From c36a1f42447de472173227a505df2afebce31384 Mon Sep 17 00:00:00 2001
From: jrhoads <jrhoads@datacite.org>
Date: Thu, 24 Feb 2022 14:36:06 -0500
Subject: [PATCH 1/9] Reference repositoy first pass

---
 app/models/reference_repository.rb                    | 11 +++++++++++
 .../20220218154500_create_reference_repositories.rb   | 10 ++++++++++
 db/schema.rb                                          | 11 ++++++++++-
 spec/models/reference_repository_spec.rb              |  5 +++++
 4 files changed, 36 insertions(+), 1 deletion(-)
 create mode 100644 app/models/reference_repository.rb
 create mode 100644 db/migrate/20220218154500_create_reference_repositories.rb
 create mode 100644 spec/models/reference_repository_spec.rb

diff --git a/app/models/reference_repository.rb b/app/models/reference_repository.rb
new file mode 100644
index 000000000..c63e57577
--- /dev/null
+++ b/app/models/reference_repository.rb
@@ -0,0 +1,11 @@
+class ReferenceRepository < ApplicationRecord
+    include Hashid::Rails
+    validates_uniqueness_of :re3doi, :allow_nil => true
+
+    def client
+        @client ||= Client.find_by_id(self[:client_id])
+    end
+    def re3repo
+        @re3repo ||= DataCatalog.find_by_id(self[:re3doi])
+    end
+end
diff --git a/db/migrate/20220218154500_create_reference_repositories.rb b/db/migrate/20220218154500_create_reference_repositories.rb
new file mode 100644
index 000000000..3b7855107
--- /dev/null
+++ b/db/migrate/20220218154500_create_reference_repositories.rb
@@ -0,0 +1,10 @@
+class CreateReferenceRepositories < ActiveRecord::Migration[5.2]
+  def change
+    create_table :reference_repositories do |t|
+      t.string :client_id, null:true
+      t.string :re3doi, null:true
+
+      t.timestamps
+    end
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index f55b1eeb4..fb9c61950 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -13,7 +13,8 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 2022_02_17_020855) do
+ActiveRecord::Schema.define(version: 2022_02_18_154500) do
+
   create_table "active_storage_attachments", options: "ENGINE=InnoDB DEFAULT CHARSET=latin1", force: :cascade do |t|
     t.string "name", limit: 191, null: false
     t.string "record_type", null: false
@@ -301,4 +302,12 @@
     t.index ["provider_id"], name: "FKE7FBD67446EBD781"
     t.index ["uid"], name: "index_provider_prefixes_on_uid", length: 128
   end
+
+  create_table "reference_repositories", options: "ENGINE=InnoDB DEFAULT CHARSET=latin1", force: :cascade do |t|
+    t.string "client_id"
+    t.string "re3doi"
+    t.datetime "created_at", null: false
+    t.datetime "updated_at", null: false
+  end
+
 end
diff --git a/spec/models/reference_repository_spec.rb b/spec/models/reference_repository_spec.rb
new file mode 100644
index 000000000..e85048bb5
--- /dev/null
+++ b/spec/models/reference_repository_spec.rb
@@ -0,0 +1,5 @@
+require 'rails_helper'
+
+RSpec.describe ReferenceRepository, type: :model do
+  pending "add some examples to (or delete) #{__FILE__}"
+end

From 8af6e5f446ab1656ed6df4e796baab3dbe30ec30 Mon Sep 17 00:00:00 2001
From: jrhoads <jrhoads@datacite.org>
Date: Fri, 25 Feb 2022 10:53:47 -0500
Subject: [PATCH 2/9] Initial indexing for reference_repositories

---
 app/models/reference_repository.rb            | 41 +++++++++--
 .../reference_repository_denormalizer.rb      | 72 +++++++++++++++++++
 2 files changed, 109 insertions(+), 4 deletions(-)
 create mode 100644 app/models/reference_repository_denormalizer.rb

diff --git a/app/models/reference_repository.rb b/app/models/reference_repository.rb
index c63e57577..9eed77dac 100644
--- a/app/models/reference_repository.rb
+++ b/app/models/reference_repository.rb
@@ -1,11 +1,44 @@
 class ReferenceRepository < ApplicationRecord
+    include Elasticsearch::Model
+    include Elasticsearch::Model::Callbacks
     include Hashid::Rails
+
+    before_save :force_index
+
     validates_uniqueness_of :re3doi, :allow_nil => true
 
