hyrax 3.0.0.pre.rc4 → 3.1.0

data/lib/wings/valkyrie/storage.rb

@@ -19,6 +19,7 @@ module Wings
       DEFAULT_CTYPE = 'application/octet-stream'
       LINK_HEADER = "<http://www.w3.org/ns/ldp#NonRDFSource>; rel=\"type\""
       FILES_PATH = 'files'
+      VERSIONS_SLUG = '/fcr:versions'
 
       attr_reader :sha1
 
@@ -27,6 +28,14 @@ module Wings
         super
       end
 
+      ##
+      # @param key [Symbol] the key for plugin behavior to check support for
+      #
+      # @return [Boolean] whether
+      def supports?(key)
+        key == :versions
+      end
+
       def upload(file:, original_filename:, resource:, content_type: DEFAULT_CTYPE, # rubocop:disable Metrics/ParameterLists
                  resource_uri_transformer: default_resource_uri_transformer, use: Hydra::PCDM::Vocab::PCDMTerms.File,
                  id_hint: 'original', **extra_arguments)
@@ -41,7 +50,49 @@ module Wings
                         id_hint: id_hint, **extra_arguments)
              end
 
-        find_by(id: ::Valkyrie::ID.new(id.to_s.sub(/^.+\/\//, PROTOCOL)))
+        find_by(id: cast_to_valkyrie_id(id))
+      end
+
+      ##
+      # @return [Enumerable<Version> ordered list of versions
+      def find_versions(id:)
+        response = connection.http.get(fedora_identifier(id: id) + VERSIONS_SLUG)
+        return [] if response.status == 404
+
+        reader = RDF::Reader.for(content_type: response.headers['content-type'])
+        version_graph = RDF::Graph.new << reader.new(response.body)
+
+        version_graph.query(predicate: RDF::Vocab::Fcrepo4.hasVersion).objects.map do |uri|
+          timestamp =
+            version_graph.query([uri, RDF::Vocab::Fcrepo4.created, :created])
+                         .first_object
+                         .object
+          Version.new(cast_to_valkyrie_id(uri.to_s), timestamp, self)
+        end.sort
+      end
+
+      ##
+      # abstractly, {Version} objects should have an {#id} and be orderable
+      # over {#<=>} (allowing e.g. `#sort` to define a consistent order---
+      # oldest to newest---for a collection of versions). the {#id} should be a
+      # globally unique identifier for the version.
+      #
+      # this implementation uses an orderable {#version_token}. in practice
+      # the token is the fcrepo created date for the version, as extracted from
+      # the versions graph.
+      Version = Struct.new(:id, :version_token, :adapter) do
+        include Comparable
+
+        ##
+        # @return [#read]
+        def io
+          adapter.find_by(id: id)
+        end
+
+        def <=>(other)
+          raise ArgumentError unless other.respond_to?(:version_token)
+          version_token <=> other.version_token
+        end
       end
 
       private
@@ -87,6 +138,10 @@ module Wings
 
         Hyrax.config.translate_id_to_uri.call(created_file.id)
       end
+
+      def cast_to_valkyrie_id(id)
+        ::Valkyrie::ID.new(id.to_s.sub(/^.+\/\//, PROTOCOL))
+      end
     end
   end
 

data/lib/wings.rb

@@ -98,27 +98,6 @@ require 'wings/valkyrie/persister'
 require 'wings/valkyrie/storage'
 require 'wings/valkyrie/query_service'
 
-Hydra::AccessControl.send(:define_method, :valkyrie_resource) do
-  attrs = attributes.symbolize_keys
-  attrs[:new_record]  = new_record?
-  attrs[:created_at]  = create_date
-  attrs[:updated_at]  = modified_date
-
-  attrs[:permissions] = permissions.map do |permission|
-    agent = permission.type == 'group' ? "group/#{permission.agent_name}" : permission.agent_name
-
-    Hyrax::Permission.new(id: permission.id,
-                          mode: permission.access.to_sym,
-                          agent: agent,
-                          access_to: Valkyrie::ID.new(permission.access_to_id),
-                          new_record: permission.new_record?)
-  end
-
-  attrs[:access_to] = attrs[:permissions].find { |p| p.access_to&.id&.present? }&.access_to
-
-  Hyrax::AccessControl.new(**attrs)
-end
-
 begin
   require 'wings/setup'
 rescue NameError, Hyrax::SimpleSchemaLoader::UndefinedSchemaError => err

