From 0b66a626556438bf177679138e7889f06462961d Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 26 Sep 2024 00:27:01 +0000 Subject: [PATCH 01/44] Match authors to openalex schema --- rails/app/models/author.rb | 9 ++------- rails/app/models/authors_counts_by_year.rb | 5 +++++ rails/app/models/authors_ids.rb | 5 +++++ .../db/migrate/20240628174722_create_authors.rb | 10 +++++----- ...0628174723_create_authors_counts_by_years.rb | 13 +++++++++++++ .../20240628174724_create_authors_ids.rb | 13 +++++++++++++ rails/spec/models/author_spec.rb | 17 +++++++++++------ 7 files changed, 54 insertions(+), 18 deletions(-) create mode 100644 rails/app/models/authors_counts_by_year.rb create mode 100644 rails/app/models/authors_ids.rb create mode 100644 rails/db/migrate/20240628174723_create_authors_counts_by_years.rb create mode 100644 rails/db/migrate/20240628174724_create_authors_ids.rb diff --git a/rails/app/models/author.rb b/rails/app/models/author.rb index df1afc8..54685df 100644 --- a/rails/app/models/author.rb +++ b/rails/app/models/author.rb @@ -1,11 +1,6 @@ # frozen_string_literal: true class Author < ApplicationRecord - validates :name, presence: true - - has_many :authorship_connections - has_many :works, through: :authorship_connections - - has_many :author_nodes - has_many :investigations, through: :author_nodes + has_one :authors_ids + has_one :authors_counts_by_year end diff --git a/rails/app/models/authors_counts_by_year.rb b/rails/app/models/authors_counts_by_year.rb new file mode 100644 index 0000000..f0fa9fe --- /dev/null +++ b/rails/app/models/authors_counts_by_year.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class AuthorsCountsByYear < ApplicationRecord + belongs_to :author +end diff --git a/rails/app/models/authors_ids.rb b/rails/app/models/authors_ids.rb new file mode 100644 index 0000000..06dbdf1 --- /dev/null +++ b/rails/app/models/authors_ids.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class AuthorsIds < ApplicationRecord + belongs_to :author +end diff --git a/rails/db/migrate/20240628174722_create_authors.rb b/rails/db/migrate/20240628174722_create_authors.rb index 6c7c81e..d1ea304 100644 --- a/rails/db/migrate/20240628174722_create_authors.rb +++ b/rails/db/migrate/20240628174722_create_authors.rb @@ -1,13 +1,13 @@ class CreateAuthors < ActiveRecord::Migration[7.1] def change create_table :authors do |t| - t.string :name t.string :orcid - t.string :openalex_id - t.integer :h_index - t.integer :i10_index - t.integer :cited_by_count + t.string :display_name + t.jsonb :display_name_alternatives t.integer :works_count + t.integer :cited_by_count + t.string :last_known_institution + t.string :works_api_url t.timestamps end diff --git a/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb b/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb new file mode 100644 index 0000000..ba68652 --- /dev/null +++ b/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb @@ -0,0 +1,13 @@ +class CreateAuthorsCountsByYears < ActiveRecord::Migration[7.1] + def change + create_table :authors_counts_by_years do |t| + t.references :author, null: false, foreign_key: true + t.integer :year, null: false + t.integer :works_count + t.integer :cited_by_count + t.integer :oa_works_count + + t.timestamps + end + end +end diff --git a/rails/db/migrate/20240628174724_create_authors_ids.rb b/rails/db/migrate/20240628174724_create_authors_ids.rb new file mode 100644 index 0000000..9a9bb61 --- /dev/null +++ b/rails/db/migrate/20240628174724_create_authors_ids.rb @@ -0,0 +1,13 @@ +class CreateAuthorsIds < ActiveRecord::Migration[7.1] + def change + create_table :authors_ids do |t| + t.references :author, null: false, foreign_key: true + t.string :openalex + t.string :orcid + t.string :wikipedia + t.integer :mag + + t.timestamps + end + end +end diff --git a/rails/spec/models/author_spec.rb b/rails/spec/models/author_spec.rb index d743404..74cd6f7 100644 --- a/rails/spec/models/author_spec.rb +++ b/rails/spec/models/author_spec.rb @@ -4,15 +4,20 @@ RSpec.describe Author, type: :model do describe 'validations' do - it { should validate_presence_of(:name) } + it { should allow_value(nil).for (:display_name) } it { should allow_value(nil).for (:orcid) } - it { should allow_value(nil).for (:openalex_id) } + it { should allow_value(nil).for (:display_name) } + it { should allow_value(nil).for (:display_name_alternatives) } + it { should allow_value(nil).for (:works_count) } + it { should allow_value(nil).for (:cited_by_count) } + it { should allow_value(nil).for (:last_known_institution) } end describe 'relationships' do - it { should have_many :author_nodes } - it { should have_many(:investigations).through(:author_nodes) } + # it { should have_many :author_nodes } + it { should have_one :authors_ids } + it { should have_one :authors_counts_by_year } - it { should have_many :authorship_connections } - it { should have_many(:works).through(:authorship_connections) } + # it { should have_many :authorship_connections } + # it { should have_many(:works).through(:authorship_connections) } end end From 8dc71b9b913e4e776ab64d35c3ba6a847bbe9042 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 26 Sep 2024 00:35:06 +0000 Subject: [PATCH 02/44] AuthorsIds spec --- rails/spec/models/authors_ids_spec.rb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 rails/spec/models/authors_ids_spec.rb diff --git a/rails/spec/models/authors_ids_spec.rb b/rails/spec/models/authors_ids_spec.rb new file mode 100644 index 0000000..069171d --- /dev/null +++ b/rails/spec/models/authors_ids_spec.rb @@ -0,0 +1,15 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe AuthorsIds, type: :model do + describe 'validations' do + it { should allow_value(nil).for (:openalex) } + it { should allow_value(nil).for (:orcid) } + it { should allow_value(nil).for (:wikipedia) } + it { should allow_value(nil).for (:mag) } + end + describe 'relationships' do + it { should belong_to :author } + end +end \ No newline at end of file From 9d75972469da1b2e80d7b1972429951cea4e4ce9 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 26 Sep 2024 01:04:38 +0000 Subject: [PATCH 03/44] Add instutions relationships --- rails/app/models/institution.rb | 7 +++++++ rails/app/models/institutions_counts_by_year.rb | 5 +++++ rails/app/models/institutions_ids.rb | 5 +++++ rails/spec/models/institution_spec.rb | 10 ++++++++++ 4 files changed, 27 insertions(+) create mode 100644 rails/app/models/institution.rb create mode 100644 rails/app/models/institutions_counts_by_year.rb create mode 100644 rails/app/models/institutions_ids.rb create mode 100644 rails/spec/models/institution_spec.rb diff --git a/rails/app/models/institution.rb b/rails/app/models/institution.rb new file mode 100644 index 0000000..15a2bcf --- /dev/null +++ b/rails/app/models/institution.rb @@ -0,0 +1,7 @@ +# frozen_string_literal: true + +class Institution < ApplicationRecord + has_one :institutions_counts_by_year + has_one :institutions_geo + has_one :institutions_ids +end diff --git a/rails/app/models/institutions_counts_by_year.rb b/rails/app/models/institutions_counts_by_year.rb new file mode 100644 index 0000000..c43db8a --- /dev/null +++ b/rails/app/models/institutions_counts_by_year.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class InstitutionsCountsByYear < ApplicationRecord + belongs_to :institution +end diff --git a/rails/app/models/institutions_ids.rb b/rails/app/models/institutions_ids.rb new file mode 100644 index 0000000..71a020d --- /dev/null +++ b/rails/app/models/institutions_ids.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class InstitutionsIds < ApplicationRecord + belongs_to :institution +end diff --git a/rails/spec/models/institution_spec.rb b/rails/spec/models/institution_spec.rb new file mode 100644 index 0000000..865fc3f --- /dev/null +++ b/rails/spec/models/institution_spec.rb @@ -0,0 +1,10 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe Institution, type: :model do + describe 'relationships' do + it { should have_one :institutions_counts_by_year } + it { should have_one :institutions_ids } + end +end \ No newline at end of file From d9024bade41bae3c7011ece8251cb35a5321515a Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 26 Sep 2024 01:41:01 +0000 Subject: [PATCH 04/44] temporarily remove nodes and edges, add work relationships --- rails/app/models/author_node.rb | 6 ---- rails/app/models/authorship_connection.rb | 4 --- rails/app/models/work.rb | 28 +++++++++---------- rails/app/models/works_authorship.rb | 5 ++++ rails/app/models/works_biblio.rb | 3 ++ rails/app/models/works_ids.rb | 5 ++++ rails/app/models/works_open_access.rb | 5 ++++ rails/app/models/works_referenced_works.rb | 11 ++++++++ rails/app/models/works_related_works.rb | 11 ++++++++ rails/spec/models/author_node_spec.rb | 17 ----------- .../models/authors_counts_by_year_spec.rb | 15 ++++++++++ rails/spec/models/authorship_edge_spec.rb | 16 ----------- rails/spec/models/connection_spec.rb | 18 ------------ rails/spec/models/investigation_spec.rb | 24 ---------------- rails/spec/models/note_node_spec.rb | 16 ----------- rails/spec/models/work_edge_spec.rb | 16 ----------- rails/spec/models/work_node_spec.rb | 17 ----------- rails/spec/models/work_spec.rb | 22 ++++++--------- ...ction_spec.rb => works_authorship_spec.rb} | 2 +- 19 files changed, 79 insertions(+), 162 deletions(-) delete mode 100644 rails/app/models/author_node.rb delete mode 100644 rails/app/models/authorship_connection.rb create mode 100644 rails/app/models/works_authorship.rb create mode 100644 rails/app/models/works_biblio.rb create mode 100644 rails/app/models/works_ids.rb create mode 100644 rails/app/models/works_open_access.rb create mode 100644 rails/app/models/works_referenced_works.rb create mode 100644 rails/app/models/works_related_works.rb delete mode 100644 rails/spec/models/author_node_spec.rb create mode 100644 rails/spec/models/authors_counts_by_year_spec.rb delete mode 100644 rails/spec/models/authorship_edge_spec.rb delete mode 100644 rails/spec/models/connection_spec.rb delete mode 