-    def client
-        @client ||= Client.find_by_id(self[:client_id])
+    def client_repo
+        if @dsclient&.symbol == self[:client_id]
+            @dsclient
+        else
+            @dsclient = ::Client.where(symbol: self[:client_id]).where(deleted_at: nil).first
+        end
     end
-    def re3repo
-        @re3repo ||= DataCatalog.find_by_id(self[:re3doi])
+
+    def re3_repo
+        @re3repo ||= DataCatalog.find_by_id(self[:re3doi]).fetch(:data, []).first
+    end
+
+    def as_indexed_json(_options = {})
+        ReferenceRepositoryDenormalizer.new(self).to_hash
+    end
+
+    settings index: { number_of_shards: 1 } do
+        mapping dynamic: 'false' do
+            indexes :id
+            indexes :client_id
+            indexes :re3doi
+            indexes :re3data_url
+            indexes :created_at, type: :date, format: :date_optional_time
+            indexes :updated_at, type: :date, format: :date_optional_time
+            indexes :name
+            indexes :description
+            indexes :pid_system, type: :keyword
+            indexes :url
+        end
+    end
+
+    def force_index
+      __elasticsearch__.instance_variable_set(:@__changed_model_attributes, nil)
     end
 end
diff --git a/app/models/reference_repository_denormalizer.rb b/app/models/reference_repository_denormalizer.rb
new file mode 100644
index 000000000..209a22655
--- /dev/null
+++ b/app/models/reference_repository_denormalizer.rb
@@ -0,0 +1,72 @@
+class ReferenceRepositoryDenormalizer
+    attr_reader :repository
+
+    def initialize(repository)
+        @repository = repository
+    end
+
+    def to_hash
+        %w[
+            id
+            client_id
+            re3doi
+            re3data_url
+            created_at
+            updated_at
+            name
+            description
+            pid_system
+            url
+        ].map { |method_name| [ method_name, send(method_name)] }.to_h
+    end
+
+    def id
+        @repository.hashid
+    end
+
+    def client_id
+        @repository.client_id
+    end
+
+    def re3doi
+        @repository.re3doi
+    end
+
+    def created_at
+        @repository.created_at
+    end
+
+    def updated_at
+        @repository.updated_at
+    end
+
+    def name
+        @repository.client_repo&.name || @repository.re3_repo.name
+    end
+
+    def description
+        @repository.client_repo&.description || @repository.re3_repo&.description
+    end
+
+    def url
+        @repository.client_repo&.url || @repository.re3_repo&.url
+    end
+
+    def re3data_url
+        doi_as_url
+    end
+
+    def pid_system
+        ret = Array.wrap(@repository.re3_repo&.pid_systems).map { |k| k.text }
+        ret += Array.wrap(@repository.client_id.nil? ? nil : 'DOI')
+        ret.uniq
+    end
+
+    def doi_as_url
+        doi = @repository.re3doi
+        return nil if doi.blank?
+        "https://doi.org/#{doi.downcase}"
+    end
+
+
+end

From c9d72aefd6fbb9fd52b363b91cc8f258a20b3659 Mon Sep 17 00:00:00 2001
From: jrhoads <jrhoads@datacite.org>
Date: Fri, 4 Mar 2022 12:08:33 -0500
Subject: [PATCH 3/9] Index additional fields for reference_repositories

---
 app/models/reference_repository.rb            | 11 ++++
 .../reference_repository_denormalizer.rb      | 63 +++++++++++++++++--
 2 files changed, 70 insertions(+), 4 deletions(-)

diff --git a/app/models/reference_repository.rb b/app/models/reference_repository.rb
index 9eed77dac..abc3919ad 100644
--- a/app/models/reference_repository.rb
+++ b/app/models/reference_repository.rb
@@ -35,6 +35,17 @@ def as_indexed_json(_options = {})
             indexes :description
             indexes :pid_system, type: :keyword
             indexes :url
+            indexes :keyword, type: :keyword
+            indexes :subject
+            indexes :contact
+            indexes :language, type: :keyword
+            indexes :certificate, type: :keyword
+            indexes :data_access, type: :keyword
+            indexes :data_upload, type: :keyword
+            indexes :provider_type, type: :keyword
+            indexes :repository_type, type: :keyword
+            indexes :data_upload_licenses, type: :keyword
+            indexes :software, type: :keyword
         end
     end
 
diff --git a/app/models/reference_repository_denormalizer.rb b/app/models/reference_repository_denormalizer.rb
index 209a22655..832bb291d 100644
--- a/app/models/reference_repository_denormalizer.rb
+++ b/app/models/reference_repository_denormalizer.rb
@@ -5,6 +5,12 @@ def initialize(repository)
         @repository = repository
     end
 