data/template.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 # Hack for https://github.com/rails/rails/issues/35153
 gsub_file 'Gemfile', /^gem ["']sqlite3["']$/, 'gem "sqlite3", "~> 1.3.0"'
-gem 'hyrax', '3.0.0-rc4'
+gem 'hyrax', '3.1.0'
 run 'bundle install'
 generate 'hyrax:install', '-f'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: hyrax
 version: !ruby/object:Gem::Version
-  version: 3.0.0.pre.rc4
+  version: 3.1.0
 platform: ruby
 authors:
 - Justin Coyne
@@ -14,7 +14,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-03-11 00:00:00.000000000 Z
+date: 2021-09-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -1178,6 +1178,8 @@ executables:
 - db-migrate-seed.sh
 - db-wait.sh
 - hyrax-entrypoint.sh
+- solrcloud-assign-configset.sh
+- solrcloud-upload-configset.sh
 extensions: []
 extra_rdoc_files: []
 files:
@@ -1720,6 +1722,8 @@ files:
 - app/forms/hyrax/forms/failed_submission_form_wrapper.rb
 - app/forms/hyrax/forms/file_manager_form.rb
 - app/forms/hyrax/forms/file_set_edit_form.rb
+- app/forms/hyrax/forms/file_set_form.rb
+- app/forms/hyrax/forms/permission.rb
 - app/forms/hyrax/forms/permission_template_form.rb
 - app/forms/hyrax/forms/resource_form.rb
 - app/forms/hyrax/forms/widgets/admin_set_embargo_period.rb
@@ -1762,6 +1766,7 @@ files:
 - app/indexers/concerns/hyrax/indexes_basic_metadata.rb
 - app/indexers/concerns/hyrax/indexes_linked_metadata.rb
 - app/indexers/hyrax/admin_set_indexer.rb
+- app/indexers/hyrax/administrative_set_indexer.rb
 - app/indexers/hyrax/basic_metadata_indexer.rb
 - app/indexers/hyrax/collection_indexer.rb
 - app/indexers/hyrax/collection_with_basic_metadata_indexer.rb
@@ -1773,6 +1778,7 @@ files:
 - app/indexers/hyrax/repository_reindexer.rb
 - app/indexers/hyrax/resource_indexer.rb
 - app/indexers/hyrax/valkyrie_collection_indexer.rb
+- app/indexers/hyrax/valkyrie_file_set_indexer.rb
 - app/indexers/hyrax/valkyrie_indexer.rb
 - app/indexers/hyrax/valkyrie_work_indexer.rb
 - app/indexers/hyrax/visibility_indexer.rb
@@ -1832,6 +1838,7 @@ files:
 - app/models/concerns/hyrax/collection_behavior.rb
 - app/models/concerns/hyrax/collection_nesting.rb
 - app/models/concerns/hyrax/core_metadata.rb
+- app/models/concerns/hyrax/embargoable.rb
 - app/models/concerns/hyrax/file_set/belongs_to_works.rb
 - app/models/concerns/hyrax/file_set/characterization.rb
 - app/models/concerns/hyrax/file_set/derivatives.rb
@@ -1935,6 +1942,7 @@ files:
 - app/presenters/hyrax/admin/workflow_roles_presenter.rb
 - app/presenters/hyrax/admin_set_options_presenter.rb
 - app/presenters/hyrax/admin_set_presenter.rb
+- app/presenters/hyrax/admin_set_selection_presenter.rb
 - app/presenters/hyrax/admin_stats_presenter.rb
 - app/presenters/hyrax/characterization_behavior.rb
 - app/presenters/hyrax/collapsable_section_presenter.rb
@@ -1956,6 +1964,7 @@ files:
 - app/presenters/hyrax/model_icon.rb
 - app/presenters/hyrax/model_proxy.rb
 - app/presenters/hyrax/page_title_decorator.rb
+- app/presenters/hyrax/pcdm_member_presenter_factory.rb
 - app/presenters/hyrax/permission_badge.rb
 - app/presenters/hyrax/presenter_factory.rb
 - app/presenters/hyrax/presenter_renderer.rb
@@ -2047,6 +2056,7 @@ files:
 - app/services/hyrax/collection_thumbnail_path_service.rb
 - app/services/hyrax/collection_types/create_service.rb
 - app/services/hyrax/collection_types/permissions_service.rb
+- app/services/hyrax/collections/collection_member_search_service.rb
 - app/services/hyrax/collections/collection_member_service.rb
 - app/services/hyrax/collections/managed_collections_service.rb
 - app/services/hyrax/collections/migration_service.rb
@@ -2069,6 +2079,7 @@ files:
