From 3d94a86b8deb64248d84d61502816d98b6d28dbd Mon Sep 17 00:00:00 2001
From: Gyan Gupta <gyan@cottagelabs.com>
Date: Tue, 1 Apr 2025 18:05:21 +0530
Subject: [PATCH] add human-readable query
---
.../complex_modalities_controller.rb | 2 +-
.../complex_sessions_controller.rb | 2 +-
.../complex_subjects_controller.rb | 2 +-
.../hyrax/crc1280_experiments_controller.rb | 11 +--
.../hyrax/dashboard/collections_controller.rb | 6 +-
.../controllers/hyrax/datasets_controller.rb | 2 +-
.../bulkrax/valkyrie_object_factory.rb | 18 ++--
hyrax/app/helpers/admin_set_helper.rb | 2 +-
.../listeners/lifecycle_listener_helper.rb | 12 +--
hyrax/app/helpers/hyrax_helper.rb | 11 +--
.../jobs/hyrax/file_sets/grant_edit_job.rb | 3 +-
.../jobs/hyrax/file_sets/grant_read_job.rb | 3 +-
.../jobs/hyrax/file_sets/revoke_edit_job.rb | 3 +-
hyrax/app/jobs/valkyrie_ingest_job.rb | 2 +-
.../crc_folder_complex_subject_entry.rb | 2 +-
hyrax/app/models/complex_modality.rb | 4 +-
hyrax/app/models/complex_session.rb | 4 +-
hyrax/app/models/complex_subject.rb | 6 +-
hyrax/app/models/concerns/common_query.rb | 93 +++++++++++++++++++
.../concerns/hyrax/tombstone_behavior.rb | 9 +-
hyrax/app/models/concerns/rdms_roles.rb | 8 +-
.../app/models/concerns/s3_file_handleable.rb | 2 +-
hyrax/app/models/crc1280_experiment.rb | 19 +---
hyrax/app/models/dataset.rb | 17 +---
hyrax/app/models/hyrax/file_set.rb | 17 +---
hyrax/app/models/hyrax/pcdm_collection.rb | 17 +---
hyrax/app/models/user.rb | 8 +-
.../hyrax/crc1280_experiment_presenter.rb | 2 +-
hyrax/app/services/doi_service.rb | 2 +-
.../collections/permissions_create_service.rb | 2 +-
hyrax/app/services/hyrax/valkyrie_upload.rb | 2 +-
.../app/services/verify_crc_dataset_import.rb | 2 +-
.../_all_children.html.erb | 2 +-
.../_parent_collection.html.erb | 2 +-
.../hyrax/crc1280_experiments/_title.html.erb | 8 --
.../hyrax/crc1280_experiments/show.html.erb | 2 +-
.../downloads_controller_override.rb | 4 +-
hyrax/config/initializers/riiif.rb | 4 +-
.../tasks/default_admin_set_for_workflow.rake | 2 +-
39 files changed, 169 insertions(+), 150 deletions(-)
create mode 100644 hyrax/app/models/concerns/common_query.rb
diff --git a/hyrax/app/controllers/hyrax/crc1280_experiments/complex_modalities_controller.rb b/hyrax/app/controllers/hyrax/crc1280_experiments/complex_modalities_controller.rb
index 9a6b84ad..0644b0e7 100644
--- a/hyrax/app/controllers/hyrax/crc1280_experiments/complex_modalities_controller.rb
+++ b/hyrax/app/controllers/hyrax/crc1280_experiments/complex_modalities_controller.rb
@@ -67,7 +67,7 @@ module Hyrax
private
def set_crc1280_experiment
- @crc1280_experiment = ::Hyrax.query_service.find_by(id: params[:crc1280_experiment_id])
+ @crc1280_experiment = Crc1280Experiment.find(params[:crc1280_experiment_id])
end
def set_complex_session
diff --git a/hyrax/app/controllers/hyrax/crc1280_experiments/complex_sessions_controller.rb b/hyrax/app/controllers/hyrax/crc1280_experiments/complex_sessions_controller.rb
index 9bd3c041..1f641c6f 100644
--- a/hyrax/app/controllers/hyrax/crc1280_experiments/complex_sessions_controller.rb
+++ b/hyrax/app/controllers/hyrax/crc1280_experiments/complex_sessions_controller.rb
@@ -70,7 +70,7 @@ module Hyrax
private
def set_crc1280_experiment
- @crc1280_experiment = ::Hyrax.query_service.find_by(id: params[:crc1280_experiment_id])
+ @crc1280_experiment = Crc1280Experiment.find(params[:crc1280_experiment_id])
end
def set_complex_subject
diff --git a/hyrax/app/controllers/hyrax/crc1280_experiments/complex_subjects_controller.rb b/hyrax/app/controllers/hyrax/crc1280_experiments/complex_subjects_controller.rb
index d99a7b38..35e17a9e 100644
--- a/hyrax/app/controllers/hyrax/crc1280_experiments/complex_subjects_controller.rb
+++ b/hyrax/app/controllers/hyrax/crc1280_experiments/complex_subjects_controller.rb
@@ -64,7 +64,7 @@ module Hyrax
private
def set_crc1280_experiment
- @crc1280_experiment = ::Hyrax.query_service.find_by(id: params[:crc1280_experiment_id])
+ @crc1280_experiment = Crc1280Experiment.find(params[:crc1280_experiment_id])
end
def set_complex_subject
diff --git a/hyrax/app/controllers/hyrax/crc1280_experiments_controller.rb b/hyrax/app/controllers/hyrax/crc1280_experiments_controller.rb
index d4672000..c1007481 100644
--- a/hyrax/app/controllers/hyrax/crc1280_experiments_controller.rb
+++ b/hyrax/app/controllers/hyrax/crc1280_experiments_controller.rb
@@ -46,7 +46,7 @@ module Hyrax
private
def check_tombstone
- @crc1280_experiment = Hyrax.query_service.find_by(id: params[:id])
+ @crc1280_experiment = Crc1280Experiment.find(params[:id])
if current_user.present? && (current_user.publication_manager? || current_user.admin?)