+    def doi_as_url
+        doi = @repository.re3doi
+        return nil if doi.blank?
+        "https://doi.org/#{doi.downcase}"
+    end
+
     def to_hash
         %w[
             id
@@ -17,6 +23,16 @@ def to_hash
             description
             pid_system
             url
+            keyword
+            contact
+            software
+            language
+            certificate
+            data_access
+            data_upload
+            provider_type
+            repository_type
+            subject
         ].map { |method_name| [ method_name, send(method_name)] }.to_h
     end
 
@@ -62,11 +78,50 @@ def pid_system
         ret.uniq
     end
 
-    def doi_as_url
-        doi = @repository.re3doi
-        return nil if doi.blank?
-        "https://doi.org/#{doi.downcase}"
+    def keyword
+        ret = Array.wrap(@repository.re3_repo&.keywords).map { |k| k.text }
+        ret.uniq
+    end
+
+    def contact
+        ret = Array.wrap(@repository.re3_repo&.contacts).map { |k| k.text}
+        ret.uniq
     end
 
+    def language
+        ret = Array.wrap(@repository.re3_repo&.repository_languages).map { |k| k.text }
+        ret += Array.wrap(@repository.client_repo&.language)
+        ret.uniq
+    end
 
+    def certificate
+        ret = Array.wrap(@repository.re3_repo&.certificates).map { |k| k.text }
+        ret += Array.wrap(@repository.client_repo&.certificate)
+        ret.uniq
+    end
+
+    def software
+        ret = Array.wrap(@repository.re3_repo&.software).map { |k| k.name }
+        ret.uniq
+    end
+
+    def data_access
+        Array.wrap(@repository.re3_repo&.data_accesses).map { |k| k.type }
+    end
+
+    def data_upload
+        Array.wrap(@repository.re3_repo&.data_uploads).map { |k| k.type }
+    end
+
+    def provider_type
+        Array.wrap(@repository.re3_repo&.provider_type).map { |k| k.text }
+    end
+
+    def repository_type
+        Array.wrap(@repository.re3_repo&.types).map { |k| k.text }
+    end
+
+    def subject
+        Array.wrap(@repository.re3_repo&.subjects).map { |k| k.text }
+    end
 end

From 3f3aadeb504e34b827d2e3511bd53291d0892974 Mon Sep 17 00:00:00 2001
From: jrhoads <jrhoads@datacite.org>
Date: Tue, 8 Mar 2022 21:03:35 -0500
Subject: [PATCH 4/9] Refactor into class methods

---
 app/models/reference_repository.rb | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/app/models/reference_repository.rb b/app/models/reference_repository.rb
index abc3919ad..c4bf7b440 100644
--- a/app/models/reference_repository.rb
+++ b/app/models/reference_repository.rb
@@ -7,16 +7,24 @@ class ReferenceRepository < ApplicationRecord
 
     validates_uniqueness_of :re3doi, :allow_nil => true
 
+    def self.find_client(client_id)
+        ::Client.where(symbol: client_id).where(deleted_at: nil).first
+    end
+
+    def self.find_re3(doi)
+        DataCatalog.find_by_id(doi).fetch(:data, []).first
+    end
+
     def client_repo
         if @dsclient&.symbol == self[:client_id]
             @dsclient
         else
-            @dsclient = ::Client.where(symbol: self[:client_id]).where(deleted_at: nil).first
+            @dsclient = ReferenceRepository.find_client(self[:client_id])
         end
     end
 
     def re3_repo
-        @re3repo ||= DataCatalog.find_by_id(self[:re3doi]).fetch(:data, []).first
+        @re3repo ||= ReferenceRepository.find_re3(self[:re3doi])
     end
 
     def as_indexed_json(_options = {})

From 6befd21a30ed2a7a2d89079d61f0e4d41d0bd46f Mon Sep 17 00:00:00 2001
From: jrhoads <jrhoads@datacite.org>
Date: Tue, 8 Mar 2022 21:04:31 -0500
Subject: [PATCH 5/9] Guard against nil