 - app/services/hyrax/custom_queries/navigators/child_works_navigator.rb
 - app/services/hyrax/custom_queries/navigators/collection_members.rb
 - app/services/hyrax/custom_queries/navigators/find_files.rb
+- app/services/hyrax/custom_queries/navigators/parent_collections_navigator.rb
 - app/services/hyrax/database_migrator.rb
 - app/services/hyrax/default_middleware_stack.rb
 - app/services/hyrax/derivative_path.rb
@@ -2082,6 +2093,7 @@ files:
 - app/services/hyrax/file_set_fixity_check_service.rb
 - app/services/hyrax/file_set_type_service.rb
 - app/services/hyrax/file_set_visibility_propagator.rb
+- app/services/hyrax/find_objects_via_solr_service.rb
 - app/services/hyrax/fixity/active_fedora_fixity_service.rb
 - app/services/hyrax/fixity/missing_content_error.rb
 - app/services/hyrax/fixity_check_failure_service.rb
@@ -2105,9 +2117,11 @@ files:
 - app/services/hyrax/listeners/batch_notification_listener.rb
 - app/services/hyrax/listeners/file_set_lifecycle_listener.rb
 - app/services/hyrax/listeners/file_set_lifecycle_notification_listener.rb
+- app/services/hyrax/listeners/member_cleanup_listener.rb
 - app/services/hyrax/listeners/metadata_index_listener.rb
 - app/services/hyrax/listeners/object_lifecycle_listener.rb
 - app/services/hyrax/listeners/proxy_deposit_listener.rb
+- app/services/hyrax/listeners/trophy_cleanup_listener.rb
 - app/services/hyrax/listeners/workflow_listener.rb
 - app/services/hyrax/local_file_service.rb
 - app/services/hyrax/lock_manager.rb
@@ -2133,6 +2147,7 @@ files:
 - app/services/hyrax/search_service.rb
 - app/services/hyrax/simple_schema_loader.rb
 - app/services/hyrax/solr_query_builder_service.rb
+- app/services/hyrax/solr_query_service.rb
 - app/services/hyrax/solr_service.rb
 - app/services/hyrax/statistics/collections/over_time.rb
 - app/services/hyrax/statistics/depositors/summary.rb
@@ -2164,6 +2179,7 @@ files:
 - app/services/hyrax/work_uploads_handler.rb
 - app/services/hyrax/workflow/abstract_notification.rb
 - app/services/hyrax/workflow/action_taken_service.rb
+- app/services/hyrax/workflow/actionable_objects.rb
 - app/services/hyrax/workflow/activate_object.rb
 - app/services/hyrax/workflow/changes_required_notification.rb
 - app/services/hyrax/workflow/deactivate_object.rb
@@ -2175,6 +2191,7 @@ files:
 - app/services/hyrax/workflow/notification_configuration_parameter.rb
 - app/services/hyrax/workflow/notification_generator.rb
 - app/services/hyrax/workflow/notification_service.rb
+- app/services/hyrax/workflow/object_in_workflow_decorator.rb
 - app/services/hyrax/workflow/pending_review_notification.rb
 - app/services/hyrax/workflow/permission_generator.rb
 - app/services/hyrax/workflow/permission_query.rb
@@ -2597,36 +2614,28 @@ files:
 - bin/db-migrate-seed.sh
 - bin/db-wait.sh
 - bin/hyrax-entrypoint.sh
-- chart/fcrepo/.gitignore
-- chart/fcrepo/.helmignore
-- chart/fcrepo/Chart.yaml
-- chart/fcrepo/README.md
-- chart/fcrepo/templates/NOTES.txt
-- chart/fcrepo/templates/_helpers.tpl
-- chart/fcrepo/templates/configmap-env.yaml
-- chart/fcrepo/templates/deployment.yaml
-- chart/fcrepo/templates/ingress.yaml
-- chart/fcrepo/templates/pvc.yaml
-- chart/fcrepo/templates/secret.yaml
-- chart/fcrepo/templates/service.yaml
-- chart/fcrepo/templates/serviceaccount.yaml
-- chart/fcrepo/templates/tests/test-connection.yaml
-- chart/fcrepo/values.yaml
+- bin/solrcloud-assign-configset.sh
+- bin/solrcloud-upload-configset.sh
 - chart/hyrax/.gitignore
 - chart/hyrax/.helmignore
 - chart/hyrax/Chart.yaml
 - chart/hyrax/README.md
 - chart/hyrax/templates/NOTES.txt
 - chart/hyrax/templates/_helpers.tpl
+- chart/hyrax/templates/branding-pvc.yaml