100644 rails/spec/models/investigation_spec.rb delete mode 100644 rails/spec/models/note_node_spec.rb delete mode 100644 rails/spec/models/work_edge_spec.rb delete mode 100644 rails/spec/models/work_node_spec.rb rename rails/spec/models/{authorship_connection_spec.rb => works_authorship_spec.rb} (75%) diff --git a/rails/app/models/author_node.rb b/rails/app/models/author_node.rb deleted file mode 100644 index efbad81..0000000 --- a/rails/app/models/author_node.rb +++ /dev/null @@ -1,6 +0,0 @@ -class AuthorNode < ApplicationRecord - validates :visible, presence: true - - belongs_to :investigation - belongs_to :author -end diff --git a/rails/app/models/authorship_connection.rb b/rails/app/models/authorship_connection.rb deleted file mode 100644 index 0795756..0000000 --- a/rails/app/models/authorship_connection.rb +++ /dev/null @@ -1,4 +0,0 @@ -class AuthorshipConnection < ApplicationRecord - belongs_to :author - belongs_to :work -end diff --git a/rails/app/models/work.rb b/rails/app/models/work.rb index f22693f..4bb8d11 100644 --- a/rails/app/models/work.rb +++ b/rails/app/models/work.rb @@ -1,27 +1,27 @@ # frozen_string_literal: true class Work < ApplicationRecord - validates :doi, presence: true - validates :title, presence: true - has_many :work_nodes - has_many :investigations, through: :work_nodes + has_many :works_authorships + has_many :authors, through: :works_authorships + has_many :institutions, through: :works_authorships - has_many :authorship_connections - has_many :authors, through: :authorship_connections + has_one :works_biblio + has_one :works_ids + has_one :works_open_access # reference_connections "names" the Connection join table for accessing through the reference association - has_many :reference_connections, - foreign_key: :citation_id, - class_name: 'Connection' + has_many :works_related_works, + foreign_key: :related_work_id, + class_name: 'WorksRelatedWorks' # source: :reference matches with the belong_to :reference identification in the Connection model - has_many :references, through: :reference_connections, source: :reference + has_many :related_works, through: :works_related_works, source: :related_work # citation_connections "names" the Connection join table for accessing through the citation association - has_many :citation_connections, - foreign_key: :reference_id, - class_name: 'Connection' + has_many :works_referenced_works, + foreign_key: :referenced_work_id, + class_name: 'WorksReferencedWorks' # source: :citation matches with the belong_to :citation identification in the Connection model - has_many :citations, through: :citation_connections, source: :citation + has_many :referenced_works, through: :works_referenced_works, source: :referenced_work end diff --git a/rails/app/models/works_authorship.rb b/rails/app/models/works_authorship.rb new file mode 100644 index 0000000..565644e --- /dev/null +++ b/rails/app/models/works_authorship.rb @@ -0,0 +1,5 @@ +class WorksAuthorship < ApplicationRecord + belongs_to :author + belongs_to :work + belongs_to :institution +end diff --git a/rails/app/models/works_biblio.rb b/rails/app/models/works_biblio.rb new file mode 100644 index 0000000..323f004 --- /dev/null +++ b/rails/app/models/works_biblio.rb @@ -0,0 +1,3 @@ +class WorksBiblio < ApplicationRecord + belongs_to :work +end diff --git a/rails/app/models/works_ids.rb b/rails/app/models/works_ids.rb new file mode 100644 index 0000000..d5496b3 --- /dev/null +++ b/rails/app/models/works_ids.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class WorksIds < ApplicationRecord + belongs_to :work +end diff --git a/rails/app/models/works_open_access.rb b/rails/app/models/works_open_access.rb new file mode 100644 index 0000000..505fcfb --- /dev/null +++ b/rails/app/models/works_open_access.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class WorksOpenAccess < ApplicationRecord + belongs_to :work +end diff --git a/rails/app/models/works_referenced_works.rb b/rails/app/models/works_referenced_works.rb new file mode 100644 index 0000000..34a7079 --- /dev/null +++ b/rails/app/models/works_referenced_works.rb @@ -0,0 +1,11 @@ +# frozen_string_literal: true + +class WorksReferencedWorks < ApplicationRecord + + validates :work_id, presence: true + validates :referenced_work_id, presence: true + + belongs_to :work, foreign_key: 'work_id', class_name: 'Work' + belongs_to :referenced_work, foreign_key: 'referenced_work_id', class_name: 'Work' + +end \ No newline at end of file diff --git a/rails/app/models/works_related_works.rb b/rails/app/models/works_related_works.rb new file mode 100644 index 0000000..be90ea2 --- /dev/null +++ b/rails/app/models/works_related_works.rb @@ -0,0 +1,11 @@ +# frozen_string_literal: true + +class WorksRelatedWorks < ApplicationRecord + + validates :work_id, presence: true + validates :related_work_id, presence: true + + belongs_to :work, foreign_key: 'work_id', class_name: 'Work' + belongs_to :related_work, foreign_key: 'related_work_id', class_name: 'Work' + +end \ No newline at end of file diff --git a/rails/spec/models/author_node_spec.rb b/rails/spec/models/author_node_spec.rb deleted file mode 100644 index 5ebdced..0000000 --- a/rails/spec/models/author_node_spec.rb +++ /dev/null @@ -1,17 +0,0 @@ -# frozen_string_literal: true - -require 'rails_helper' - -RSpec.describe AuthorNode, type: :model do - describe 'validations' do - it { should allow_value(nil).for(:x_coordinate) } - it { should allow_value(nil).for(:y_coordinate) } - - it { should validate_presence_of(:visible) } - end - - describe 'relationships' do - it { should belong_to :investigation } - it { should belong_to :author } - end -end diff --git a/rails/spec/models/authors_counts_by_year_spec.rb b/rails/spec/models/authors_counts_by_year_spec.rb new file mode 100644 index 0000000..069171d --- /dev/null +++ b/rails/spec/models/authors_counts_by_year_spec.rb @@ -0,0 +1,15 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe AuthorsIds, type: :model do + describe 'validations' do + it { should allow_value(nil).for (:openalex) } + it { should allow_value(nil).for (:orcid) } + it { should allow_value(nil).for (:wikipedia) } + it { should allow_value(nil).for (:mag) } + end + describe 'relationships' do + it { should belong_to :author } + end +end \ No newline at end of file diff --git a/rails/spec/models/authorship_edge_spec.rb b/rails/spec/models/authorship_edge_spec.rb deleted file mode 100644 index 449925e..0000000 --- a/rails/spec/models/authorship_edge_spec.rb +++ /dev/null @@ -1,16 +0,0 @@ -# frozen_string_literal - -require 'rails_helper' - -RSpec.describe AuthorshipEdge, type: :model do - describe 'validations' do - it { should validate_presence_of(:investigation_id) } - it { should validate_presence_of(:authorship_connection_id) } - it { should validate_presence_of(:visible) } - end - - describe 'relationships' do - it { should belong_to :investigation } - it { should belong_to :authorship_connection } - end -end diff --git a/rails/spec/models/connection_spec.rb b/rails/spec/models/connection_spec.rb deleted file mode 100644 index 1142a70..0000000 --- a/rails/spec/models/connection_spec.rb +++ /dev/null @@ -1,18 +0,0 @@ -# frozen_string_literal: true - -require 'rails_helper' - -RSpec.describe Connection, type: :model do - describe 'validations' do - it { should validate_presence_of :reference_id } - it { should validate_presence_of :citation_id } - end - - describe 'relationships' do - it { should belong_to :reference } - it { should belong_to :citation } - - it { should have_many(:work_edges) } - it { should have_many(:investigations).through(:work_edges) } - end -end diff --git a/rails/spec/models/investigation_spec.rb b/rails/spec/models/investigation_spec.rb deleted file mode 100644 index cc83370..0000000 --- a/rails/spec/models/investigation_spec.rb +++ /dev/null @@ -1,24 +0,0 @@ -# frozen_string_literal: true - -require 'rails_helper' - -RSpec.describe Investigation, type: :model do - describe 'validations' do - it { should validate_presence_of :name } - end - - describe 'relationships' do - it { should have_many :work_nodes } - it { should have_many(:works).through(:work_nodes) } - - it { should have_many(:author_nodes) } - it { should have_many(:authors).through(:author_nodes) } - - it { should have_many(:note_nodes) } - - it { should have_many(:work_edges) } - it { should have_many(:connections).through(:work_edges) } - - it { should belong_to :user } - end -end diff --git a/rails/spec/models/note_node_spec.rb b/rails/spec/models/note_node_spec.rb deleted file mode 100644 index 9f92a3e..0000000 --- a/rails/spec/models/note_node_spec.rb +++ /dev/null @@ -1,16 +0,0 @@ -# frozen_string_literal: true - -require 'rails_helper' - -RSpec.describe NoteNode, type: :model do - describe 'validations' do - it { should allow_value(nil).for (:x_coordinate) } - it { should allow_value(nil).for (:y_coordinate) } - - it { should validate_presence_of(:visible) } - end - - describe 'relationships' do - it { should belong_to :investigation } - end -end diff --git a/rails/spec/models/work_edge_spec.rb b/rails/spec/models/work_edge_spec.rb deleted file mode 100644 index 3cf4bad..0000000 --- a/rails/spec/models/work_edge_spec.rb +++ /dev/null @@ -1,16 +0,0 @@ -# frozen_string_literal: true - -require 'rails_helper' - -RSpec.describe WorkEdge, type: :model do - describe 'validations' do - it { should validate_presence_of(:investigation_id) } - it { should validate_presence_of(:connection_id) } - it { should validate_presence_of(:visible) } - end - - describe 'relationships' do - it { should belong_to :investigation } - it { should belong_to :connection } - end -end diff --git a/rails/spec/models/work_node_spec.rb b/rails/spec/models/work_node_spec.rb deleted file mode 100644 index 745e0ff..0000000 --- a/rails/spec/models/work_node_spec.rb +++ /dev/null @@ -1,17 +0,0 @@ -# frozen_string_literal: true - -require 'rails_helper' - -RSpec.describe WorkNode, type: :model do - describe 'validations' do - it { should allow_value(nil).for(:x_coordinate) } - it { should allow_value(nil).for(:y_coordinate) } - - it { should validate_presence_of(:visible) } - end - - describe 'relationships' do - it { should belong_to :investigation } - it { should belong_to :work } - end -end diff --git a/rails/spec/models/work_spec.rb b/rails/spec/models/work_spec.rb index 456b61a..d9f7094 100644 --- a/rails/spec/models/work_spec.rb +++ b/rails/spec/models/work_spec.rb @@ -4,21 +4,17 @@ RSpec.describe Work, type: :model do describe 'validations' do - it { should validate_presence_of(:doi) } - it { should validate_presence_of(:title) } + # it { should validate_presence_of(:doi) } + # it { should validate_presence_of(:title) } end describe 'relationships' do - it { should have_many :work_nodes } - it { should have_many(:investigations).through(:work_nodes) } - - it { should have_many :authorship_connections } - it { should have_many(:authors).through(:authorship_connections) } - - it { should have_many :reference_connections } - it { should have_many(:references).through(:reference_connections) } - - it { should have_many :citation_connections } - it { should have_many(:citations).through(:citation_connections) } + it { should have_one :works_biblio } + it { should have_one :works_ids } + it { should have_one :works_open_access } + it { should have_many :works_related_works } + it { should have_many(:related_works).through(:works_related_works) } + it { should have_many :works_referenced_works } + it { should have_many(:referenced_works).through(:works_referenced_works) } end end diff --git a/rails/spec/models/authorship_connection_spec.rb b/rails/spec/models/works_authorship_spec.rb similarity index 75% rename from rails/spec/models/authorship_connection_spec.rb rename to rails/spec/models/works_authorship_spec.rb index b4db8ae..6dfd8e0 100644 --- a/rails/spec/models/authorship_connection_spec.rb +++ b/rails/spec/models/works_authorship_spec.rb @@ -2,7 +2,7 @@ require 'rails_helper' -RSpec.describe AuthorshipConnection, type: :model do +RSpec.describe WorksAuthorship, type: :model do describe 'relationships' do it { should belong_to :author } it { should belong_to :work } From f4a8e504d2ccee17ff9a3f93833fd2558c247ccc Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Mon, 30 Sep 2024 19:27:36 +0000 Subject: [PATCH 05/44] Add models to match openalex db --- rails/app/models/author.rb | 2 ++ rails/app/models/authorship_edge.rb | 8 -------- rails/app/models/concept.rb | 14 ++++++++++++++ rails/app/models/concepts_counts_by_year.rb | 5 +++++ rails/app/models/concepts_ids.rb | 5 +++++ rails/app/models/concepts_related_concepts.rb | 8 ++++++++ rails/app/models/connection.rb | 12 ------------ rails/app/models/institution.rb | 6 ++++++ .../institutions_associated_institutions.rb | 11 +++++++++++ rails/app/models/institutions_geo.rb | 5 +++++ rails/app/models/investigation.rb | 19 ------------------- rails/app/models/note_node.rb | 7 ------- rails/app/models/venue.rb | 8 ++++++++ rails/app/models/venues_counts_by_year.rb | 5 +++++ rails/app/models/venues_ids.rb | 5 +++++ rails/app/models/work.rb | 4 ++++ rails/app/models/work_edge.rb | 8 -------- rails/app/models/work_node.rb | 6 ------ rails/app/models/works_concept.rb | 6 ++++++ rails/app/models/works_mesh.rb | 5 +++++ 20 files changed, 89 insertions(+), 60 deletions(-) delete mode 100644 rails/app/models/authorship_edge.rb create mode 100644 rails/app/models/concept.rb create mode 100644 rails/app/models/concepts_counts_by_year.rb create mode 100644 rails/app/models/concepts_ids.rb create mode 100644 rails/app/models/concepts_related_concepts.rb delete mode 100644 rails/app/models/connection.rb create mode 100644 rails/app/models/institutions_associated_institutions.rb create mode 100644 rails/app/models/institutions_geo.rb delete mode 100644 rails/app/models/investigation.rb delete mode 100644 rails/app/models/note_node.rb create mode 100644 rails/app/models/venue.rb create mode 100644 rails/app/models/venues_counts_by_year.rb create mode 100644 rails/app/models/venues_ids.rb delete mode 100644 rails/app/models/work_edge.rb delete mode 100644 rails/app/models/work_node.rb create mode 100644 rails/app/models/works_concept.rb create mode 100644 rails/app/models/works_mesh.rb diff --git a/rails/app/models/author.rb b/rails/app/models/author.rb index 54685df..b2a5ece 100644 --- a/rails/app/models/author.rb +++ b/rails/app/models/author.rb @@ -3,4 +3,6 @@ class Author < ApplicationRecord has_one :authors_ids has_one :authors_counts_by_year + has_many :works_authorships + has_many :institutions, through: :works_authorships end diff --git a/rails/app/models/authorship_edge.rb b/rails/app/models/authorship_edge.rb deleted file mode 100644 index b1954f6..0000000 --- a/rails/app/models/authorship_edge.rb +++ /dev/null @@ -1,8 +0,0 @@ -class AuthorshipEdge < ApplicationRecord - validates :investigation_id, presence: true - validates :authorship_connection_id, presence: true - validates :visible, presence: true - - belongs_to :investigation - belongs_to :authorship_connection -end diff --git a/rails/app/models/concept.rb b/rails/app/models/concept.rb new file mode 100644 index 0000000..c081e3e --- /dev/null +++ b/rails/app/models/concept.rb @@ -0,0 +1,14 @@ +# frozen_string_literal: true + +class Concept < ApplicationRecord + has_many :works_concepts + has_many :works, through: :works_concepts + has_one :concepts_counts_by_year + has_one :concepts_ids + + has_many :concepts_related_concepts, + foreign_key: :related_concept_id, + class_name: 'ConceptsRelatedConcepts' + + has_many :related_concepts, through: :concepts_related_concepts, source: :related_concept +end diff --git a/rails/app/models/concepts_counts_by_year.rb b/rails/app/models/concepts_counts_by_year.rb new file mode 100644 index 0000000..dff941f --- /dev/null +++ b/rails/app/models/concepts_counts_by_year.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class ConceptsCountsByYear < ApplicationRecord + belongs_to :concept +end diff --git a/rails/app/models/concepts_ids.rb b/rails/app/models/concepts_ids.rb new file mode 100644 index 0000000..13bf08c --- /dev/null +++ b/rails/app/models/concepts_ids.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class ConceptsIds < ApplicationRecord + belongs_to :concept +end diff --git a/rails/app/models/concepts_related_concepts.rb b/rails/app/models/concepts_related_concepts.rb new file mode 100644 index 0000000..d2f9847 --- /dev/null +++ b/rails/app/models/concepts_related_concepts.rb @@ -0,0 +1,8 @@ +# frozen_string_literal: true + +class ConceptsRelatedConcepts < ApplicationRecord + + belongs_to :concept, foreign_key: 'concept_id', class_name: 'Concept' + belongs_to :related_concept, foreign_key: 'related_concept_id', class_name: 'Concept' + +end \ No newline at end of file diff --git a/rails/app/models/connection.rb b/rails/app/models/connection.rb deleted file mode 100644 index ed9cea9..0000000 --- a/rails/app/models/connection.rb +++ /dev/null @@ -1,12 +0,0 @@ -# frozen_string_literal: true - -class Connection < ApplicationRecord - validates :reference_id, presence: true - validates :citation_id, presence: true - - belongs_to :reference, foreign_key: 'reference_id', class_name: 'Work' - belongs_to :citation, foreign_key: 'citation_id', class_name: 'Work' - - has_many :work_edges - has_many :investigations, through: :work_edges -end diff --git a/rails/app/models/institution.rb b/rails/app/models/institution.rb index 15a2bcf..6f396f8 100644 --- a/rails/app/models/institution.rb +++ b/rails/app/models/institution.rb @@ -4,4 +4,10 @@ class Institution < ApplicationRecord has_one :institutions_counts_by_year has_one :institutions_geo has_one :institutions_ids + + has_many :institutions_associated_institutions, + foreign_key: :associated_institution_id, + class_name: 'InstitutionsAssociatedInstitutions' + + has_many :associated_institutions, through: :institutions_associated_institutions, source: :associated_institution end diff --git a/rails/app/models/institutions_associated_institutions.rb b/rails/app/models/institutions_associated_institutions.rb new file mode 100644 index 0000000..14b9e32 --- /dev/null +++ b/rails/app/models/institutions_associated_institutions.rb @@ -0,0 +1,11 @@ +# frozen_string_literal: true + +class InstitutionsAssociatedInstitutions < ApplicationRecord + + validates :institution_id, presence: true + validates :associated_institution_id, presence: true + + belongs_to :institution, foreign_key: 'institution_id', class_name: 'Institution' + belongs_to :associated_institution, foreign_key: 'associated_institution_id', class_name: 'Institution' + +end \ No newline at end of file diff --git a/rails/app/models/institutions_geo.rb b/rails/app/models/institutions_geo.rb new file mode 100644 index 0000000..e0ded7a --- /dev/null +++ b/rails/app/models/institutions_geo.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class InstitutionsGeo < ApplicationRecord + belongs_to :institution +end diff --git a/rails/app/models/investigation.rb b/rails/app/models/investigation.rb deleted file mode 100644 index b337651..0000000 --- a/rails/app/models/investigation.rb +++ /dev/null @@ -1,19 +0,0 @@ -# frozen_string_literal: true - -class Investigation < ApplicationRecord - validates :name, presence: true - - has_many :work_nodes - has_many :author_nodes - has_many :note_nodes - has_many :work_edges - has_many :authorship_edges - - has_many :works, through: :work_nodes - has_many :authors, through: :author_nodes - - has_many :connections, through: :work_edges - has_many :authorship_connections, through: :authorship_edges - - belongs_to :user -end diff --git a/rails/app/models/note_node.rb b/rails/app/models/note_node.rb deleted file mode 100644 index 1b3f1fb..0000000 --- a/rails/app/models/note_node.rb +++ /dev/null @@ -1,7 +0,0 @@ -# frozen_string_literal: true - -class NoteNode < ApplicationRecord - validates :visible, presence: true - - belongs_to :investigation -end diff --git a/rails/app/models/venue.rb b/rails/app/models/venue.rb new file mode 100644 index 0000000..44584d1 --- /dev/null +++ b/rails/app/models/venue.rb @@ -0,0 +1,8 @@ +# frozen_string_literal: true + +class Venue < ApplicationRecord + has_one :venues_counts_by_year + has_one :venues_ids + has_many :works + has_many :works_alternate_host_venues +end diff --git a/rails/app/models/venues_counts_by_year.rb b/rails/app/models/venues_counts_by_year.rb new file mode 100644 index 0000000..4a1303b --- /dev/null +++ b/rails/app/models/venues_counts_by_year.