---
 app/models/reference_repository_denormalizer.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/reference_repository_denormalizer.rb b/app/models/reference_repository_denormalizer.rb
index 832bb291d..639046102 100644
--- a/app/models/reference_repository_denormalizer.rb
+++ b/app/models/reference_repository_denormalizer.rb
@@ -57,7 +57,7 @@ def updated_at
     end
 
     def name
-        @repository.client_repo&.name || @repository.re3_repo.name
+        @repository.client_repo&.name || @repository.re3_repo&.name
     end
 
     def description

From 66cf3797f94a7fa9ebaeb31108fd2a136d3b5ad6 Mon Sep 17 00:00:00 2001
From: jrhoads <jrhoads@datacite.org>
Date: Tue, 8 Mar 2022 21:05:42 -0500
Subject: [PATCH 6/9] Add rake tasks to load Client and Re3data Repositories
 into ReferenceRepositories

---
 lib/tasks/repository.rake | 44 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 lib/tasks/repository.rake

diff --git a/lib/tasks/repository.rake b/lib/tasks/repository.rake
new file mode 100644
index 000000000..99aa2d486
--- /dev/null
+++ b/lib/tasks/repository.rake
@@ -0,0 +1,44 @@
+namespace :repository do
+  desc "Load all Clients into Reference Repostories"
+  task load_client_repos: :environment do
+    puts "Processing Client Repositories"
+    progressbar = ProgressBar.create(
+      format: "%a %e %P% Processed: %c from %C %t",
+      title: "Client Repositories",
+      total: Client.all.count
+    )
+    Client.all.each do |c|
+      progressbar.increment
+      ReferenceRepository.find_or_create_by(
+        client_id: c.symbol,
+        re3doi: c.re3data_id
+      )
+    end
+  end
+
+  desc "Load all Re3data Repositories into Reference Repostories"
+  task :load_re3data_repos, [:pages] => :environment do |t, args|
+    pages = (args[:pages] || 3).to_i
+    re3repos = []
+    (1..pages).each do |page|
+      puts "Fetching Re3Data Repositories: Fetch Group #{page}"
+      re3repos += DataCatalog.query("", limit: 1000, offset:page).fetch(:data, [])
+    end
+    re3repos.uniq!
+    puts "Processing Re3Data Repositories"
+    progressbar = ProgressBar.create(
+      format: "%a %e %P% Processed: %c from %C %t",
+      title: "Re3data Repositories",
+      total: re3repos.length
+    )
+    re3repos.each  do |repo|
+      progressbar.increment
+      doi = repo.id&.gsub('https://doi.org/','')
+      if not doi.blank?
+        ReferenceRepository.find_or_create_by(
+          re3doi: doi
+        )
+      end
+    end
+  end
+end

From 13a976d6e2fb7385dd25504fcb24afbe38c41418 Mon Sep 17 00:00:00 2001
From: jrhoads <jrhoads@datacite.org>
Date: Tue, 8 Mar 2022 22:06:13 -0500
Subject: [PATCH 7/9] Appease the rubocop

---
 app/models/reference_repository.rb            | 102 +++----
 .../reference_repository_denormalizer.rb      | 252 +++++++++---------
 ...218154500_create_reference_repositories.rb |   6 +-
 db/schema.rb                                  |   2 -
 lib/tasks/repository.rake                     |   6 +-
 spec/models/reference_repository_spec.rb      |   4 +-
 6 files changed, 190 insertions(+), 182 deletions(-)

diff --git a/app/models/reference_repository.rb b/app/models/reference_repository.rb
index c4bf7b440..e8aa5fa72 100644
--- a/app/models/reference_repository.rb
+++ b/app/models/reference_repository.rb
@@ -1,63 +1,65 @@
+# frozen_string_literal: true
+
 class ReferenceRepository < ApplicationRecord
-    include Elasticsearch::Model
-    include Elasticsearch::Model::Callbacks
-    include Hashid::Rails
+  include Elasticsearch::Model
+  include Elasticsearch::Model::Callbacks
+  include Hashid::Rails
 
-    before_save :force_index
+  before_save :force_index
 
-    validates_uniqueness_of :re3doi, :allow_nil => true
+  validates_uniqueness_of :re3doi, allow_nil: true
 
-    def self.find_client(client_id)
-        ::Client.where(symbol: client_id).where(deleted_at: nil).first
-    end
+  def self.find_client(client_id)
+    ::Client.where(symbol: client_id).where(deleted_at: nil).first
+  end
 
