From 43e471e678cd1d42f9914175a951e32b18906460 Mon Sep 17 00:00:00 2001
From: Anusha Ranganathan <anusha@cottagelabs.com>
Date: Sat, 25 Feb 2023 00:35:47 +0000
Subject: [PATCH] Save ARK in metadata, remove identifier from form, DRY code
---
.env.template | 14 +++---
.env.template.development | 2 +-
hyrax/app/forms/hyrax/crc_dataset_form.rb | 14 ------
hyrax/app/forms/hyrax/dataset_form.rb | 17 +------
.../app/models/concerns/external_services.rb | 48 +++++++++++++++++++
hyrax/app/models/crc_dataset.rb | 35 +-------------
hyrax/app/models/dataset.rb | 28 ++---------
.../nested_identifier_attribute_renderer.rb | 2 +-
hyrax/app/services/ark_service.rb | 2 +-
.../services/hyrax/workflow/register_doi.rb | 9 ++--
10 files changed, 68 insertions(+), 103 deletions(-)
create mode 100644 hyrax/app/models/concerns/external_services.rb
diff --git a/.env.template b/.env.template
index 900d99c0..a017d488 100644
--- a/.env.template
+++ b/.env.template
@@ -146,6 +146,13 @@ ORCID_SANDBOX=true
# If Authorization is restricted, only existing users with an Orcid are allowed access
ORCID_RESTRICT_AUTHORIZATION=true
+# DOI
+REGISTER_DOI=true
+DOI_URL=https://api.test.datacite.org/
+DOI_USERNAME=
+DOI_PASSWORD=
+DOI_PREFIX=
+
# ARK
REGISTER_ARK=true
ARK_ENDPOINT=
@@ -155,13 +162,6 @@ ARK_NAMESPACE=
# ARK name assigning authority number
ARK_NAAN=
-# DOI
-USE_DOI_REGISTRATION=true
-DOI_URL=https://api.test.datacite.org/
-DOI_USERNAME=
-DOI_PASSWORD=
-DOI_PREFIX=
-
# Download
DOWNLOAD_SIZE_LIMIT=100000000
DOWNLOAD_PATH=tmp/downloads
diff --git a/.env.template.development b/.env.template.development
index 24346983..718a4f80 100644
--- a/.env.template.development
+++ b/.env.template.development
@@ -159,7 +159,7 @@ ARK_NAMESPACE=
ARK_NAAN=
# DOI
-USE_DOI_REGISTRATION=false
+REGISTER_DOI=false
DOI_URL=
DOI_USERNAME=
DOI_PASSWORD=
diff --git a/hyrax/app/forms/hyrax/crc_dataset_form.rb b/hyrax/app/forms/hyrax/crc_dataset_form.rb
index 21bc1512..f0335be1 100644
--- a/hyrax/app/forms/hyrax/crc_dataset_form.rb
+++ b/hyrax/app/forms/hyrax/crc_dataset_form.rb
@@ -28,7 +28,6 @@ module Hyrax
:approval_number,
:extra_information,
:modality,
- :complex_identifier,
:complex_date,
:subject,
:publisher,
@@ -153,17 +152,6 @@ module Hyrax
]
end
- def self.permitted_identifier_params
- [:id,
- :_destroy,
- {
- identifier: [],
- scheme: [],
- label: []
- }
- ]
- end
-
def self.permitted_person_params
[:id,
:_destroy,
@@ -186,7 +174,6 @@ module Hyrax
{
title: [],
url: [],
- complex_identifier_attributes: permitted_identifier_params,
relationship: []
}
]
@@ -219,7 +206,6 @@ module Hyrax
permitted << :experiment_title
permitted << :experiment_description
permitted << { complex_date_attributes: permitted_date_params }
- permitted << { complex_identifier_attributes: permitted_identifier_params }
permitted << { complex_person_attributes: permitted_person_params }
permitted << { complex_relation_attributes: permitted_relation_params }
permitted << { complex_funding_reference_attributes: permitted_fundref_params }
diff --git a/hyrax/app/forms/hyrax/dataset_form.rb b/hyrax/app/forms/hyrax/dataset_form.rb
index 0581287b..260cd125 100644
--- a/hyrax/app/forms/hyrax/dataset_form.rb
+++ b/hyrax/app/forms/hyrax/dataset_form.rb
@@ -37,7 +37,6 @@ module Hyrax
# :technical_information,
:based_near,
:complex_funding_reference,
- :complex_identifier,
:publisher,
:doi,
]
@@ -73,8 +72,7 @@ module Hyrax
def references_tab_terms
[
# Related Items, ID
- :complex_relation,
- :complex_identifier,
+ :complex_relation
]
end
@@ -96,17 +94,6 @@ module Hyrax
]
end
- def self.permitted_identifier_params
- [:id,
- :_destroy,
- {
- identifier: [],
- scheme: [],
- label: []
- }
- ]
- end
-
def self.permitted_person_params
[:id,
:_destroy,
@@ -129,7 +116,6 @@ module Hyrax
{
title: [],
url: [],
- complex_identifier_attributes: permitted_identifier_params,
relationship: []
}
]
@@ -152,7 +138,6 @@ module Hyrax
permitted = super
permitted << :doi
permitted << { complex_date_attributes: permitted_date_params }