if @crc1280_experiment.is_tombstoned == true && params[:action] == 'edit'
redirect_to main_app.polymorphic_path(@crc1280_experiment)
@@ -62,7 +62,7 @@ module Hyrax
def redirect_to_default_collection
return if params.has_key?(:add_works_to_collection)
- collection = Hyrax::PcdmCollection.where(title: [ENV.fetch('CRC_1280_COLLECTION', "CRC 1280")]).first
+ collection = Hyrax::PcdmCollection.find_by(title: [ENV.fetch('CRC_1280_COLLECTION', "CRC 1280")])
flash[:notice] = "You need to navigate to your group to create an experiment."
redirect_to dashboard_collection_path(collection.id)
@@ -70,10 +70,9 @@ module Hyrax
def build_breadcrumbs
return super if ['show', 'edit'].exclude?(action_name)
-
- work = Hyrax.query_service.find_by(id: presenter.id)
- parent_group_collection = Hyrax.query_service.custom_queries.find_parent_collections(resource: work).first
- crc_1280_collection = Hyrax.query_service.custom_queries.find_parent_collections(resource: parent_group_collection).first if parent_group_collection
+ work = Crc1280Experiment.find(presenter.id)
+ parent_group_collection = work.parent_collections.first
+ crc_1280_collection = parent_group_collection.parent_collections.first if parent_group_collection
add_breadcrumb t(:'hyrax.controls.home'), root_path
add_breadcrumb crc_1280_collection.title.first, dashboard_collection_path(crc_1280_collection.id) if crc_1280_collection.present?
diff --git a/hyrax/app/controllers/hyrax/dashboard/collections_controller.rb b/hyrax/app/controllers/hyrax/dashboard/collections_controller.rb
index e2df45ef..ea9f4eca 100644
--- a/hyrax/app/controllers/hyrax/dashboard/collections_controller.rb
+++ b/hyrax/app/controllers/hyrax/dashboard/collections_controller.rb
@@ -485,17 +485,17 @@ module Hyrax
end
def move_members_between_collections
+
remove_members_from_collection
add_members_to_collection(collection_id: params[:destination_collection_id])
-
destination_title =
- Hyrax.query_service.find_by(id: params[:destination_collection_id]).title.first ||
+ Hyrax::PcdmCollection.find(params[:destination_collection_id]).title.first ||
params[:destination_collection_id]
flash[:notice] = "Successfully moved #{batch.count} files to #{destination_title} Collection."
rescue StandardError => err
Hyrax.logger.error(err)
destination_title =
- Hyrax.query_service.find_by(id: params[:destination_collection_id]).title.first ||
+ Hyrax::PcdmCollection.find(params[:destination_collection_id]).title.first ||
destination_id
flash[:error] = "An error occured. Files were not moved to #{destination_title} Collection."
end
diff --git a/hyrax/app/controllers/hyrax/datasets_controller.rb b/hyrax/app/controllers/hyrax/datasets_controller.rb
index 0e549fb7..e68042f1 100644
--- a/hyrax/app/controllers/hyrax/datasets_controller.rb
+++ b/hyrax/app/controllers/hyrax/datasets_controller.rb
@@ -22,7 +22,7 @@ module Hyrax
private
def check_tombstone
- @dataset = Hyrax.query_service.find_by(id: params[:id])
+ @dataset = Dataset.find(params[:id])
if current_user.nil?
if @dataset.is_tombstoned == true
diff --git a/hyrax/app/factories/bulkrax/valkyrie_object_factory.rb b/hyrax/app/factories/bulkrax/valkyrie_object_factory.rb
index 837330b0..3eec53a9 100644
--- a/hyrax/app/factories/bulkrax/valkyrie_object_factory.rb
+++ b/hyrax/app/factories/bulkrax/valkyrie_object_factory.rb
@@ -142,9 +142,9 @@ module Bulkrax
if resource.respond_to?(:save!)
resource.save!
else
- result = Hyrax.persister.save(resource: resource)
+ result = resource.save
raise Valkyrie::Persistence::ObjectNotFoundError unless result
- Hyrax.index_adapter.save(resource: result)
+ result.save_index
if result.collection?
publish('collection.metadata.updated', collection: result, user: user)
else
@@ -156,7 +156,7 @@ module Bulkrax
def self.update_index(resources:)
Array(resources).each do |resource|
- Hyrax.index_adapter.save(resource: resource)
+ resource.save_index
end
end
@@ -202,16 +202,14 @@ module Bulkrax
def self.ordered_file_sets_for(object)
return [] if object.blank?
-
- Hyrax.custom_queries.find_child_file_sets(resource: object)
+ object.child_filesets
end
def delete(user)
obj = find
return false unless obj
-
- Hyrax.persister.delete(resource: obj)
- Hyrax.index_adapter.delete(resource: obj)
+ obj.delete
+ obj.delete_index
self.class.publish(event: 'object.deleted', object: obj, user: user)
end
@@ -230,7 +228,7 @@ module Bulkrax
return if @object.depositor.present?