-    def self.find_re3(doi)
-        DataCatalog.find_by_id(doi).fetch(:data, []).first
-    end
+  def self.find_re3(doi)
+    DataCatalog.find_by_id(doi).fetch(:data, []).first
+  end
 
-    def client_repo
-        if @dsclient&.symbol == self[:client_id]
-            @dsclient
-        else
-            @dsclient = ReferenceRepository.find_client(self[:client_id])
-        end
+  def client_repo
+    if @dsclient&.symbol == self[:client_id]
+      @dsclient
+    else
+      @dsclient = ReferenceRepository.find_client(self[:client_id])
     end
+  end
 
-    def re3_repo
-        @re3repo ||= ReferenceRepository.find_re3(self[:re3doi])
-    end
+  def re3_repo
+    @re3repo ||= ReferenceRepository.find_re3(self[:re3doi])
+  end
 
-    def as_indexed_json(_options = {})
-        ReferenceRepositoryDenormalizer.new(self).to_hash
-    end
+  def as_indexed_json(_options = {})
+    ReferenceRepositoryDenormalizer.new(self).to_hash
+  end
 
-    settings index: { number_of_shards: 1 } do
-        mapping dynamic: 'false' do
-            indexes :id
-            indexes :client_id
-            indexes :re3doi
-            indexes :re3data_url
-            indexes :created_at, type: :date, format: :date_optional_time
-            indexes :updated_at, type: :date, format: :date_optional_time
-            indexes :name
-            indexes :description
-            indexes :pid_system, type: :keyword
-            indexes :url
-            indexes :keyword, type: :keyword
-            indexes :subject
-            indexes :contact
-            indexes :language, type: :keyword
-            indexes :certificate, type: :keyword
-            indexes :data_access, type: :keyword
-            indexes :data_upload, type: :keyword
-            indexes :provider_type, type: :keyword
-            indexes :repository_type, type: :keyword
-            indexes :data_upload_licenses, type: :keyword
-            indexes :software, type: :keyword
-        end
+  settings index: { number_of_shards: 1 } do
+    mapping dynamic: "false" do
+      indexes :id
+      indexes :client_id
+      indexes :re3doi
+      indexes :re3data_url
+      indexes :created_at, type: :date, format: :date_optional_time
+      indexes :updated_at, type: :date, format: :date_optional_time
+      indexes :name
+      indexes :description
+      indexes :pid_system, type: :keyword
+      indexes :url
+      indexes :keyword, type: :keyword
+      indexes :subject
+      indexes :contact
+      indexes :language, type: :keyword
+      indexes :certificate, type: :keyword
+      indexes :data_access, type: :keyword
+      indexes :data_upload, type: :keyword
+      indexes :provider_type, type: :keyword
+      indexes :repository_type, type: :keyword
+      indexes :data_upload_licenses, type: :keyword
+      indexes :software, type: :keyword
     end
+  end
 