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class VenuesCountsByYear < ApplicationRecord + belongs_to :venue +end diff --git a/rails/app/models/venues_ids.rb b/rails/app/models/venues_ids.rb new file mode 100644 index 0000000..bb32b95 --- /dev/null +++ b/rails/app/models/venues_ids.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class VenuesIds < ApplicationRecord + belongs_to :venue +end diff --git a/rails/app/models/work.rb b/rails/app/models/work.rb index 4bb8d11..ed53faa 100644 --- a/rails/app/models/work.rb +++ b/rails/app/models/work.rb @@ -9,6 +9,10 @@ class Work < ApplicationRecord has_one :works_biblio has_one :works_ids has_one :works_open_access + has_one :works_mesh + + has_many :works_concepts + has_many :concepts, through: :works_concepts # reference_connections "names" the Connection join table for accessing through the reference association has_many :works_related_works, diff --git a/rails/app/models/work_edge.rb b/rails/app/models/work_edge.rb deleted file mode 100644 index 7fa0393..0000000 --- a/rails/app/models/work_edge.rb +++ /dev/null @@ -1,8 +0,0 @@ -class WorkEdge < ApplicationRecord - validates :investigation_id, presence: true - validates :connection_id, presence: true - validates :visible, presence: true - - belongs_to :investigation - belongs_to :connection -end diff --git a/rails/app/models/work_node.rb b/rails/app/models/work_node.rb deleted file mode 100644 index 1026eff..0000000 --- a/rails/app/models/work_node.rb +++ /dev/null @@ -1,6 +0,0 @@ -class WorkNode < ApplicationRecord - validates :visible, presence: true - - belongs_to :investigation - belongs_to :work -end diff --git a/rails/app/models/works_concept.rb b/rails/app/models/works_concept.rb new file mode 100644 index 0000000..69bdeea --- /dev/null +++ b/rails/app/models/works_concept.rb @@ -0,0 +1,6 @@ +# frozen_string_literal: true + +class WorksConcept < ApplicationRecord + belongs_to :work + belongs_to :concept +end diff --git a/rails/app/models/works_mesh.rb b/rails/app/models/works_mesh.rb new file mode 100644 index 0000000..b21276e --- /dev/null +++ b/rails/app/models/works_mesh.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class WorksMesh < ApplicationRecord + belongs_to :work +end From a72af23cc7320df3bf4f905389a21cd0d6c7899a Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Mon, 30 Sep 2024 19:27:56 +0000 Subject: [PATCH 06/44] Add db migrations to match openalex db --- .../20240402200952_create_investigations.rb | 12 - .../db/migrate/20240418013207_create_works.rb | 20 - .../20240422153043_create_connections.rb | 18 - .../20240621193206_create_work_nodes.rb | 15 - .../migrate/20240628174725_create_topics.rb | 20 + .../migrate/20240628174726_create_concepts.rb | 16 + ...0240628174727_create_concepts_ancestors.rb | 11 + ...8174728_create_concepts_counts_by_years.rb | 11 + .../20240628174729_create_concepts_ids.rb | 13 + ...174730_create_concepts_related_concepts.rb | 11 + .../20240628174731_create_institutions.rb | 19 + ...te_institutions_associated_institutions.rb | 10 + ...733_create_institutions_counts_by_years.rb | 11 + ...20240628174734_create_institutions_geos.rb | 15 + .../20240628174735_create_institutions_ids.rb | 14 + .../20240628174736_create_publishers.rb | 15 + ...74737_create_publishers_counts_by_years.rb | 12 + .../20240628174738_create_publishers_ids.rb | 11 + .../migrate/20240628174739_create_sources.rb | 17 + ...28174740_create_sources_counts_by_years.rb | 12 + .../20240628174741_create_sources_ids.rb | 14 + .../db/migrate/20240628174742_create_works.rb | 21 + ...28174743_create_works_primary_locations.rb | 16 + .../20240628174744_create_works_locations.rb | 16 + ...28174745_create_works_best_oa_locations.rb | 16 + ...628174746_create_authorship_connections.rb | 10 - ...20240628174746_create_works_authorships.rb | 13 + .../20240628174747_create_works_biblios.rb | 13 + .../20240628174748_create_works_topics.rb | 10 + .../20240628174749_create_works_concepts.rb | 11 + .../20240628174750_create_works_ids.rb | 13 + .../20240628174751_create_works_meshes.rb | 13 + ...240628174752_create_works_open_accesses.rb | 12 + ...628174753_create_works_referenced_works.rb | 11 + ...240628174754_create_works_related_works.rb | 10 + .../migrate/20240628174755_create_venues.rb | 17 + ...628174756_create_venues_counts_by_years.rb | 11 + .../20240628174757_create_venues_ids.rb | 12 + .../20240702195645_devise_create_users.rb | 48 -- .../20240708215131_create_author_nodes.rb | 14 - .../20240709200009_create_note_nodes.rb | 14 - .../20240804025750_create_work_edges.rb | 11 - .../20240812193606_create_authorship_edges.rb | 11 - rails/db/schema.rb | 452 ++++++++++++++---- 44 files changed, 808 insertions(+), 264 deletions(-) delete mode 100644 rails/db/migrate/20240402200952_create_investigations.rb delete mode 100644 rails/db/migrate/20240418013207_create_works.rb delete mode 100644 rails/db/migrate/20240422153043_create_connections.rb delete mode 100644 rails/db/migrate/20240621193206_create_work_nodes.rb create mode 100644 rails/db/migrate/20240628174725_create_topics.rb create mode 100644 rails/db/migrate/20240628174726_create_concepts.rb create mode 100644 rails/db/migrate/20240628174727_create_concepts_ancestors.rb create mode 100644 rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb create mode 100644 rails/db/migrate/20240628174729_create_concepts_ids.rb create mode 100644 rails/db/migrate/20240628174730_create_concepts_related_concepts.rb create mode 100644 rails/db/migrate/20240628174731_create_institutions.rb create mode 100644 rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb create mode 100644 rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb create mode 100644 rails/db/migrate/20240628174734_create_institutions_geos.rb create mode 100644 rails/db/migrate/20240628174735_create_institutions_ids.rb create mode 100644 rails/db/migrate/20240628174736_create_publishers.rb create mode 100644 rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb create mode 100644 rails/db/migrate/20240628174738_create_publishers_ids.rb create mode 100644 rails/db/migrate/20240628174739_create_sources.rb create mode 100644 rails/db/migrate/20240628174740_create_sources_counts_by_years.rb create mode 100644 rails/db/migrate/20240628174741_create_sources_ids.rb create mode 100644 rails/db/migrate/20240628174742_create_works.rb create mode 100644 rails/db/migrate/20240628174743_create_works_primary_locations.rb create mode 100644 rails/db/migrate/20240628174744_create_works_locations.rb create mode 100644 rails/db/migrate/20240628174745_create_works_best_oa_locations.rb delete mode 100644 rails/db/migrate/20240628174746_create_authorship_connections.rb create mode 100644 rails/db/migrate/20240628174746_create_works_authorships.rb create mode 100644 rails/db/migrate/20240628174747_create_works_biblios.rb create mode 100644 rails/db/migrate/20240628174748_create_works_topics.rb create mode 100644 rails/db/migrate/20240628174749_create_works_concepts.rb create mode 100644 rails/db/migrate/20240628174750_create_works_ids.rb create mode 100644 rails/db/migrate/20240628174751_create_works_meshes.rb create mode 100644 rails/db/migrate/20240628174752_create_works_open_accesses.rb create mode 100644 rails/db/migrate/20240628174753_create_works_referenced_works.rb create mode 100644 rails/db/migrate/20240628174754_create_works_related_works.rb create mode 100644 rails/db/migrate/20240628174755_create_venues.rb create mode 100644 rails/db/migrate/20240628174756_create_venues_counts_by_years.rb create mode 100644 rails/db/migrate/20240628174757_create_venues_ids.rb delete mode 100644 rails/db/migrate/20240702195645_devise_create_users.rb delete mode 100644 rails/db/migrate/20240708215131_create_author_nodes.rb delete mode 100644 rails/db/migrate/20240709200009_create_note_nodes.rb delete mode 100644 rails/db/migrate/20240804025750_create_work_edges.rb delete mode 100644 rails/db/migrate/20240812193606_create_authorship_edges.rb diff --git a/rails/db/migrate/20240402200952_create_investigations.rb b/rails/db/migrate/20240402200952_create_investigations.rb deleted file mode 100644 index 8285948..0000000 --- a/rails/db/migrate/20240402200952_create_investigations.rb +++ /dev/null @@ -1,12 +0,0 @@ -# frozen_string_literal: true - -class CreateInvestigations < ActiveRecord::Migration[7.1] - def change - create_table :investigations do |t| - t.integer :user_id - t.string :name - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240418013207_create_works.rb b/rails/db/migrate/20240418013207_create_works.rb deleted file mode 100644 index b98ec0a..0000000 --- a/rails/db/migrate/20240418013207_create_works.rb +++ /dev/null @@ -1,20 +0,0 @@ -# frozen_string_literal: true - -class CreateWorks < ActiveRecord::Migration[7.1] - def change - create_table :works do |t| - t.string :doi - t.string :title - t.string :openalex_id - t.string :language - t.string :publication_year - t.string :keywords, array: true, default: [] - t.string :topics, array: true, default: [] - t.boolean :is_open_access, default: false - t.string :open_access_url - t.string :abstract, default: "" - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240422153043_create_connections.rb b/rails/db/migrate/20240422153043_create_connections.rb deleted file mode 100644 index 92d7b5b..0000000 --- a/rails/db/migrate/20240422153043_create_connections.rb +++ /dev/null @@ -1,18 +0,0 @@ -# frozen_string_literal: true - -class CreateConnections < ActiveRecord::Migration[7.1] - def change - create_table :connections do |t| - t.integer :reference_id, null: false - t.integer :citation_id, null: false - - t.timestamps - end - end -end - -# create an InvestigationConnection