@object.depositor = @user.email
- object = Hyrax.persister.save(resource: @object)
+ object = @object.save
self.class.publish(event: "object.metadata.updated", object: object, user: @user)
object
end
@@ -476,7 +474,7 @@ module Bulkrax
# @Override Destroy existing files with Hyrax::Transactions
def destroy_existing_files
- existing_files = Hyrax.custom_queries.find_child_file_sets(resource: object)
+ existing_files = object.child_filesets
existing_files.each do |fs|
transactions["file_set.destroy"]
diff --git a/hyrax/app/helpers/admin_set_helper.rb b/hyrax/app/helpers/admin_set_helper.rb
index 1db3b1f2..d30b0bcf 100644
--- a/hyrax/app/helpers/admin_set_helper.rb
+++ b/hyrax/app/helpers/admin_set_helper.rb
@@ -1,5 +1,5 @@
module AdminSetHelper
- def self.find_admin_set_by_property(**args)
+ def self.find_by(**args)
query = <<-SQL
SELECT * FROM orm_resources
WHERE metadata @> ?
diff --git a/hyrax/app/helpers/hyrax/listeners/lifecycle_listener_helper.rb b/hyrax/app/helpers/hyrax/listeners/lifecycle_listener_helper.rb
index 795bda0c..5a95a55b 100644
--- a/hyrax/app/helpers/hyrax/listeners/lifecycle_listener_helper.rb
+++ b/hyrax/app/helpers/hyrax/listeners/lifecycle_listener_helper.rb
@@ -14,8 +14,8 @@ module Hyrax
object = object.register_ark(user: user)
end
- object = save_object!(object)
- Hyrax.index_adapter.save(resource: object)
+ object.save
+ object.save_index
object
end
@@ -25,8 +25,8 @@ module Hyrax
object = object.set_format_and_size
end
- object = save_object!(object)
- Hyrax.index_adapter.save(resource: object)
+ object.save
+ object.save_index
object
end
@@ -74,10 +74,6 @@ module Hyrax
s3.delete_object(bucket_name, self.object_key_on_s3)
parent.update(date_modified: DateTime.now)
end
-
- def save_object!(object)
- Hyrax.persister.save(resource: object)
- end
end
end
end
\ No newline at end of file
diff --git a/hyrax/app/helpers/hyrax_helper.rb b/hyrax/app/helpers/hyrax_helper.rb
index 850e896e..32cba110 100644
--- a/hyrax/app/helpers/hyrax_helper.rb
+++ b/hyrax/app/helpers/hyrax_helper.rb
@@ -45,19 +45,19 @@ module HyraxHelper
end
def manager_role(presenter)
- Hyrax.query_service.find_by(id: presenter.id).manager_role
+ Hyrax::PcdmCollection.find(presenter.id).manager_role
end
def member_role(presenter)
- Hyrax.query_service.find_by(id: presenter.id).member_role
+ Hyrax::PcdmCollection.find(presenter.id).member_role
end
def manager_role_for_group(presenter)
- Hyrax.query_service.find_by(id: presenter.id).manager_role_for_group
+ Hyrax::PcdmCollection.find(presenter.id).manager_role_for_group
end
def member_role_for_group(presenter)
- Hyrax.query_service.find_by(id: presenter.id).member_role_for_group
+ Hyrax::PcdmCollection.find(presenter.id).member_role_for_group
end
def can_create_work_in_group?(group_id)
@@ -151,8 +151,7 @@ module HyraxHelper
def s3_file_download_url_for_file_set(file_set_id)
s3 = S3StorageService.new
s3.init_client
-
- file_set = Hyrax.query_service.find_by(id: file_set_id)
+ file_set = Hyrax::FileSet.find(file_set_id)
bucket_name = s3.sanitise_name(file_set.parent_work.id)
s3.presigned_url_for_download(bucket_name, file_set.object_key_on_s3)
diff --git a/hyrax/app/jobs/hyrax/file_sets/grant_edit_job.rb b/hyrax/app/jobs/hyrax/file_sets/grant_edit_job.rb
index 093735ea..99802379 100644
--- a/hyrax/app/jobs/hyrax/file_sets/grant_edit_job.rb
+++ b/hyrax/app/jobs/hyrax/file_sets/grant_edit_job.rb
@@ -6,8 +6,7 @@ module Hyrax
include PermissionJobBehavior
def perform(file_set_id, group_key)
- file_set = Hyrax.query_service.find_by(id: file_set_id)
-
+ file_set = Hyrax::FileSet.find(file_set_id)
file_set.edit_groups = file_set.edit_groups.to_a + Array.wrap(group_key) # += works in Ruby 2.6+
file_set.try(:permission_manager)&.acl&.save
end
diff --git a/hyrax/app/jobs/hyrax/file_sets/grant_read_job.rb b/hyrax/app/jobs/hyrax/file_sets/grant_read_job.rb
index 23707d08..b34e52f6 100644
--- a/hyrax/app/jobs/hyrax/file_sets/grant_read_job.rb
+++ b/hyrax/app/jobs/hyrax/file_sets/grant_read_job.rb
@@ -8,8 +8,7 @@ module Hyrax
include PermissionJobBehavior
def perform(file_set_id, group_key)
- file_set = Hyrax.query_service.find_by(id: file_set_id)
-
+ file_set = Hyrax::FileSet.find(file_set_id)
file_set.read_groups = file_set.read_groups.to_a + Array.wrap(group_key) # += works in Ruby 2.6+
file_set.try(:permission_manager)&.acl&.save
end
diff --git a/hyrax/app/jobs/hyrax/file_sets/revoke_edit_job.rb b/hyrax/app/jobs/hyrax/file_sets/revoke_edit_job.rb
index db5349c1..133bda9e 100644
--- a/hyrax/app/jobs/hyrax/file_sets/revoke_edit_job.rb
+++ b/hyrax/app/jobs/hyrax/file_sets/revoke_edit_job.rb
@@ -8,8 +8,7 @@ module Hyrax
include PermissionJobBehavior
def perform(file_set_id, group_key)
- file_set = Hyrax.query_service.find_by(id: file_set_id)
-
+ file_set = Hyrax::FileSet.find(file_set_id)
file_set.edit_groups = file_set.edit_groups.to_a - Array.wrap(group_key) # += works in Ruby 2.6+
file_set.try(:permission_manager)&.acl&.save
end
diff --git a/hyrax/app/jobs/valkyrie_ingest_job.rb b/hyrax/app/jobs/valkyrie_ingest_job.rb
index e29c2bde..33e01664 100644
--- a/hyrax/app/jobs/valkyrie_ingest_job.rb
+++ b/hyrax/app/jobs/valkyrie_ingest_job.rb
@@ -24,7 +24,7 @@ class ValkyrieIngestJob < Hyrax::ApplicationJob
# @return [void]
def ingest(file:, pcdm_use:)
file_set_uri = Valkyrie::ID.new(file.file_set_uri)
- file_set = Hyrax.query_service.find_by(id: file_set_uri)
+ file_set = Hyrax::FileSet.find(file_set_uri)
upload_file(
file: file,
file_set: file_set,
diff --git a/hyrax/app/models/bulkrax/crc_folder_complex_subject_entry.rb b/hyrax/app/models/bulkrax/crc_folder_complex_subject_entry.rb
index d96587ab..91ba8b9d 100644
--- a/hyrax/app/models/bulkrax/crc_folder_complex_subject_entry.rb
+++ b/hyrax/app/models/bulkrax/crc_folder_complex_subject_entry.rb
@@ -29,7 +29,7 @@ module Bulkrax
end
def crc1280_experiment_created?