-    def force_index
-      __elasticsearch__.instance_variable_set(:@__changed_model_attributes, nil)
-    end
+  def force_index
+    __elasticsearch__.instance_variable_set(:@__changed_model_attributes, nil)
+  end
 end
diff --git a/app/models/reference_repository_denormalizer.rb b/app/models/reference_repository_denormalizer.rb
index 639046102..cc07fd567 100644
--- a/app/models/reference_repository_denormalizer.rb
+++ b/app/models/reference_repository_denormalizer.rb
@@ -1,127 +1,129 @@
+# frozen_string_literal: true
+
 class ReferenceRepositoryDenormalizer
-    attr_reader :repository
-
-    def initialize(repository)
-        @repository = repository
-    end
-
-    def doi_as_url
-        doi = @repository.re3doi
-        return nil if doi.blank?
-        "https://doi.org/#{doi.downcase}"
-    end
-
-    def to_hash
-        %w[
-            id
-            client_id
-            re3doi
-            re3data_url
-            created_at
-            updated_at
-            name
-            description
-            pid_system
-            url
-            keyword
-            contact
-            software
-            language
-            certificate
-            data_access
-            data_upload
-            provider_type
-            repository_type
-            subject
-        ].map { |method_name| [ method_name, send(method_name)] }.to_h
-    end
-
-    def id
-        @repository.hashid
-    end
-
-    def client_id
-        @repository.client_id
-    end
-
-    def re3doi
-        @repository.re3doi
-    end
-
-    def created_at
-        @repository.created_at
-    end
-
-    def updated_at
-        @repository.updated_at
-    end
-
-    def name
-        @repository.client_repo&.name || @repository.re3_repo&.name
-    end
-
-    def description
-        @repository.client_repo&.description || @repository.re3_repo&.description
-    end
-
-    def url
-        @repository.client_repo&.url || @repository.re3_repo&.url
-    end
-
-    def re3data_url
-        doi_as_url
-    end
-
-    def pid_system
-        ret = Array.wrap(@repository.re3_repo&.pid_systems).map { |k| k.text }
-        ret += Array.wrap(@repository.client_id.nil? ? nil : 'DOI')
-        ret.uniq
-    end
-
-    def keyword
-        ret = Array.wrap(@repository.re3_repo&.keywords).map { |k| k.text }
-        ret.uniq
-    end
-
-    def contact
-        ret = Array.wrap(@repository.re3_repo&.contacts).map { |k| k.text}
-        ret.uniq
-    end
-
-    def language
-        ret = Array.wrap(@repository.re3_repo&.repository_languages).map { |k| k.text }
-        ret += Array.wrap(@repository.client_repo&.language)
-        ret.uniq
-    end
-
-    def certificate
-        ret = Array.wrap(@repository.re3_repo&.certificates).map { |k| k.text }
-        ret += Array.wrap(@repository.client_repo&.certificate)
-        ret.uniq
-    end
-
-    def software
-        ret = Array.wrap(@repository.re3_repo&.software).map { |k| k.name }
-        ret.uniq
-    end
-
-    def data_access
-        Array.wrap(@repository.re3_repo&.data_accesses).map { |k| k.type }
-    end
-
-    def data_upload
-        Array.wrap(@repository.re3_repo&.data_uploads).map { |k| k.type }
-    end
-
-    def provider_type
-        Array.wrap(@repository.re3_repo&.provider_type).map { |k| k.text }
-    end
-
-    def repository_type
-        Array.wrap(@repository.re3_repo&.types).map { |k| k.text }
-    end
-
-    def subject
-        Array.wrap(@repository.re3_repo&.subjects).map { |k| k.text }
-    end
+  attr_reader :repository
+
+  def initialize(repository)
+    @repository = repository
+  end
+
+  def doi_as_url
+    doi = @repository.re3doi
+    return nil if doi.blank?
+    "https://doi.org/#{doi.downcase}"
+  end
+
+  def to_hash
+    %w[
+        id
+        client_id
+        re3doi
+        re3data_url
+        created_at
+        updated_at
+        name
+        description
+        pid_system
+        url
+        keyword
+        contact
+        software
+        language
+        certificate
+        data_access
+        data_upload
+        provider_type
+        repository_type
+        subject
+    ].map { |method_name| [ method_name, send(method_name)] }.to_h
+  end
+
+  def id
+    @repository.hashid
+  end
+
+  def client_id
+    @repository.client_id
+  end
+
+  def re3doi
+    @repository.re3doi
+  end
+
+  def created_at
+    @repository.created_at
+  end
+
+  def updated_at
+    @repository.updated_at
+  end
+
+  def name
+    @repository.client_repo&.name || @repository.re3_repo&.name
+  end
+
+  def description
+    @repository.client_repo&.description || @repository.re3_repo&.description
+  end
+
+  def url
+    @repository.client_repo&.url || @repository.re3_repo&.url
+  end
+
+  def re3data_url
+    doi_as_url
+  end
+
+  def pid_system
+    ret = Array.wrap(@repository.re3_repo&.pid_systems).map { |k| k.text }
+    ret += Array.wrap(@repository.client_id.nil? ? nil : "DOI")
+    ret.uniq
+  end
+
+  def keyword
+    ret = Array.wrap(@repository.re3_repo&.keywords).map { |k| k.text }
+    ret.uniq
+  end
+
+  def contact
+    ret = Array.wrap(@repository.re3_repo&.contacts).map { |k| k.text }
+    ret.uniq
+  end
+
+  def language
+    ret = Array.wrap(@repository.re3_repo&.repository_languages).map { |k| k.text }
+    ret += Array.wrap(@repository.client_repo&.language)
+    ret.uniq
+  end
+
+  def certificate
+    ret = Array.wrap(@repository.re3_repo&.certificates).map { |k| k.text }
+    ret += Array.wrap(@repository.client_repo&.certificate)
+    ret.uniq
+  end
+
+  def software
+    ret = Array.wrap(@repository.re3_repo&.software).map { |k| k.name }
+    ret.uniq
+  end
+
+  def data_access
+    Array.wrap(@repository.re3_repo&.data_accesses).map { |k| k.type }
+  end
+
+  def data_upload
+    Array.wrap(@repository.re3_repo&.data_uploads).map { |k| k.type }
+  end
+
+  def provider_type
+    Array.wrap(@repository.re3_repo&.provider_type).map { |k| k.text }
+  end
+
+  def repository_type
+    Array.wrap(@repository.re3_repo&.types).map { |k| k.text }
+  end
+
+  def subject
+    Array.wrap(@repository.re3_repo&.subjects).map { |k| k.text }
+  end
 end
diff --git a/db/migrate/20220218154500_create_reference_repositories.rb b/db/migrate/20220218154500_create_reference_repositories.rb
index 3b7855107..f7456a994 100644
--- a/db/migrate/20220218154500_create_reference_repositories.rb
+++ b/db/migrate/20220218154500_create_reference_repositories.rb
@@ -1,8 +1,10 @@
+# frozen_string_literal: true
+
 class CreateReferenceRepositories < ActiveRecord::Migration[5.2]
   def change
     create_table :reference_repositories do |t|
-      t.string :client_id, null:true
-      t.string :re3doi, null:true
+      t.string :client_id, null: true
+      t.string :re3doi, null: true
 