model, for associating edges with an investigation? - -# how else to represent edges? - -# just make edges lol diff --git a/rails/db/migrate/20240621193206_create_work_nodes.rb b/rails/db/migrate/20240621193206_create_work_nodes.rb deleted file mode 100644 index 1879309..0000000 --- a/rails/db/migrate/20240621193206_create_work_nodes.rb +++ /dev/null @@ -1,15 +0,0 @@ -class CreateWorkNodes < ActiveRecord::Migration[7.1] - def change - create_table :work_nodes do |t| - t.integer :x_coordinate - t.integer :y_coordinate - - t.references :investigation, null: false, foreign_key: true - t.references :work, null: false, foreign_key: true - - t.boolean :visible, null: false, default: true - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240628174725_create_topics.rb b/rails/db/migrate/20240628174725_create_topics.rb new file mode 100644 index 0000000..7cba1fd --- /dev/null +++ b/rails/db/migrate/20240628174725_create_topics.rb @@ -0,0 +1,20 @@ +class CreateTopics < ActiveRecord::Migration[7.1] + def change + create_table :topics do |t| + t.string :display_name + t.string :subfield_id + t.string :subfield_display_name + t.string :field_id + t.string :field_display_name + t.string :domain_id + t.string :domain_display_name + t.string :description + t.string :keywords + t.string :works_api_url + t.string :wikipedia_id + t.integer :works_count + t.integer :cited_by_count + t.timestamps + end + end +end diff --git a/rails/db/migrate/20240628174726_create_concepts.rb b/rails/db/migrate/20240628174726_create_concepts.rb new file mode 100644 index 0000000..f2b6433 --- /dev/null +++ b/rails/db/migrate/20240628174726_create_concepts.rb @@ -0,0 +1,16 @@ +class CreateConcepts < ActiveRecord::Migration[7.1] + def change + create_table :concepts do |t| + t.string :wikidata + t.string :display_name + t.integer :level + t.string :description + t.integer :works_count + t.integer :cited_by_count + t.string :image_url + t.string :image_thumbnail_url + t.string :works_api_url + + end + end +end diff --git a/rails/db/migrate/20240628174727_create_concepts_ancestors.rb b/rails/db/migrate/20240628174727_create_concepts_ancestors.rb new file mode 100644 index 0000000..6c3d709 --- /dev/null +++ b/rails/db/migrate/20240628174727_create_concepts_ancestors.rb @@ -0,0 +1,11 @@ +class CreateConceptsAncestors < ActiveRecord::Migration[7.1] + def change + create_table :concepts_ancestors do |t| + t.string :concept_id, null: false + t.string :ancestor_id, null: false + # this needs to be that self-referential many-to-many situation + + t.timestamps + end + end +end diff --git a/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb b/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb new file mode 100644 index 0000000..2dc7364 --- /dev/null +++ b/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb @@ -0,0 +1,11 @@ +class CreateConceptsCountsByYears < ActiveRecord::Migration[7.1] + def change + create_table :concepts_counts_by_years do |t| + t.references :concept, null: false, foreign_key: true + t.integer :year, null: false + t.integer :works_count + t.integer :cited_by_count + t.integer :oa_works_count + end + end +end diff --git a/rails/db/migrate/20240628174729_create_concepts_ids.rb b/rails/db/migrate/20240628174729_create_concepts_ids.rb new file mode 100644 index 0000000..0a201f4 --- /dev/null +++ b/rails/db/migrate/20240628174729_create_concepts_ids.rb @@ -0,0 +1,13 @@ +class CreateConceptsIds < ActiveRecord::Migration[7.1] + def change + create_table :concepts_ids do |t| + t.references :concept, null: false, foreign_key: true + t.string :openalex + t.string :wikidata + t.string :wikipedia + t.jsonb :umls_aui + t.jsonb :umls_cui + t.integer :mag + end + end +end diff --git a/rails/db/migrate/20240628174730_create_concepts_related_concepts.rb b/rails/db/migrate/20240628174730_create_concepts_related_concepts.rb new file mode 100644 index 0000000..ac4bc88 --- /dev/null +++ b/rails/db/migrate/20240628174730_create_concepts_related_concepts.rb @@ -0,0 +1,11 @@ +class CreateConceptsRelatedConcepts < ActiveRecord::Migration[7.1] + def change + create_table :concepts_related_concepts do |t| + t.string :concept_id + t.string :related_concept_id + t.float :score + + # another self-referential many-to-many + end + end +end diff --git a/rails/db/migrate/20240628174731_create_institutions.rb b/rails/db/migrate/20240628174731_create_institutions.rb new file mode 100644 index 0000000..f2f55ce --- /dev/null +++ b/rails/db/migrate/20240628174731_create_institutions.rb @@ -0,0 +1,19 @@ +class CreateInstitutions < ActiveRecord::Migration[7.1] + def change + create_table :institutions do |t| + t.string :ror + t.string :display_name + t.string :country_code + t.string :type + t.string :homepage_url + t.string :image_url + t.string :image_thumbnail_url + t.jsonb :display_name_acronyms + t.jsonb :display_name_alternatives + t.integer :works_count + t.integer :cited_by_count + t.string :works_api_url + + end + end +end diff --git a/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb b/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb new file mode 100644 index 0000000..53b6b00 --- /dev/null +++ b/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb @@ -0,0 +1,10 @@ +class CreateInstitutionsAssociatedInstitutions < ActiveRecord::Migration[7.1] + def change + create_table :institutions_associated_institutions do |t| + t.string :institution_id + t.string :associated_institution_id + t.string :relationship + + end + end +end diff --git a/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb b/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb new file mode 100644 index 0000000..ed56ca7 --- /dev/null +++ b/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb @@ -0,0 +1,11 @@ +class CreateInstitutionsCountsByYears < ActiveRecord::Migration[7.1] + def change + create_table :institutions_counts_by_years do |t| + t.references :institution, null: false, foreign_key: true + t.integer :year + t.integer :works_count + t.integer :oa_works_count + + end + end +end diff --git a/rails/db/migrate/20240628174734_create_institutions_geos.rb b/rails/db/migrate/20240628174734_create_institutions_geos.rb new file mode 100644 index 0000000..f354452 --- /dev/null +++ b/rails/db/migrate/20240628174734_create_institutions_geos.rb @@ -0,0 +1,15 @@ +class CreateInstitutionsGeos < ActiveRecord::Migration[7.1] + def change + create_table :institutions_geos do |t| + t.references :institution, null: false, foreign_key: true + t.string :city + t.string :geonames_city_id + t.string :region + t.string :country_code + t.string :country + t.float :latitude + t.float :longitude + + end + end +end diff --git a/rails/db/migrate/20240628174735_create_institutions_ids.rb b/rails/db/migrate/20240628174735_create_institutions_ids.rb new file mode 100644 index 0000000..67cf257 --- /dev/null +++ b/rails/db/migrate/20240628174735_create_institutions_ids.rb @@ -0,0 +1,14 @@ +class CreateInstitutionsIds < ActiveRecord::Migration[7.1] + def change + create_table :institutions_ids do |t| + t.references :institution, null: false, foreign_key: true + t.string :openalex + t.string :ror + t.string :grid + t.string :wikipedia + t.string :wikidata + t.integer :mag + + end + end +end diff --git a/rails/db/migrate/20240628174736_create_publishers.rb b/rails/db/migrate/20240628174736_create_publishers.rb new file mode 100644 index 0000000..fcde5e3 --- /dev/null +++ b/rails/db/migrate/20240628174736_create_publishers.rb @@ -0,0 +1,15 @@ +class CreatePublishers < ActiveRecord::Migration[7.1] + def change + create_table :publishers do |t| + t.string :display_name + t.jsonb :alternate_titles + t.jsonb :country_codes + t.integer :hierarchy_level + t.string :parent_publisher + t.integer :works_count + t.integer :cited_by_count + t.string :sources_api_url + + end + end +end diff --git a/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb b/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb new file mode 100644 index 0000000..b064cfe --- /dev/null +++ b/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb @@ -0,0 +1,12 @@ +class CreatePublishersCountsByYears < ActiveRecord::Migration[7.1] + def change + create_table :publishers_counts_by_years do |t| + t.references :publisher, null: false, foreign_key: true + t.integer :year + t.integer :works_count + t.integer :cited_by_count + t.integer :oa_works_count + + end + end +end diff --git a/rails/db/migrate/20240628174738_create_publishers_ids.rb b/rails/db/migrate/20240628174738_create_publishers_ids.rb new file mode 100644 index 0000000..7fb683f --- /dev/null +++ b/rails/db/migrate/20240628174738_create_publishers_ids.rb @@ -0,0 +1,11 @@ +class CreatePublishersIds < ActiveRecord::Migration[7.1] + def change + create_table :publishers_ids do |t| + t.references :publisher, null: false, foreign_key: true + t.string :openalex + t.string :ror + t.string :wikidata + + end + end +end diff --git a/rails/db/migrate/20240628174739_create_sources.rb b/rails/db/migrate/20240628174739_create_sources.rb new file mode 100644 index 0000000..98a9a02 --- /dev/null +++ b/rails/db/migrate/20240628174739_create_sources.rb @@ -0,0 +1,17 @@ +class CreateSources < ActiveRecord::Migration[7.1] + def change + create_table :sources do |t| + t.string :issn_l + t.jsonb :issn + t.string :display_name + t.string :publisher + t.integer :works_count + t.integer :cited_by_count + t.boolean :is_oa + t.boolean :is_in_doaj + t.string :homepage_url + t.string :works_api_url + + end + end +end diff --git a/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb b/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb new file mode 100644 index 0000000..060e27e --- /dev/null +++ b/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb @@ -0,0 +1,12 @@ +class CreateSourcesCountsByYears < ActiveRecord::Migration[7.1] + def change + create_table :sources_counts_by_years do |t| + t.references :source, null: false, foreign_key: true + t.integer :year + t.integer :works_count + t.integer :cited_by_count + t.integer :oa_works_count + + end + end +end diff --git