- permitted << { complex_identifier_attributes: permitted_identifier_params }
permitted << { complex_person_attributes: permitted_person_params }
permitted << { complex_relation_attributes: permitted_relation_params }
permitted << { complex_funding_reference_attributes: permitted_fundref_params }
diff --git a/hyrax/app/models/concerns/external_services.rb b/hyrax/app/models/concerns/external_services.rb
new file mode 100644
index 00000000..d5a1168e
--- /dev/null
+++ b/hyrax/app/models/concerns/external_services.rb
@@ -0,0 +1,48 @@
+module ExternalServices
+ extend ActiveSupport::Concern
+
+ included do
+
+ def register_ark
+ return true if ENV.fetch('REGISTER_ARK', 'true') == 'false'
+ ark = ArkService.new
+ ark.authenticate
+
+ creators = self.complex_person.map{|person| "#{person.first_name.first},#{person.last_name.first}" }.compact
+
+ metadata = {
+ 'creator': creators.join(';'),
+ 'title': self.title.first,
+ 'date_created': self.create_date
+ }
+ url = "#{ENV['APPLICATION_URL']}/concern/crc_datasets/#{self.id}"
+ resp = ark.create_ark(self.id, url, metadata)
+ if resp and resp[0]
+ # Save ark to metadata
+ complex_identifier = ComplexIdentifier.new(RDF::Node.new, ActiveTriples::Resource.new)
+ complex_identifier.identifier = resp[2]
+ complex_identifier.scheme = 'ARK'
+ self.update(complex_identifier: [complex_identifier])
+ self.save
+ end
+ end
+
+ def total_file_size
+ s3 = S3StorageService.new
+ s3.init_client
+ bucket_name = s3.sanitise_name(self.id)
+ return 0 unless s3.bucket_exists?(bucket_name)
+ _list_of_objects, size = s3.list_all_objects(bucket_name)
+ size
+ end
+
+ def save_work_meta_json_file_to_s3
+ s3 = S3StorageService.new
+ s3.init_client
+ bucket_name = s3.sanitise_name(id)
+ s3.create_bucket(bucket_name) unless s3.bucket_exists?(bucket_name)
+ s3.add_content(bucket_name, 'metadata.json', to_json)
+ end
+
+ end
+end
\ No newline at end of file
diff --git a/hyrax/app/models/crc_dataset.rb b/hyrax/app/models/crc_dataset.rb
index e1dd279f..63748473 100644
--- a/hyrax/app/models/crc_dataset.rb
+++ b/hyrax/app/models/crc_dataset.rb
@@ -5,6 +5,7 @@
class CrcDataset < ActiveFedora::Base
include ::Hyrax::WorkBehavior
include ::Hyrax::TombstoneBehavior
+ include ExternalServices
self.indexer = CrcDatasetIndexer
# Change this to restrict which works can be added as a child.
# self.valid_child_concerns = []
@@ -12,7 +13,7 @@ class CrcDataset < ActiveFedora::Base
after_save :save_work_meta_json_file_to_s3
after_create :set_default_source_and_tombstone_status
- after_create :update_ark
+ after_create :register_ark
# ------ properties from core metadata ------
# property date_modified - not displayed (filled in by the system)
@@ -149,42 +150,10 @@ class CrcDataset < ActiveFedora::Base
private
- def save_work_meta_json_file_to_s3
- s3 = S3StorageService.new
- s3.init_client
- bucket_name = s3.sanitise_name(id)
- s3.create_bucket(bucket_name) unless s3.bucket_exists?(bucket_name)
- s3.add_content(bucket_name, 'metadata.json', to_json)
- end
-
def set_default_source_and_tombstone_status
self.source = source.present? ? source : [SecureRandom.uuid]
self.is_tombstoned = false
self.save
end
- def update_ark
- ark = ArkService.new
- ark.authenticate
-
- creators = self.complex_person.map{|person| "#{person.first_name.first},#{person.last_name.first}" }.compact
-
- metadata = {
- 'creator': creators.join(';'),
- 'title': self.title.first,
- 'date_created': self.create_date
- }
- url = "#{ENV['APPLICATION_URL']}/concern/crc_datasets/#{self.id}"
- ark.create_ark(self.id, url, metadata)
- end
-
- def total_file_size
- s3 = S3StorageService.new
- s3.init_client
- bucket_name = s3.sanitise_name(self.id)
- return 0 unless s3.bucket_exists?(bucket_name)
- _list_of_objects, size = s3.list_all_objects(bucket_name)
- size
- end
-
end
diff --git a/hyrax/app/models/dataset.rb b/hyrax/app/models/dataset.rb
index bf258dc7..af76216e 100644
--- a/hyrax/app/models/dataset.rb
+++ b/hyrax/app/models/dataset.rb
@@ -4,13 +4,16 @@ require "./lib/vocabularies/rdms"