       t.timestamps
     end
diff --git a/db/schema.rb b/db/schema.rb
index fb9c61950..f730af62b 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -14,7 +14,6 @@
 # It's strongly recommended that you check this file into your version control system.
 
 ActiveRecord::Schema.define(version: 2022_02_18_154500) do
-
   create_table "active_storage_attachments", options: "ENGINE=InnoDB DEFAULT CHARSET=latin1", force: :cascade do |t|
     t.string "name", limit: 191, null: false
     t.string "record_type", null: false
@@ -309,5 +308,4 @@
     t.datetime "created_at", null: false
     t.datetime "updated_at", null: false
   end
-
 end
diff --git a/lib/tasks/repository.rake b/lib/tasks/repository.rake
index 99aa2d486..c0381eadf 100644
--- a/lib/tasks/repository.rake
+++ b/lib/tasks/repository.rake
@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 namespace :repository do
   desc "Load all Clients into Reference Repostories"
   task load_client_repos: :environment do
@@ -22,7 +24,7 @@ namespace :repository do
     re3repos = []
     (1..pages).each do |page|
       puts "Fetching Re3Data Repositories: Fetch Group #{page}"
-      re3repos += DataCatalog.query("", limit: 1000, offset:page).fetch(:data, [])
+      re3repos += DataCatalog.query("", limit: 1000, offset: page).fetch(:data, [])
     end
     re3repos.uniq!
     puts "Processing Re3Data Repositories"
@@ -33,7 +35,7 @@ namespace :repository do
     )
     re3repos.each  do |repo|
       progressbar.increment
-      doi = repo.id&.gsub('https://doi.org/','')
+      doi = repo.id&.gsub("https://doi.org/", "")
       if not doi.blank?
         ReferenceRepository.find_or_create_by(
           re3doi: doi
diff --git a/spec/models/reference_repository_spec.rb b/spec/models/reference_repository_spec.rb
index e85048bb5..c88d34f32 100644
--- a/spec/models/reference_repository_spec.rb
+++ b/spec/models/reference_repository_spec.rb
@@ -1,4 +1,6 @@
-require 'rails_helper'
+# frozen_string_literal: true
+
+require "rails_helper"
 
 RSpec.describe ReferenceRepository, type: :model do
   pending "add some examples to (or delete) #{__FILE__}"

From 48f484955479627f8316c02f05c347de722071ac Mon Sep 17 00:00:00 2001
From: jrhoads <jrhoads@datacite.org>
Date: Tue, 8 Mar 2022 22:43:16 -0500
Subject: [PATCH 8/9] Update Gemfile/lock