- ::Crc1280Experiment.find_by_property(source: [self.raw_metadata['parents']]).present?
+ ::Crc1280Experiment.find_by(source: [self.raw_metadata['parents']]).present?
end
def validate_and_fix_title
diff --git a/hyrax/app/models/complex_modality.rb b/hyrax/app/models/complex_modality.rb
index c2f08822..637da4be 100644
--- a/hyrax/app/models/complex_modality.rb
+++ b/hyrax/app/models/complex_modality.rb
@@ -31,7 +31,7 @@ class ComplexModality < ActiveRecord::Base
}
def file_sets
- @file_sets ||= FileSet.where(for_complex_type: ["ComplexModality"], for_complex_identifier: [self.source_identifier])
+ @file_sets ||= Hyrax::FileSet.where(for_complex_type: ["ComplexModality"], for_complex_identifier: [self.source_identifier])
end
def s3_object_prefix
@@ -69,6 +69,6 @@ class ComplexModality < ActiveRecord::Base
end
def reindex_parent_work
- Hyrax.index_adapter.save(resource: crc1280_experiment)
+ crc1280_experiment.save_index
end
end
diff --git a/hyrax/app/models/complex_session.rb b/hyrax/app/models/complex_session.rb
index 38ecb059..2bd9dfcb 100644
--- a/hyrax/app/models/complex_session.rb
+++ b/hyrax/app/models/complex_session.rb
@@ -32,7 +32,7 @@ class ComplexSession < ActiveRecord::Base
}
def file_sets
- @file_sets ||= FileSet.where(for_complex_type: ["ComplexSession"], for_complex_identifier: [self.source_identifier])
+ @file_sets ||= Hyrax::FileSet.where(for_complex_type: ["ComplexSession"], for_complex_identifier: [self.source_identifier])
end
def display_date_recorded
@@ -74,6 +74,6 @@ class ComplexSession < ActiveRecord::Base
end
def reindex_parent_work
- Hyrax.index_adapter.save(resource: crc1280_experiment)
+ crc1280_experiment.save_index
end
end
diff --git a/hyrax/app/models/complex_subject.rb b/hyrax/app/models/complex_subject.rb
index cccbae8f..fdb2ca2e 100644
--- a/hyrax/app/models/complex_subject.rb
+++ b/hyrax/app/models/complex_subject.rb
@@ -30,11 +30,11 @@ class ComplexSubject < ActiveRecord::Base
} #Thu, 05 Dec 2024 05:36:17 +0000
def crc1280_experiment
- @crc1280_experiment ||= Crc1280Experiment.find_by_property(source: [parent_source_identifier])
+ @crc1280_experiment ||= Crc1280Experiment.find_by(source: [parent_source_identifier])
end
def file_sets
- @file_sets ||= FileSet.where(for_complex_type: ["ComplexSubject"], for_complex_identifier: [self.source_identifier])
+ @file_sets ||= Hyrax::FileSet.where(for_complex_type: ["ComplexSubject"], for_complex_identifier: [self.source_identifier])
end
def s3_object_prefix
@@ -72,6 +72,6 @@ class ComplexSubject < ActiveRecord::Base
end
def reindex_parent_work
- Hyrax.index_adapter.save(resource: crc1280_experiment)
+ crc1280_experiment.save_index
end
end
diff --git a/hyrax/app/models/concerns/common_query.rb b/hyrax/app/models/concerns/common_query.rb
new file mode 100644
index 00000000..a590fb5f
--- /dev/null
+++ b/hyrax/app/models/concerns/common_query.rb
@@ -0,0 +1,93 @@
+module CommonQuery
+ extend ActiveSupport::Concern
+
+ def parent_collections
+ return [] unless self.persisted?
