(classifier: nil)
-      first('has_model_ssim')&.safe_constantize ||
-        model_classifier(classifier).classifier(self).best_model
+      model = first('has_model_ssim')&.safe_constantize
+      model = (first('has_model_ssim')&.+ 'Resource')&.safe_constantize if Hyrax.config.valkyrie_transition?
+      model || model_classifier(classifier).classifier(self).best_model
     end
 
     def depositor(default = '')
@@ -135,6 +142,10 @@ module Hyrax
       self['visibility_ssi'] == indexed_lease_visibility
     end
 
+    def extensions_and_mime_types
+      JSON.parse(self['extensions_and_mime_types_ssm'].first).map(&:with_indifferent_access) if self['extensions_and_mime_types_ssm']
+    end
+
     private
 
     def model_classifier(classifier)