---
 Gemfile      | 2 ++
 Gemfile.lock | 7 ++++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/Gemfile b/Gemfile
index 62f9dceec..983668d4c 100644
--- a/Gemfile
+++ b/Gemfile
@@ -113,3 +113,5 @@ group :test do
   gem "vcr", "~> 5.1"
   gem "webmock", "~> 3.1"
 end
+
+gem "hashid-rails", "~> 1.4"
diff --git a/Gemfile.lock b/Gemfile.lock
index 755c54136..62fcdfbdc 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -273,6 +273,10 @@ GEM
     hamster (3.0.0)
       concurrent-ruby (~> 1.0)
     hashdiff (1.0.1)
+    hashid-rails (1.4.1)
+      activerecord (>= 4.0)
+      hashids (~> 1.0)
+    hashids (1.0.6)
     hashie (4.1.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
@@ -669,6 +673,7 @@ DEPENDENCIES
   graphql-cache (~> 0.6.0)
   graphql-errors (~> 0.4.0)
   hashdiff (>= 1.0.0.beta1, < 2.0.0)
+  hashid-rails
   iso-639 (~> 0.3.5)
   iso8601 (~> 0.9.0)
   jsonlint (~> 0.3.0)
@@ -722,4 +727,4 @@ DEPENDENCIES
   webmock (~> 3.1)
 
 BUNDLED WITH
-   2.2.30
+   2.2.33

From 27fda4997e32375fe57345f313a0a083b497386c Mon Sep 17 00:00:00 2001
From: jrhoads <jrhoads@datacite.org>
Date: Tue, 15 Mar 2022 14:51:54 -0400
Subject: [PATCH 9/9] Add Indexable concern to RefereceRepository model as well
 as associated rake tasks

---
 app/models/reference_repository.rb |  1 +
 lib/tasks/repository.rake          | 65 ++++++++++++++++++++++++++++++
 2 files changed, 66 insertions(+)

diff --git a/app/models/reference_repository.rb b/app/models/reference_repository.rb
index e8aa5fa72..32f643453 100644
--- a/app/models/reference_repository.rb
+++ b/app/models/reference_repository.rb
@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 class ReferenceRepository < ApplicationRecord
+  include Indexable
   include Elasticsearch::Model
   include Elasticsearch::Model::Callbacks
   include Hashid::Rails
diff --git a/lib/tasks/repository.rake b/lib/tasks/repository.rake
index c0381eadf..7606bd159 100644
--- a/lib/tasks/repository.rake
+++ b/lib/tasks/repository.rake
@@ -43,4 +43,69 @@ namespace :repository do
       end
     end
   end
+
+  desc "Create index for reference_repositories"
+  task create_index: :environment do
+    puts ReferenceRepository.create_index
+  end
+
+  desc "Delete index for reference_repositories"
+  task delete_index: :environment do
+    puts ReferenceRepository.delete_index(index: ENV["INDEX"])
+  end
+
+  desc "Upgrade index for reference_repositories"
+  task upgrade_index: :environment do
+    puts ReferenceRepository.upgrade_index
+  end
+
+  desc "Show index stats for reference_repositories"
+  task index_stats: :environment do
+    puts ReferenceRepository.index_stats
+  end
+
+  desc "Switch index for reference_repositories"
+  task switch_index: :environment do
+    puts ReferenceRepository.switch_index
+  end
+
+  desc "Return active index for reference_repositories"
+  task active_index: :environment do
+    puts ReferenceRepository.active_index + " is the active index."
+  end
+
+  desc "Monitor reindexing for reference_repositories"
+  task monitor_reindex: :environment do
+    puts ReferenceRepository.monitor_reindex
+  end
+
+  desc "Create alias for reference_repositories"
+  task create_alias: :environment do
+    puts ReferenceRepository.create_alias(index: ENV["INDEX"], alias: ENV["ALIAS"])
+  end
+
+  desc "List aliases for reference_repositories"
+  task list_aliases: :environment do
+    puts ReferenceRepository.list_aliases
+  end
+
+  desc "Delete alias for reference_repositories"
+  task delete_alias: :environment do
+    puts ReferenceRepository.delete_alias(index: ENV["INDEX"], alias: ENV["ALIAS"])
+  end
+
+  desc "Import all reference_repositories"
+  task import: :environment do
+    ReferenceRepository.import(index: ReferenceRepository.inactive_index)
+  end
+
+  desc "Delete from index by query"
+  task delete_by_query: :environment do
+    if ENV["QUERY"].nil?
+      puts "ENV['QUERY'] is required"
+      exit
+    end
+
+    puts ReferenceRepository.delete_by_query(index: ENV["INDEX"], query: ENV["QUERY"])
+  end
 end