+ Hyrax.query_service.custom_queries.find_parent_collections(resource: self)
+ end
+
+ def parent_work
+ Hyrax.custom_queries.find_parent_work(resource: self)
+ end
+
+ def child_filesets
+ Hyrax.custom_queries.find_child_file_sets(resource: self)
+ end
+
+
+ # save resource
+ def save
+ Hyrax.persister.save(resource: self)
+ end
+
+ def save_index
+ Hyrax.index_adapter.save(resource: self)
+ end
+
+
+ # delete resource
+ def delete
+ Hyrax.persister.delete(resource: self)
+ end
+
+ def delete_index
+ Hyrax.index_adapter.delete(resource: self)
+ end
+
+
+ # clss methods
+ class_methods do
+ def find_by(**args)
+ conditions = ["metadata @> ?"]
+ id = args.delete(:id)
+ jsonb_query = args.to_json
+
+ if id.present?
+ if valid_uuid?(id)
+ conditions << "id = '#{id}'"
+ else
+ raise Valkyrie::Persistence::ObjectNotFoundError, "Invalid or missing UUID for id=#{id}"
+ end
+ end
+
+ conditions << "internal_resource = '#{name}'"
+
+ query = <<-SQL
+ SELECT * FROM orm_resources
+ WHERE #{conditions.join(' AND ')};
+ SQL
+
+ Hyrax.query_service.run_query(query, jsonb_query).first
+ end
+
+ def where(**args)
+ query = <<-SQL
+ SELECT * FROM orm_resources
+ WHERE metadata @> ?
+ AND internal_resource = '#{name}';
+ SQL
+
+ jsonb_query = args.to_json
+ Hyrax.query_service.run_query(query, jsonb_query).to_a
+ end
+
+ def find(id)
+ unless id.present? && valid_uuid?(id)
+ raise Valkyrie::Persistence::ObjectNotFoundError, "Invalid or missing UUID for id=#{id}"
+ end
+
+ result = find_by(id: id)
+
+ if result.nil?
+ raise Valkyrie::Persistence::ObjectNotFoundError, "Couldn't find resource with id=#{id}"
+ end
+
+ result
+ end
+
+ def valid_uuid?(string)
+ uuid_regex = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i
+ uuid_regex.match?(string)
+ end
+ end
+end
diff --git a/hyrax/app/models/concerns/hyrax/tombstone_behavior.rb b/hyrax/app/models/concerns/hyrax/tombstone_behavior.rb
index 9d983f9f..12f415f7 100644
--- a/hyrax/app/models/concerns/hyrax/tombstone_behavior.rb
+++ b/hyrax/app/models/concerns/hyrax/tombstone_behavior.rb
@@ -5,8 +5,7 @@ module Hyrax
self.is_tombstoned = true
self.tombstone_status = "initiated"
self.tombstone_date = DateTime.now
-
- work = Hyrax.persister.save(resource: self)
+ work = self.save
Hyrax.publisher.publish('object.metadata.updated', object: work, user: user)
end
@@ -14,8 +13,7 @@ module Hyrax
return false unless self.is_tombstoned || self.tombstone_status == "initiated"
self.tombstone_status = "deleted"
-
- work = Hyrax.persister.save(resource: self)
+ work = self.save
Hyrax.publisher.publish('object.metadata.updated', object: work, user: user)
Hyrax::RemoveAssociatedObjectsJob.perform_later(work.id.to_s, user.id)
@@ -27,8 +25,7 @@ module Hyrax
self.is_tombstoned = false
self.tombstone_status = "restored"
-
- work = Hyrax.persister.save(resource: self)
+ work = self.save
Hyrax.publisher.publish('object.metadata.updated', object: work, user: user)
end
end
diff --git a/hyrax/app/models/concerns/rdms_roles.rb b/hyrax/app/models/concerns/rdms_roles.rb
index 35c4cbf6..4f53bef1 100644
--- a/hyrax/app/models/concerns/rdms_roles.rb
+++ b/hyrax/app/models/concerns/rdms_roles.rb
@@ -26,7 +26,7 @@ module RdmsRoles
end
def crc_manager_for?(group_id)
- group = Hyrax.query_service.find_by(id: group_id) rescue nil
+ group = Hyrax::PcdmCollection.find(group_id) rescue nil
return false unless group
@@ -35,7 +35,7 @@ module RdmsRoles
end
def group_manager_for?(group_id)
- group = Hyrax.query_service.find_by(id: group_id) rescue nil
+ group = Hyrax::PcdmCollection.find(group_id) rescue nil
return false unless group
@@ -44,7 +44,7 @@ module RdmsRoles
end
def crc_member_for?(group_id)
- group = Hyrax.query_service.find_by(id: group_id) rescue nil
+ group = Hyrax::PcdmCollection.find(group_id) rescue nil
return false unless group
@@ -53,7 +53,7 @@ module RdmsRoles
end
def group_member_for?(group_id)
- group = Hyrax.query_service.find_by(id: group_id) rescue nil
+ group = Hyrax::PcdmCollection.find(group_id) rescue nil
return false unless group
diff --git a/hyrax/app/models/concerns/s3_file_handleable.rb b/hyrax/app/models/concerns/s3_file_handleable.rb
index 73c40f99..6cccc4dc 100644
--- a/hyrax/app/models/concerns/s3_file_handleable.rb
+++ b/hyrax/app/models/concerns/s3_file_handleable.rb
@@ -75,7 +75,7 @@ module S3FileHandleable
crc1280_experiment.files_size = [total_size.to_s]
crc1280_experiment.format = list_of_format
- Hyrax.persister.save(resource: crc1280_experiment)
+ crc1280_experiment.save
end
diff --git a/hyrax/app/models/crc1280_experiment.rb b/hyrax/app/models/crc1280_experiment.rb
index d71d299f..efe74a41 100644
--- a/hyrax/app/models/crc1280_experiment.rb
+++ b/hyrax/app/models/crc1280_experiment.rb
@@ -10,7 +10,7 @@ class Crc1280Experiment < Hyrax::Work
attribute :complex_identifier , Valkyrie::Types::Array.of(Valkyrie::Types::String)
include Hyrax::Schema(:basic_metadata)
include Hyrax::Schema(:crc1280_experiment)
- include CommonWorksQuery
+ include CommonQuery
include ::Hyrax::TombstoneBehavior
include ExternalServices
include S3FileHandleable
@@ -32,22 +32,11 @@ class Crc1280Experiment < Hyrax::Work
] + CRC_FILTER_FACET_FIELDS
def default_admin_set
- AdminSetHelper.find_admin_set_by_property(title: [ENV.fetch('CRC_ADMIN_SET_TITLE', 'CRC 1280 Publishing Workflow')])
- end
-
- def self.find_by_property(**args)
- query = <<-SQL
- SELECT * FROM orm_resources
- WHERE metadata @> ?