 - chart/hyrax/templates/configmap-env.yaml
+- chart/hyrax/templates/cron-embargo.yaml
+- chart/hyrax/templates/cron-lease.yaml
+- chart/hyrax/templates/deployment-worker.yaml
 - chart/hyrax/templates/deployment.yaml
-- chart/hyrax/templates/fcrepo-secret.yaml
+- chart/hyrax/templates/derivatives-pvc.yaml
 - chart/hyrax/templates/hpa.yaml
 - chart/hyrax/templates/ingress.yaml
 - chart/hyrax/templates/secrets.yaml
 - chart/hyrax/templates/service.yaml
 - chart/hyrax/templates/serviceaccount.yaml
 - chart/hyrax/templates/tests/test-connection.yaml
+- chart/hyrax/templates/uploads-pvc.yaml
 - chart/hyrax/values.yaml
 - config/brakeman.ignore
 - config/features.rb
@@ -2636,6 +2645,7 @@ files:
 - config/initializers/listeners.rb
 - config/initializers/nesting_indexer_initializer.rb
 - config/initializers/simple_form.rb
+- config/initializers/valkryrie_storage.rb
 - config/initializers/valkyrie_id_equality.rb
 - config/locales/hyrax.de.yml
 - config/locales/hyrax.en.yml
@@ -2798,6 +2808,7 @@ files:
 - lib/generators/hyrax/work_resource/templates/work_spec.rb.erb
 - lib/generators/hyrax/work_resource/work_resource_generator.rb
 - lib/hyrax.rb
+- lib/hyrax/active_fedora_dummy_model.rb
 - lib/hyrax/arkivo.rb
 - lib/hyrax/arkivo/actor.rb
 - lib/hyrax/arkivo/config.rb
@@ -2847,6 +2858,7 @@ files:
 - lib/hyrax/specs/shared_specs/identifiers.rb
 - lib/hyrax/specs/shared_specs/indexers.rb
 - lib/hyrax/specs/shared_specs/metadata.rb
+- lib/hyrax/specs/shared_specs/valkyrie_storage_versions.rb
 - lib/hyrax/specs/shared_specs/workflow_method.rb
 - lib/hyrax/specs/spy_listener.rb
 - lib/hyrax/transactions.rb
@@ -2854,14 +2866,18 @@ files:
 - lib/hyrax/transactions/container.rb
 - lib/hyrax/transactions/create_work.rb
 - lib/hyrax/transactions/destroy_work.rb
+- lib/hyrax/transactions/file_set_destroy.rb
 - lib/hyrax/transactions/steps/add_file_sets.rb
 - lib/hyrax/transactions/steps/add_to_collections.rb
+- lib/hyrax/transactions/steps/add_to_parent.rb
 - lib/hyrax/transactions/steps/apply_collection_permission_template.rb
 - lib/hyrax/transactions/steps/apply_permission_template.rb
 - lib/hyrax/transactions/steps/apply_visibility.rb
+- lib/hyrax/transactions/steps/delete_resource.rb
 - lib/hyrax/transactions/steps/destroy_work.rb
 - lib/hyrax/transactions/steps/ensure_admin_set.rb
 - lib/hyrax/transactions/steps/ensure_permission_template.rb
+- lib/hyrax/transactions/steps/remove_file_set_from_work.rb
 - lib/hyrax/transactions/steps/save.rb
 - lib/hyrax/transactions/steps/save_access_control.rb
 - lib/hyrax/transactions/steps/save_work.rb
@@ -2873,7 +2889,9 @@ files:
 - lib/hyrax/transactions/transaction.rb
 - lib/hyrax/transactions/update_work.rb
 - lib/hyrax/transactions/work_create.rb
+- lib/hyrax/transactions/work_destroy.rb
 - lib/hyrax/valkyrie_can_can_adapter.rb
+- lib/hyrax/valkyrie_simple_path_generator.rb
 - lib/hyrax/version.rb
 - lib/hyrax/zotero.rb
 - lib/hyrax/zotero/config.rb
@@ -2881,10 +2899,12 @@ files:
 - lib/tasks/controlled_vocabularies.rake
 - lib/tasks/default_admin_set.rake
 - lib/tasks/default_collection_type.rake
+- lib/tasks/embargo_lease.rake
 - lib/tasks/hyrax.rake
 - lib/tasks/hyrax_user.rake
 - lib/tasks/install.rake
 - lib/tasks/migrate.rake
+- lib/tasks/regenerate_derivatives.rake
 - lib/tasks/reindex.rake
 - lib/tasks/stats_tasks.rake
 - lib/tasks/universal_viewer.rake
@@ -2954,11 +2974,11 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '2.5'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
-rubygems_version: 3.1.4
+rubygems_version: 3.1.6
 signing_key:
 specification_version: 4
 summary: Hyrax is a front-end based on the robust Samvera framework, providing a user