class Dataset < ActiveFedora::Base
include ::Hyrax::WorkBehavior
include ::Hyrax::TombstoneBehavior
+ include ExternalServices
self.indexer = DatasetIndexer
# Change this to restrict which works can be added as a child.
# self.valid_child_concerns = []
validates :title, presence: { message: 'Your dataset must have a title.' }
+ after_save :save_work_meta_json_file_to_s3
after_create :set_default_tombstone_status
- after_create :update_ark
+ after_create :register_ark
+
# ------ properties from core metadata ------
# property date_modified - not displayed (filled in by the system)
# property date_uploaded - not displayed (filled in by the system)
@@ -113,15 +116,6 @@ class Dataset < ActiveFedora::Base
accepts_nested_attributes_for :complex_relation, reject_if: :relation_blank, allow_destroy: true
accepts_nested_attributes_for :updated_subresources, allow_destroy: true
- def total_file_size
- s3 = S3StorageService.new
- s3.init_client
- bucket_name = s3.sanitise_name(self.id)
- return 0 unless s3.bucket_exists?(bucket_name)
- _list_of_objects, size = s3.list_all_objects(bucket_name)
- size
- end
-
private
def set_default_tombstone_status
@@ -129,18 +123,4 @@ class Dataset < ActiveFedora::Base
self.save
end
- def update_ark
- ark = ArkService.new
- ark.authenticate
-
- creators = self.complex_person.map{|person| "#{person.last_name.first},#{person.first_name.first}" }.compact
- metadata = {
- creator: creators.join(';'),
- title: self.title.first,
- date_created: self.create_date
- }
- url = "#{ENV['APPLICATION_URL']}/concern/datasets/#{self.id}"
- ark.create_ark(self.id, url, metadata)
- end
-
end
diff --git a/hyrax/app/renderers/nested_identifier_attribute_renderer.rb b/hyrax/app/renderers/nested_identifier_attribute_renderer.rb
index 31070367..744abbfb 100644
--- a/hyrax/app/renderers/nested_identifier_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_identifier_attribute_renderer.rb
@@ -13,7 +13,7 @@ class NestedIdentifierAttributeRenderer < NestedAttributeRenderer
end
unless v.dig('identifier').blank?
- val = v['identifier'][0]
+ val = link_to(v['identifier'][0], v['identifier'][0])
end
html += get_row(scheme, val)
diff --git a/hyrax/app/services/ark_service.rb b/hyrax/app/services/ark_service.rb
index 31c91a13..c532f160 100644
--- a/hyrax/app/services/ark_service.rb
+++ b/hyrax/app/services/ark_service.rb
@@ -191,7 +191,7 @@ class ArkService
# request.body = data
request.set_form_data(data)
success, _response_body, _response = _do_request(request)
- return success, _response_body
+ return success, _response_body, uri.to_s
end
def _prepare_metadata(where, work_url, metadata)
diff --git a/hyrax/app/services/hyrax/workflow/register_doi.rb b/hyrax/app/services/hyrax/workflow/register_doi.rb
index f1cbd706..bdef119a 100644
--- a/hyrax/app/services/hyrax/workflow/register_doi.rb
+++ b/hyrax/app/services/hyrax/workflow/register_doi.rb
@@ -11,18 +11,15 @@ module Hyrax
# Genrate DOI for dataset
module RegisterDoi
def self.call(target:, **)
- return true unless ENV['USE_DOI_REGISTRATION']
+ return true if ENV.fetch('REGISTER_DOI', 'true') == 'false'
@dataset = target
- collection = @dataset.parent_collections.first
- collection_type = collection&.collection_type&.title
url = URI(ENV['DOI_URL'])
http = Net::HTTP.new(url.host, url.port)
http.use_ssl = true
- creators = @dataset.complex_person.select { |person| person.role == ['creator'] }
- creators_hash = creators.map do |person|
+ creators_hash = @dataset.complex_person.map do |person|
{ name: "#{person.last_name.first},#{person.first_name.first}" }
end.compact
@@ -38,7 +35,7 @@ module Hyrax
"doi": "#{ENV['DOI_PREFIX']}/#{@dataset.id}",
"creators": creators_hash,
"titles": [{ title: @dataset.title&.first }],
- "publisher": collection_type == 'CRC 1280' ? 'SFB1280' : 'Ruhr-University Bochum',
+ "publisher": @dataset.publisher&.first || 'Ruhr-University Bochum',
"publicationYear": Date.today.year,
"types": {
"resourceTypeGeneral": @dataset.resource_type&.first
--
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