- AND internal_resource = 'Crc1280Experiment';
- SQL
-
- jsonb_query = args.to_json
- Hyrax.query_service.run_query(query, jsonb_query).first
+ AdminSetHelper.find_by(title: [ENV.fetch('CRC_ADMIN_SET_TITLE', 'CRC 1280 Publishing Workflow')])
end
def file_sets
- @file_sets ||= FileSet.where(for_complex_type: ["Crc1280Experiment"], for_complex_identifier: self.source)
+ @file_sets ||= Hyrax::FileSet.where(for_complex_type: ["Crc1280Experiment"], for_complex_identifier: self.source)
end
def complex_subjects
@@ -63,7 +52,7 @@ class Crc1280Experiment < Hyrax::Work
end
def apply_parent_permissions
- parent = Hyrax.custom_queries.find_parent_collections(resource: self).first
+ parent = self.parent_collections.first
if parent.present?
template = Hyrax::PermissionTemplate.find_by(source_id: parent.id.to_s)
self.edit_groups += template.agent_ids_for(agent_type: 'group', access: 'manage')
diff --git a/hyrax/app/models/dataset.rb b/hyrax/app/models/dataset.rb
index b12f4b88..48f2af82 100644
--- a/hyrax/app/models/dataset.rb
+++ b/hyrax/app/models/dataset.rb
@@ -10,28 +10,17 @@ class Dataset < Hyrax::Work
attribute :complex_identifier , Valkyrie::Types::Array.of(Valkyrie::Types::String)
include Hyrax::Schema(:basic_metadata)
include Hyrax::Schema(:dataset)
- include CommonWorksQuery
+ include CommonQuery
include ::Hyrax::TombstoneBehavior
include ExternalServices
include S3FileHandleable
def default_admin_set
- AdminSetHelper.find_admin_set_by_property(title: [ENV.fetch('RUB_ADMIN_SET_TITLE', 'RUB publication workflow')])
- end
-
- def self.find_by_property(**args)
- query = <<-SQL
- SELECT * FROM orm_resources
- WHERE metadata @> ?
- AND internal_resource = 'Dataset';
- SQL
-
- jsonb_query = args.to_json
- Hyrax.query_service.run_query(query, jsonb_query).first
+ AdminSetHelper.find_by(title: [ENV.fetch('RUB_ADMIN_SET_TITLE', 'RUB publication workflow')])
end
def file_sets
- @file_sets ||= Hyrax.custom_queries.find_child_file_sets(resource: self)
+ @file_sets ||= self.child_filesets
end
end
diff --git a/hyrax/app/models/hyrax/file_set.rb b/hyrax/app/models/hyrax/file_set.rb
index f5b38e39..5cdad76c 100644
--- a/hyrax/app/models/hyrax/file_set.rb
+++ b/hyrax/app/models/hyrax/file_set.rb
@@ -51,6 +51,7 @@ module Hyrax
class FileSet < Hyrax::Resource
include Hyrax::Schema(:core_metadata)
include Hyrax::Schema(:file_set_metadata)
+ include CommonQuery
attribute :for_complex_identifier, Valkyrie::Types::String
attribute :for_complex_type, Valkyrie::Types::String
@@ -128,22 +129,6 @@ module Hyrax
true
end
- def self.where(**args)
- query = <<-SQL
- SELECT * FROM orm_resources
- WHERE metadata @> ?
- AND internal_resource = 'Hyrax::FileSet';
- SQL
-
- jsonb_query = args.to_json
-
- Hyrax.query_service.run_query(query, jsonb_query).to_a
- end
-
- def parent_work
- Hyrax.custom_queries.find_parent_work(resource: self)
- end
-
def parent_object
case for_complex_type
when 'ComplexSubject'
diff --git a/hyrax/app/models/hyrax/pcdm_collection.rb b/hyrax/app/models/hyrax/pcdm_collection.rb
index 41fe97e6..c5c213ec 100644
--- a/hyrax/app/models/hyrax/pcdm_collection.rb
+++ b/hyrax/app/models/hyrax/pcdm_collection.rb
@@ -42,6 +42,7 @@ module Hyrax
class PcdmCollection < Hyrax::Resource
include Hyrax::Schema(:core_metadata)
include Hyrax::Schema(:collection_metadata)
+ include CommonQuery
attribute :collection_type_gid, Valkyrie::Types::String
attribute :member_ids, Valkyrie::Types::Array.of(Valkyrie::Types::ID).meta(ordered: true)
@@ -94,22 +95,6 @@ module Hyrax
Role.find_by_name("#{collection_type.title.parameterize(separator: '_')}_#{id}_member")
end
- def parent_collections
- Hyrax.custom_queries.find_parent_collections(resource: self)
-
- end
-
- def self.where(**args)
- query = <<-SQL
- SELECT * FROM orm_resources
- WHERE metadata @> ?