data/chart/fcrepo/.gitignore

@@ -1,2 +0,0 @@
-charts/*
-Chart.lock

data/chart/fcrepo/.helmignore

@@ -1,23 +0,0 @@
-# Patterns to ignore when building packages.
-# This supports shell glob matching, relative path matching, and
-# negation (prefixed with !). Only one pattern per line.
-.DS_Store
-# Common VCS dirs
-.git/
-.gitignore
-.bzr/
-.bzrignore
-.hg/
-.hgignore
-.svn/
-# Common backup files
-*.swp
-*.bak
-*.tmp
-*.orig
-*~
-# Various IDEs
-.project
-.idea/
-*.tmproj
-.vscode/

data/chart/fcrepo/Chart.yaml

@@ -1,11 +0,0 @@
-apiVersion: v2
-name: fcrepo
-description: Fedora Commons Repository 4
-type: application
-version: 0.4.1
-appVersion: 4.7
-dependencies:
-  - name: postgresql
-    version: 9.3.3
-    repository: https://charts.bitnami.com/bitnami
-    condition: postgresql.enabled

data/chart/fcrepo/README.md

@@ -1,50 +0,0 @@
-Fedora Commons Helm Chart
-=========================
-
-Fedora is the flexible, modular, open source repository platform with native
-linked data support.
-
-## Installation
-
-```sh
-helm dep up chart/fcrepo
-helm install fcrepo chart/fcrepo
-```
-
-## Configuration
-
-By default, this chart deploys with Postgresql as the backend for Fedora.
-Without other configuration, it will deploy a new Postgresql instance/database
-as a service available to the `fcrepo` deployment.
-
-In practice, users may want to forego installing postgres for two reasons:
-
-_First_, when you are deploying Fedora into a more complex application
-environment you may wish to reuse an existing Postgres instance already
-maintained with that environment.
-
-In this case, `fcrepo` should be deployed with postgresql explictly disabled, an
-`exernalDatabaseUsername`, and an `fcrepoSecretName`. `fcrepoSecretName` must
-correspond to an existing secret providing `DATABASE_PASSWORD`, `DATABASE_HOST`,
-and `JAVA_OPTS`.
-
-Optionally, a `externalDatabaseName` may be given to avoid collissions in the
-case that the default `fcrepo` is not an acceptable database name.
-
-This is usually done in the context of a parent chart which provides the postgresql instance, for example:
-
-```yaml
-fcrepo:
-  enabled: true
-  fcrepoSecretName: "mychart.fcrepo.fullname"
-  externalDatabaseUsername: "mydbuser"
-  servicePort: 8080
-  postgresql:
-    enabled: false
-```
-
-_Second_, because they want to use another backend for Fedora. This use case is broadly unsupported here. In theory, you can get a default (Infinispan) configuration by setting `postgresql.enabled` to `false`. **THIS CONFIGURATION IS UNTESTED AND UNSUPPORTED**:
-
-```sh
-helm install --set postgresql.enabled=false fcrepo-test chart/fcrepo
-```