- AND internal_resource = 'Hyrax::PcdmCollection';
- SQL
-
- jsonb_query = args.to_json
- Hyrax.query_service.run_query(query, jsonb_query)
- end
-
protected
def visibility_writer
diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index 06557226..1b1b76e8 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -238,7 +238,7 @@ class User < ApplicationRecord
private
def handle_crc_1280_manager_role(action)
- admin_set = AdminSetHelper.find_admin_set_by_property(title: [ENV.fetch('CRC_ADMIN_SET_TITLE', 'CRC 1280 Publishing Workflow')])
+ admin_set = AdminSetHelper.find_by(title: [ENV.fetch('CRC_ADMIN_SET_TITLE', 'CRC 1280 Publishing Workflow')])
add_or_remove_responsibility(admin_set, 'approving_crc_manager', action)
end
@@ -249,19 +249,19 @@ class User < ApplicationRecord
]
titles.each do |title|
- admin_set = AdminSetHelper.find_admin_set_by_property(title: [title])
+ admin_set = AdminSetHelper.find_by(title: [title])
next if admin_set.nil?
add_or_remove_responsibility(admin_set, 'approving_publication_manager', action)
end
end
def handle_group_manager_role(action)
- admin_set = AdminSetHelper.find_admin_set_by_property(title: [ENV.fetch('CRC_ADMIN_SET_TITLE', 'CRC 1280 Publishing Workflow')])
+ admin_set = AdminSetHelper.find_by(title: [ENV.fetch('CRC_ADMIN_SET_TITLE', 'CRC 1280 Publishing Workflow')])
add_or_remove_responsibility(admin_set, 'approving_group_manager', action)
end
def handle_group_member_role(action)
- admin_set = AdminSetHelper.find_admin_set_by_property(title: [ENV.fetch('CRC_ADMIN_SET_TITLE', 'CRC 1280 Publishing Workflow')])
+ admin_set = AdminSetHelper.find_by(title: [ENV.fetch('CRC_ADMIN_SET_TITLE', 'CRC 1280 Publishing Workflow')])
add_or_remove_responsibility(admin_set, 'depositor', action)
end
diff --git a/hyrax/app/presenters/hyrax/crc1280_experiment_presenter.rb b/hyrax/app/presenters/hyrax/crc1280_experiment_presenter.rb
index 79a3f411..648aa612 100644
--- a/hyrax/app/presenters/hyrax/crc1280_experiment_presenter.rb
+++ b/hyrax/app/presenters/hyrax/crc1280_experiment_presenter.rb
@@ -15,7 +15,7 @@ module Hyrax
'session' => {},
'modality' => {}
}
- experiment = Hyrax.query_service.find_by(id: self.id)
+ experiment = Crc1280Experiment.find(self.id)
# subject filter query if filter available
subject_query = build_query(subject_field_mappings, options[:filter])
diff --git a/hyrax/app/services/doi_service.rb b/hyrax/app/services/doi_service.rb
index 6c5531db..bc6fa2e0 100644
--- a/hyrax/app/services/doi_service.rb
+++ b/hyrax/app/services/doi_service.rb
@@ -66,7 +66,7 @@ class DoiService
@work.complex_identifier = @work.complex_identifier + [complex_identifier]
@work.complex_date = @work.complex_date + [complex_date]
- Hyrax.persister.save(resource: @work)
+ @work.save
Hyrax.publisher.publish('object.metadata.updated', object: @work, user: user)
end
end
\ No newline at end of file
diff --git a/hyrax/app/services/hyrax/collections/permissions_create_service.rb b/hyrax/app/services/hyrax/collections/permissions_create_service.rb
index e341d838..0d09910a 100644
--- a/hyrax/app/services/hyrax/collections/permissions_create_service.rb
+++ b/hyrax/app/services/hyrax/collections/permissions_create_service.rb
@@ -44,7 +44,7 @@ module Hyrax
# access: Hyrax::PermissionTemplateAccess::DEPOSIT } ]
# @see Hyrax::PermissionTemplateAccess for valid values for agent_type and access
def add_access(collection_id:, grants:)
- collection = Hyrax.query_service.find_by(id: collection_id)
+ collection = Hyrax::PcdmCollection.find(collection_id)
template = Hyrax::PermissionTemplate.find_by!(source_id: collection_id.to_s)
grants.each do |grant|
Hyrax::PermissionTemplateAccess.find_or_create_by(permission_template_id: template.id.to_s,
diff --git a/hyrax/app/services/hyrax/valkyrie_upload.rb b/hyrax/app/services/hyrax/valkyrie_upload.rb
index ef52eafa..ff9749c2 100644
--- a/hyrax/app/services/hyrax/valkyrie_upload.rb
+++ b/hyrax/app/services/hyrax/valkyrie_upload.rb
@@ -143,7 +143,7 @@ class Hyrax::ValkyrieUpload
# @return [Hyrax::FileSet] updated file set
def add_file_to_file_set(file_set:, file_metadata:, user:)
file_set.file_ids += [file_metadata.id]
- Hyrax.persister.save(resource: file_set)
+ file_set.save
Hyrax.publisher.publish('object.membership.updated', object: file_set, user: user)
end
diff --git a/hyrax/app/services/verify_crc_dataset_import.rb b/hyrax/app/services/verify_crc_dataset_import.rb
index 462bb017..0719695b 100644
--- a/hyrax/app/services/verify_crc_dataset_import.rb
+++ b/hyrax/app/services/verify_crc_dataset_import.rb
@@ -119,7 +119,7 @@ class VerifyCrcDatasetImport
end
# Get CrcDataset for the entry
- works = Crc1280Experiment.find_by_property(source: [entry.identifier])
+ works = Crc1280Experiment.find_by(source: [entry.identifier])
unless works.present?
msg = "The CrcDataset with source identifier #{entry.identifier} was not found"
return false, msg, paths_compared, nil
diff --git a/hyrax/app/views/hyrax/crc1280_experiments/_all_children.html.erb b/hyrax/app/views/hyrax/crc1280_experiments/_all_children.html.erb
index fa3c6712..0c9cdddd 100644
--- a/hyrax/app/views/hyrax/crc1280_experiments/_all_children.html.erb
+++ b/hyrax/app/views/hyrax/crc1280_experiments/_all_children.html.erb
@@ -1,5 +1,5 @@
<%
- member_ids = Hyrax.query_service.custom_queries.find_child_file_sets(resource: work).to_a #+ experiment.complex_subjects&.ids
+ member_ids = work.child_filesets.to_a #+ experiment.complex_subjects&.ids
%>
<% if presenter.crc_work_type.present? && presenter.crc_work_type[0] == 'experiment' %>
diff --git a/hyrax/app/views/hyrax/crc1280_experiments/_parent_collection.html.erb b/hyrax/app/views/hyrax/crc1280_experiments/_parent_collection.html.erb
index e20a5e9c..2053a322 100644
--- a/hyrax/app/views/hyrax/crc1280_experiments/_parent_collection.html.erb
+++ b/hyrax/app/views/hyrax/crc1280_experiments/_parent_collection.html.erb
@@ -1,4 +1,4 @@
-<% parent_collections = Hyrax.query_service.custom_queries.find_parent_collections(resource: collection) %>
+<% parent_collections = collection.parent_collections %>
<% if parent_collections.present? %>
<% parent_collections.each do |collection| %>
<%= render 'parent_collection', collection: collection %>
diff --git a/hyrax/app/views/hyrax/crc1280_experiments/_title.html.erb b/hyrax/app/views/hyrax/crc1280_experiments/_title.html.erb
index 09c40f39..122f7572 100644
--- a/hyrax/app/views/hyrax/crc1280_experiments/_title.html.erb
+++ b/hyrax/app/views/hyrax/crc1280_experiments/_title.html.erb
@@ -14,14 +14,6 @@
</h2>
<% end %>
<% end %>
- <div class="row">
- <% if is_published?(presenter) %>
- <div class="col-md-3">
- <%= render 'citations', presenter: @presenter %>
- <%= render 'social_media' %>
- </div>
- <% end %>
- </div>
</div>
</div>
</div>
\ No newline at end of file
diff --git a/hyrax/app/views/hyrax/crc1280_experiments/show.html.erb b/hyrax/app/views/hyrax/crc1280_experiments/show.html.erb
index 202e8e76..108f4354 100644
--- a/hyrax/app/views/hyrax/crc1280_experiments/show.html.erb
+++ b/hyrax/app/views/hyrax/crc1280_experiments/show.html.erb
@@ -1,5 +1,5 @@
<% presenter ||= @presenter %>
-<% work = Hyrax.query_service.find_by(id: presenter.id) %>
+<% work = Crc1280Experiment.find(presenter.id) %>
<% filter = params[:filter].present? ? params[:filter].permit!.to_h : {} %>
<div class="row show-work">
<div class="col-md-12 work-type">
diff --git a/hyrax/config/initializers/downloads_controller_override.rb b/hyrax/config/initializers/downloads_controller_override.rb
index 7fd9bd02..f5efb423 100644
--- a/hyrax/config/initializers/downloads_controller_override.rb
+++ b/hyrax/config/initializers/downloads_controller_override.rb
@@ -10,12 +10,12 @@ Rails.application.config.to_prepare do
use_valkyrie: Hyrax.config.use_valkyrie?
)
else
- Hyrax.query_service.find_by(id: file_set_id)
+ Hyrax::FileSet.find(file_set_id)
end
@parent ||=
case file_set
when Hyrax::Resource
- Hyrax.query_service.find_parents(resource: file_set).first
+ file_set.parent_work
else
file_set.parent
end
diff --git a/hyrax/config/initializers/riiif.rb b/hyrax/config/initializers/riiif.rb
index eace5cda..25edd426 100644
--- a/hyrax/config/initializers/riiif.rb
+++ b/hyrax/config/initializers/riiif.rb
@@ -97,8 +97,8 @@ module Hyrax
def load_file(id)
benchmark "RiiifFileResolver loaded #{id}", level: :debug do
fs_id = id.sub(/\A([^\/]*)\/.*/, '\1')
- file_set = Hyrax.query_service.find_by(id: fs_id)
- file_metadata = Hyrax.custom_queries.find_original_file(file_set: file_set)
+ file_set = Hyrax::FileSet.find(fs_id)
+ file_metadata = file_set.original_file
file_metadata.file.disk_path.to_s # Stores a local copy in tmpdir
end
end
diff --git a/hyrax/lib/tasks/default_admin_set_for_workflow.rake b/hyrax/lib/tasks/default_admin_set_for_workflow.rake
index c0a5b776..5955eabf 100644
--- a/hyrax/lib/tasks/default_admin_set_for_workflow.rake
+++ b/hyrax/lib/tasks/default_admin_set_for_workflow.rake
@@ -12,7 +12,7 @@ namespace :hyrax do
crc_default_admin_set_title = ENV.fetch('CRC_ADMIN_SET_TITLE', 'CRC 1280 Publishing Workflow')
[rub_default_admin_set_title, crc_default_admin_set_title].each do |title|
- unless AdminSetHelper.find_admin_set_by_property(title: [title]).present?
+ unless AdminSetHelper.find_by(title: [title]).present?
admin_set = Hyrax::AdministrativeSet.new(title: [title])
updated_admin_set = Hyrax.persister.save(resource: admin_set)
--
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