a/rails/db/migrate/20240628174741_create_sources_ids.rb b/rails/db/migrate/20240628174741_create_sources_ids.rb new file mode 100644 index 0000000..08b651f --- /dev/null +++ b/rails/db/migrate/20240628174741_create_sources_ids.rb @@ -0,0 +1,14 @@ +class CreateSourcesIds < ActiveRecord::Migration[7.1] + def change + create_table :sources_ids do |t| + t.references :source, null: false, foreign_key: true + t.string :openalex + t.string :issn_l + t.jsonb :issn + t.integer :mag + t.string :wikidata + t.string :fatcat + + end + end +end diff --git a/rails/db/migrate/20240628174742_create_works.rb b/rails/db/migrate/20240628174742_create_works.rb new file mode 100644 index 0000000..625da67 --- /dev/null +++ b/rails/db/migrate/20240628174742_create_works.rb @@ -0,0 +1,21 @@ +# frozen_string_literal: true + +class CreateWorks < ActiveRecord::Migration[7.1] + def change + create_table :works do |t| + t.string :doi + t.string :title + t.string :display_name + t.integer :publication_year + t.string :publication_date + t.string :type + t.integer :cited_by_count + t.boolean :is_retracted + t.boolean :is_paratext + t.string :cited_by_api_url + t.jsonb :abstract_inverted_index + t.string :language + + end + end +end diff --git a/rails/db/migrate/20240628174743_create_works_primary_locations.rb b/rails/db/migrate/20240628174743_create_works_primary_locations.rb new file mode 100644 index 0000000..39a02b8 --- /dev/null +++ b/rails/db/migrate/20240628174743_create_works_primary_locations.rb @@ -0,0 +1,16 @@ +# frozen_string_literal: true + +class CreateWorksPrimaryLocations < ActiveRecord::Migration[7.1] + def change + create_table :works_primary_locations do |t| + t.references :work, null: false, foreign_key: true + t.references :source, null: false, foreign_key: true + t.string :landing_page_url + t.string :pdf_url + t.boolean :is_oa + t.string :version + t.string :license + + end + end +end diff --git a/rails/db/migrate/20240628174744_create_works_locations.rb b/rails/db/migrate/20240628174744_create_works_locations.rb new file mode 100644 index 0000000..587d4c5 --- /dev/null +++ b/rails/db/migrate/20240628174744_create_works_locations.rb @@ -0,0 +1,16 @@ +# frozen_string_literal: true + +class CreateWorksLocations < ActiveRecord::Migration[7.1] + def change + create_table :works_locations do |t| + t.references :work, null: false, foreign_key: true + t.references :source, null: false, foreign_key: true + t.string :landing_page_url + t.string :pdf_url + t.boolean :is_oa + t.string :version + t.string :license + + end + end +end diff --git a/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb b/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb new file mode 100644 index 0000000..f8f190d --- /dev/null +++ b/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb @@ -0,0 +1,16 @@ +# frozen_string_literal: true + +class CreateWorksBestOaLocations < ActiveRecord::Migration[7.1] + def change + create_table :works_best_oa_locations do |t| + t.references :work, null: false, foreign_key: true + t.references :source, null: false, foreign_key: true + t.string :landing_page_url + t.string :pdf_url + t.boolean :is_oa + t.string :version + t.string :license + + end + end +end diff --git a/rails/db/migrate/20240628174746_create_authorship_connections.rb b/rails/db/migrate/20240628174746_create_authorship_connections.rb deleted file mode 100644 index bc7feb7..0000000 --- a/rails/db/migrate/20240628174746_create_authorship_connections.rb +++ /dev/null @@ -1,10 +0,0 @@ -class CreateAuthorshipConnections < ActiveRecord::Migration[7.1] - def change - create_table :authorship_connections do |t| - t.references :author, null: false, foreign_key: true - t.references :work, null: false, foreign_key: true - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240628174746_create_works_authorships.rb b/rails/db/migrate/20240628174746_create_works_authorships.rb new file mode 100644 index 0000000..d9466c1 --- /dev/null +++ b/rails/db/migrate/20240628174746_create_works_authorships.rb @@ -0,0 +1,13 @@ +class CreateWorksAuthorships < ActiveRecord::Migration[7.1] + def change + create_table :works_authorships do |t| + t.references :work, null: false, foreign_key: true + t.references :author, null: false, foreign_key: true + t.references :institution, null: false, foreign_key: true + t.string :author_position + t.string :raw_affiliation_string + + t.timestamps + end + end +end diff --git a/rails/db/migrate/20240628174747_create_works_biblios.rb b/rails/db/migrate/20240628174747_create_works_biblios.rb new file mode 100644 index 0000000..fc2602a --- /dev/null +++ b/rails/db/migrate/20240628174747_create_works_biblios.rb @@ -0,0 +1,13 @@ +class CreateWorksBiblios < ActiveRecord::Migration[7.1] + def change + create_table :works_biblios do |t| + t.references :work, null: false, foreign_key: true + t.string :volume + t.string :issue + t.string :first_page + t.string :last_page + + t.timestamps + end + end +end diff --git a/rails/db/migrate/20240628174748_create_works_topics.rb b/rails/db/migrate/20240628174748_create_works_topics.rb new file mode 100644 index 0000000..63a00d1 --- /dev/null +++ b/rails/db/migrate/20240628174748_create_works_topics.rb @@ -0,0 +1,10 @@ +class CreateWorksTopics < ActiveRecord::Migration[7.1] + def change + create_table :works_topics do |t| + t.references :work, null: false, foreign_key: true + t.references :topic, null: false, foreign_key: true + t.float :score + + end + end +end diff --git a/rails/db/migrate/20240628174749_create_works_concepts.rb b/rails/db/migrate/20240628174749_create_works_concepts.rb new file mode 100644 index 0000000..b2d3f5a --- /dev/null +++ b/rails/db/migrate/20240628174749_create_works_concepts.rb @@ -0,0 +1,11 @@ +class CreateWorksConcepts < ActiveRecord::Migration[7.1] + def change + create_table :works_concepts do |t| + t.references :work, null: false, foreign_key: true + t.references :concept, null: false, foreign_key: true + + t.float :score + + end + end +end diff --git a/rails/db/migrate/20240628174750_create_works_ids.rb b/rails/db/migrate/20240628174750_create_works_ids.rb new file mode 100644 index 0000000..bcd82c9 --- /dev/null +++ b/rails/db/migrate/20240628174750_create_works_ids.rb @@ -0,0 +1,13 @@ +class CreateWorksIds < ActiveRecord::Migration[7.1] + def change + create_table :works_ids do |t| + t.references :work, null: false, foreign_key: true + t.string :openalex + t.string :doi + t.integer :mag + t.string :pmid + t.string :pmcid + + end + end +end diff --git a/rails/db/migrate/20240628174751_create_works_meshes.rb b/rails/db/migrate/20240628174751_create_works_meshes.rb new file mode 100644 index 0000000..a18b6cc --- /dev/null +++ b/rails/db/migrate/20240628174751_create_works_meshes.rb @@ -0,0 +1,13 @@ +class CreateWorksMeshes < ActiveRecord::Migration[7.1] + def change + create_table :works_meshes do |t| + t.references :work, null: false, foreign_key: true + t.string :descriptor_ui + t.string :descriptor_name + t.string :qualifier_ui + t.string :qualifier_name + t.boolean :is_major_topic + + end + end +end diff --git a/rails/db/migrate/20240628174752_create_works_open_accesses.rb b/rails/db/migrate/20240628174752_create_works_open_accesses.rb new file mode 100644 index 0000000..c030b59 --- /dev/null +++ b/rails/db/migrate/20240628174752_create_works_open_accesses.rb @@ -0,0 +1,12 @@ +class CreateWorksOpenAccesses < ActiveRecord::Migration[7.1] + def change + create_table :works_open_accesses do |t| + t.references :work, null: false, foreign_key: true + t.boolean :is_oa + t.string :oa_status + t.string :oa_url + t.boolean :any_repository_has_fulltext + + end + end +end diff --git a/rails/db/migrate/20240628174753_create_works_referenced_works.rb b/rails/db/migrate/20240628174753_create_works_referenced_works.rb new file mode 100644 index 0000000..9e7c5ef --- /dev/null +++ b/rails/db/migrate/20240628174753_create_works_referenced_works.rb @@ -0,0 +1,11 @@ +class CreateWorksReferencedWorks < ActiveRecord::Migration[7.1] + def change + create_table :works_referenced_works do |t| + t.string :work_id + t.string :referenced_work_id + + # self-referential many-to-many + + end + end +end diff --git a/rails/db/migrate/20240628174754_create_works_related_works.rb b/rails/db/migrate/20240628174754_create_works_related_works.rb new file mode 100644 index 0000000..18bf6b8 --- /dev/null +++ b/rails/db/migrate/20240628174754_create_works_related_works.rb @@ -0,0 +1,10 @@ +class CreateWorksRelatedWorks < ActiveRecord::Migration[7.1] + def change + create_table :works_related_works do |t| + t.string :work_id + t.string :related_work_id + + # self referential many-to-many + end + end +end diff --git a/rails/db/migrate/20240628174755_create_venues.rb b/rails/db/migrate/20240628174755_create_venues.rb new file mode 100644 index 0000000..af6bf7f --- /dev/null +++ b/rails/db/migrate/20240628174755_create_venues.rb @@ -0,0 +1,17 @@ +class CreateVenues < ActiveRecord::Migration[7.1] + def change + create_table :venues do |t| + t.string :issn_l + t.string :issn + t.string :display_name + t.string :publisher + t.integer :works_count + t.integer :cited_by_count + t.boolean :is_oa + t.boolean :is_in_doaj + t.string :homepage_url + t.string :works_api_url + + end + end +end diff --git a/rails/db/migrate/20240628174756_create_venues_counts_by_years.rb b/rails/db/migrate/20240628174756_create_venues_counts_by_years.rb new file mode 100644 index 0000000..e7100fa --- /dev/null +++ b/rails/db/migrate/20240628174756_create_venues_counts_by_years.rb @@ -0,0 +1,11 @@ +class CreateVenuesCountsByYears < ActiveRecord::Migration[7.1] + def change + create_table :venues_counts_by_years do |t| + t.references :venue, null: false, foreign_key: true + t.integer :year + t.integer :works_count + t.integer :cited_by_count + + end + end +end diff --git a/rails/db/migrate/20240628174757_create_venues_ids.rb b/rails/db/migrate/20240628174757_create_venues_ids.rb new file mode 100644 index 0000000..2630d34 --- /dev/null +++ b/rails/db/migrate/20240628174757_create_venues_ids.rb @@ -0,0 +1,12 @@ +class CreateVenuesIds < ActiveRecord::Migration[7.1] + def change + create_table :venues_ids do |t| + t.references :venue, null: false, foreign_key: true + t.string :openalex + t.string :issn_l + t.string :issn + t.integer :mag + + end + end +end diff --git a/rails/db/migrate/20240702195645_devise_create_users.rb b/rails/db/migrate/20240702195645_devise_create_users.rb deleted file mode 100644 index 73c7c3c..0000000 --- a/rails/db/migrate/20240702195645_devise_create_users.rb +++ /dev/null @@ -1,48 +0,0 @@ -# frozen_string_literal: true - -class DeviseCreateUsers < ActiveRecord::Migration[7.1] - def change - create_table :users do |t| - ## Database authenticatable - t.string :email, null: false, default: '' - t.string :encrypted_password, null: false, default: '' - - ## Recoverable - t.string :reset_password_token - t.datetime :reset_password_sent_at - - ## Rememberable - t.datetime :remember_created_at - - ## Trackable - # t.integer :sign_in_count, default: 0, null: false - # t.datetime :current_sign_in_at - # t.datetime :last_sign_in_at - # t.string :current_sign_in_ip - # t.string :last_sign_in_ip - - ## Confirmable - # t.string :confirmation_token - # t.datetime :confirmed_at - # t.datetime :confirmation_sent_at - # t.string :unconfirmed_email # Only if using reconfirmable - - ## Lockable - # t.integer :failed_attempts, default: 0, null: false # Only if lock strategy is :failed_attempts - # t.string :unlock_token # Only if unlock strategy is :email or :both - # t.datetime :locked_at - - # token authentication - t.string :authentication_token - t.datetime :authentication_token_created_at, :datetime - - t.timestamps null: false - end - - add_index :users, :email, unique: true - add_index :users, :reset_password_token, unique: true - add_index :users, :authentication_token, unique: true - # add_index :users, :confirmation_token, unique: true - # add_index :users, :unlock_token, unique: true - end -end diff --git a/rails/db/migrate/20240708215131_create_author_nodes.rb b/rails/db/migrate/20240708215131_create_author_nodes.rb deleted file mode 100644 index 6f6decc..0000000 --- a/rails/db/migrate/20240708215131_create_author_nodes.rb +++ /dev/null @@ -1,14 +0,0 @@ -class CreateAuthorNodes < ActiveRecord::Migration[7.1] - def change - create_table :author_nodes do |t| - t.integer :x_coordinate - t.integer :y_coordinate - t.boolean :visible, null: false, default: true - - t.references :investigation, null: false, foreign_key: true - t.references :author, null: false, foreign_key: true - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240709200009_create_note_nodes.rb b/rails/db/migrate/20240709200009_create_note_nodes.rb deleted file mode 100644 index db652f5..0000000 --- a/rails/db/migrate/20240709200009_create_note_nodes.rb +++ /dev/null @@ -1,14 +0,0 @@ -class CreateNoteNodes < ActiveRecord::Migration[7.1] - def change - create_table :note_nodes do |t| - t.integer :x_coordinate - t.integer :y_coordinate - t.boolean :visible - - t.integer :investigation_id - t.string :body_text - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240804025750_create_work_edges.rb b/rails/db/migrate/20240804025750_create_work_edges.rb deleted file mode 100644 index c46c29f..0000000 --- a/rails/db/migrate/20240804025750_create_work_edges.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreateWorkEdges < ActiveRecord::Migration[7.1] - def change - create_table :work_edges do |t| - t.references :investigation, null: false, foreign_key: true - t.references :connection, null: false, foreign_key: true - t.boolean :visible, null: false, default: true - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240812193606_create_authorship_edges.rb b/rails/db/migrate/20240812193606_create_authorship_edges.rb deleted file mode 100644 index 80d55bd..0000000 --- a/rails/db/migrate/20240812193606_create_authorship_edges.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreateAuthorshipEdges < ActiveRecord::Migration[7.1] - def change - create_table :authorship_edges do |t| - t.references :investigation, null: false, foreign_key: true - t.references :authorship_connection, null: false, foreign_key: true - t.boolean :visible, null: false, default: true - - t.timestamps - end - end -end diff --git a/rails/db/schema.rb b/rails/db/schema.rb index 31f1ce6..1f31511 100644 --- a/rails/db/schema.rb +++ b/rails/db/schema.rb @@ -10,138 +10,408 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema[7.1].define(version: 2024_08_12_193606) do +ActiveRecord::Schema[7.1].define(version: 2024_06_28_174757) do # These are extensions that must be enabled in order to support this database enable_extension "plpgsql" - create_table "author_nodes", force: :cascade do |t| - t.integer "x_coordinate" - t.integer "y_coordinate" - t.boolean "visible", default: true, null: false - t.bigint "investigation_id", null: false - t.bigint "author_id", null: false - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.index ["author_id"], name: "index_author_nodes_on_author_id" - t.index ["investigation_id"], name: "index_author_nodes_on_investigation_id" - end - create_table "authors", force: :cascade do |t| - t.string "name" t.string "orcid" - t.string "openalex_id" - t.integer "h_index" - t.integer "i10_index" - t.integer "cited_by_count" + t.string "display_name" + t.jsonb "display_name_alternatives" t.integer "works_count" + t.integer "cited_by_count" + t.string "last_known_institution" + t.string "works_api_url" t.datetime "created_at", null: false t.datetime "updated_at", null: false end - create_table "authorship_connections", force: :cascade do |t| + create_table "authors_counts_by_years", force: :cascade do |t| t.bigint "author_id", null: false - t.bigint "work_id", null: false + t.integer "year", null: false + t.integer "works_count" + t.integer "cited_by_count" + t.integer "oa_works_count" t.datetime "created_at", null: false t.datetime "updated_at", null: false - t.index ["author_id"], name: "index_authorship_connections_on_author_id" - t.index ["work_id"], name: "index_authorship_connections_on_work_id" + t.index ["author_id"], name: "index_authors_counts_by_years_on_author_id" end - create_table "authorship_edges", force: :cascade do |t| - t.bigint "investigation_id", null: false - t.bigint "authorship_connection_id", null: false - t.boolean "visible", default: true, null: false + create_table "authors_ids", force: :cascade do |t| + t.bigint "author_id", null: false + t.string "openalex" + t.string "orcid" + t.string "wikipedia" + t.integer "mag" t.datetime "created_at", null: false t.datetime "updated_at", null: false - t.index ["authorship_connection_id"], name: "index_authorship_edges_on_authorship_connection_id" - t.index ["investigation_id"], name: "index_authorship_edges_on_investigation_id" + t.index ["author_id"], name: "index_authors_ids_on_author_id" end - create_table "connections", force: :cascade do |t| - t.integer "reference_id", null: false - t.integer "citation_id", null: false - t.datetime "created_at", null: false - t.datetime "updated_at", null: false + create_table "concepts", force: :cascade do |t| + t.string "wikidata" + t.string "display_name" + t.integer "level" + t.string "description" + t.integer "works_count" + t.integer "cited_by_count" + t.string "image_url" + t.string "image_thumbnail_url" + t.string "works_api_url" end - create_table "investigations", force: :cascade do |t| - t.integer "user_id" - t.string "name" + create_table "concepts_ancestors", force: :cascade do |t| + t.string "concept_id", null: false + t.string "ancestor_id", null: false t.datetime "created_at", null: false t.datetime "updated_at", null: false end - create_table "note_nodes", force: :cascade do |t| - t.integer "x_coordinate" - t.integer "y_coordinate" - t.boolean "visible" - t.integer "investigation_id" - t.string "body_text" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false + create_table "concepts_counts_by_years", force: :cascade do |t| + t.bigint "concept_id", null: false + t.integer "year", null: false + t.integer "works_count" + t.integer "cited_by_count" + t.integer "oa_works_count" + t.index ["concept_id"], name: "index_concepts_counts_by_years_on_concept_id" end - create_table "users", force: :cascade do |t| - t.string "email", default: "", null: false - t.string "encrypted_password", default: "", null: false - t.string "reset_password_token" - t.datetime "reset_password_sent_at" - t.datetime "remember_created_at" - t.string "authentication_token" - t.datetime "authentication_token_created_at" - t.datetime "datetime" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.index ["authentication_token"], name: "index_users_on_authentication_token", unique: true - t.index ["email"], name: "index_users_on_email", unique: true - t.index ["reset_password_token"], name: "index_users_on_reset_password_token", unique: true + create_table "concepts_ids", force: :cascade do |t| + t.bigint "concept_id", null: false + t.string "openalex" + t.string "wikidata" + t.string "wikipedia" + t.jsonb "umls_aui" + t.jsonb "umls_cui" + t.integer "mag" + t.index ["concept_id"], name: "index_concepts_ids_on_concept_id" end - create_table "work_edges", force: :cascade do |t| - t.bigint "investigation_id", null: false - t.bigint "connection_id", null: false - t.boolean "visible", default: true, null: false - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.index ["connection_id"], name: "index_work_edges_on_connection_id" - t.index ["investigation_id"], name: "index_work_edges_on_investigation_id" + create_table "concepts_related_concepts", force: :cascade do |t| + t.string "concept_id" + t.string "related_concept_id" + t.float "score" end - create_table "work_nodes", force: :cascade do |t| - t.integer "x_coordinate" - t.integer "y_coordinate" - t.bigint "investigation_id", null: false - t.bigint "work_id", null: false - t.boolean "visible", default: true, null: false + create_table "institutions", force: :cascade do |t| + t.string "ror" + t.string "display_name" + t.string "country_code" + t.string "type" + t.string "homepage_url" + t.string "image_url" + t.string "image_thumbnail_url" + t.jsonb "display_name_acronyms" + t.jsonb "display_name_alternatives" + t.integer "works_count" + t.integer "cited_by_count" + t.string "works_api_url" + end + + create_table "institutions_associated_institutions", force: :cascade do |t| + t.string "institution_id" + t.string "associated_institution_id" + t.string "relationship" + end + + create_table "institutions_counts_by_years", force: :cascade do |t| + t.bigint "institution_id", null: false + t.integer "year" + t.integer "works_count" + t.integer "oa_works_count" + t.index ["institution_id"], name: "index_institutions_counts_by_years_on_institution_id" + end + + create_table "institutions_geos", force: :cascade do |t| + t.bigint "institution_id", null: false + t.string "city" + t.string "geonames_city_id" + t.string "region" + t.string "country_code" + t.string "country" + t.float "latitude" + t.float "longitude" + t.index ["institution_id"], name: "index_institutions_geos_on_institution_id" + end + + create_table "institutions_ids", force: :cascade do |t| + t.bigint "institution_id", null: false + t.string "openalex" + t.string "ror" + t.string "grid" + t.string "wikipedia" + t.string "wikidata" + t.integer "mag" + t.index ["institution_id"], name: "index_institutions_ids_on_institution_id" + end + + create_table "publishers", force: :cascade do |t| + t.string "display_name" + t.jsonb "alternate_titles" + t.jsonb "country_codes" + t.integer "hierarchy_level" + t.string "parent_publisher" + t.integer "works_count" + t.integer "cited_by_count" + t.string "sources_api_url" + end + + create_table "publishers_counts_by_years", force: :cascade do |t| + t.bigint "publisher_id", null: false + t.integer "year" + t.integer "works_count" + t.integer "cited_by_count" + t.integer "oa_works_count" + t.index ["publisher_id"], name: "index_publishers_counts_by_years_on_publisher_id" + end + + create_table "publishers_ids", force: :cascade do |t| + t.bigint "publisher_id", null: false + t.string "openalex" + t.string "ror" + t.string "wikidata" + t.index ["publisher_id"], name: "index_publishers_ids_on_publisher_id" + end + + create_table "sources", force: :cascade do |t| + t.string "issn_l" + t.jsonb "issn" + t.string "display_name" + t.string "publisher" + t.integer "works_count" + t.integer "cited_by_count" + t.boolean "is_oa" + t.boolean "is_in_doaj" + t.string "homepage_url" + t.string "works_api_url" + end + + create_table "sources_counts_by_years", force: :cascade do |t| + t.bigint "source_id", null: false + t.integer "year" + t.integer "works_count" + t.integer "cited_by_count" + t.integer "oa_works_count" + t.index ["source_id"], name: "index_sources_counts_by_years_on_source_id" + end + + create_table "sources_ids", force: :cascade do |t| + t.bigint "source_id", null: false + t.string "openalex" + t.string "issn_l" + t.jsonb "issn" + t.integer "mag" + t.string "wikidata" + t.string "fatcat" + t.index ["source_id"], name: "index_sources_ids_on_source_id" + end + + create_table "topics", force: :cascade do |t| + t.string "display_name" + t.string "subfield_id" + t.string "subfield_display_name" + t.string "field_id" + t.string "field_display_name" + t.string "domain_id" + t.string "domain_display_name" + t.string "description" + t.string "keywords" + t.string "works_api_url" + t.string "wikipedia_id" + t.integer "works_count" + t.integer "cited_by_count" t.datetime "created_at", null: false t.datetime "updated_at", null: false - t.index ["investigation_id"], name: "index_work_nodes_on_investigation_id" - t.index ["work_id"], name: "index_work_nodes_on_work_id" + end + + create_table "venues", force: :cascade do |t| + t.string "issn_l" + t.string "issn" + t.string "display_name" + t.string "publisher" + t.integer "works_count" + t.integer "cited_by_count" + t.boolean "is_oa" + t.boolean "is_in_doaj" + t.string "homepage_url" + t.string "works_api_url" + end + + create_table "venues_counts_by_years", force: :cascade do |t| + t.bigint "venue_id", null: false + t.integer "year" + t.integer "works_count" + t.integer "cited_by_count" + t.index ["venue_id"], name: "index_venues_counts_by_years_on_venue_id" + end + + create_table "venues_ids", force: :cascade do |t| + t.bigint "venue_id", null: false + t.string "openalex" + t.string "issn_l" + t.string "issn" + t.integer "mag" + t.index ["venue_id"], name: "index_venues_ids_on_venue_id" end create_table "works", force: :cascade do |t| t.string "doi" t.string "title" - t.string "openalex_id" + t.string "display_name" + t.integer "publication_year" + t.string "publication_date" + t.string "type" + t.integer "cited_by_count" + t.boolean "is_retracted" + t.boolean "is_paratext" + t.string "cited_by_api_url" + t.jsonb "abstract_inverted_index" t.string "language" - t.string "publication_year" - t.string "keywords", default: [], array: true - t.string "topics", default: [], array: true - t.boolean "is_open_access", default: false - t.string "open_access_url" - t.string "abstract", default: "" + end + + create_table "works_authorships", force: :cascade do |t| + t.bigint "work_id", null: false + t.bigint "author_id", null: false + t.bigint "institution_id", null: false + t.string "author_position" + t.string "raw_affiliation_string" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["author_id"], name: "index_works_authorships_on_author_id" + t.index ["institution_id"], name: "index_works_authorships_on_institution_id" + t.index ["work_id"], name: "index_works_authorships_on_work_id" + end + + create_table "works_best_oa_locations", force: :cascade do |t| + t.bigint "work_id", null: false + t.bigint "source_id", null: false + t.string "landing_page_url" + t.string "pdf_url" + t.boolean "is_oa" + t.string "version" + t.string "license" + t.index ["source_id"], name: "index_works_best_oa_locations_on_source_id" + t.index ["work_id"], name: "index_works_best_oa_locations_on_work_id" + end + + create_table "works_biblios", force: :cascade do |t| + t.bigint "work_id", null: false + t.string "volume" + t.string "issue" + t.string "first_page" + t.string "last_page" t.datetime "created_at", null: false t.datetime "updated_at", null: false + t.index ["work_id"], name: "index_works_biblios_on_work_id" + end + + create_table "works_concepts", force: :cascade do |t| + t.bigint "work_id", null: false + t.bigint "concept_id", null: false + t.float "score" + t.index ["concept_id"], name: "index_works_concepts_on_concept_id" + t.index ["work_id"], name: "index_works_concepts_on_work_id" + end + + create_table "works_ids", force: :cascade do |t| + t.bigint "work_id", null: false + t.string "openalex" + t.string "doi" + t.integer "mag" + t.string "pmid" + t.string "pmcid" + t.index ["work_id"], name: "index_works_ids_on_work_id" + end + + create_table "works_locations", force: :cascade do |t| + t.bigint "work_id", null: false + t.bigint "source_id", null: false + t.string "landing_page_url" + t.string "pdf_url" + t.boolean "is_oa" + t.string "version" + t.string "license" + t.index ["source_id"], name: "index_works_locations_on_source_id" + t.index ["work_id"], name: "index_works_locations_on_work_id" + end + + create_table "works_meshes", force: :cascade do |t| + t.bigint "work_id", null: false + t.string "descriptor_ui" + t.string "descriptor_name" + t.string "qualifier_ui" + t.string "qualifier_name" + t.boolean "is_major_topic" + t.index ["work_id"], name: "index_works_meshes_on_work_id" + end + + create_table "works_open_accesses", force: :cascade do |t| + t.bigint "work_id", null: false + t.boolean "is_oa" + t.string "oa_status" + t.string "oa_url" + t.boolean "any_repository_has_fulltext" + t.index ["work_id"], name: "index_works_open_accesses_on_work_id" + end + + create_table "works_primary_locations", force: :cascade do |t| + t.bigint "work_id", null: false + t.bigint "source_id", null: false + t.string "landing_page_url" + t.string "pdf_url" + t.boolean "is_oa" + t.string "version" + t.string "license" + t.index ["source_id"], name: "index_works_primary_locations_on_source_id" + t.index ["work_id"], name: "index_works_primary_locations_on_work_id" + end + + create_table "works_referenced_works", force: :cascade do |t| + t.string "work_id" + t.string "referenced_work_id" + end + + create_table "works_related_works", force: :cascade do |t| + t.string "work_id" + t.string "related_work_id" + end + + create_table "works_topics", force: :cascade do |t| + t.bigint "work_id", null: false + t.bigint "topic_id", null: false + t.float "score" + t.index ["topic_id"], name: "index_works_topics_on_topic_id" + t.index ["work_id"], name: "index_works_topics_on_work_id" end - add_foreign_key "author_nodes", "authors" - add_foreign_key "author_nodes", "investigations" - add_foreign_key "authorship_connections", "authors" - add_foreign_key "authorship_connections", "works" - add_foreign_key "authorship_edges", "authorship_connections" - add_foreign_key "authorship_edges", "investigations" - add_foreign_key "work_edges", "connections" - add_foreign_key "work_edges", "investigations" - add_foreign_key "work_nodes", "investigations" - add_foreign_key "work_nodes", "works" + add_foreign_key "authors_counts_by_years", "authors" + add_foreign_key "authors_ids", "authors" + add_foreign_key "concepts_counts_by_years", "concepts" + add_foreign_key "concepts_ids", "concepts" + add_foreign_key "institutions_counts_by_years", "institutions" + add_foreign_key "institutions_geos", "institutions" + add_foreign_key "institutions_ids", "institutions" + add_foreign_key "publishers_counts_by_years", "publishers" + add_foreign_key "publishers_ids", "publishers" + add_foreign_key "sources_counts_by_years", "sources" + add_foreign_key "sources_ids", "sources" + add_foreign_key "venues_counts_by_years", "venues" + add_foreign_key "venues_ids", "venues" + add_foreign_key "works_authorships", "authors" + add_foreign_key "works_authorships", "institutions" + add_foreign_key "works_authorships", "works" + add_foreign_key "works_best_oa_locations", "sources" + add_foreign_key "works_best_oa_locations", "works" + add_foreign_key "works_biblios", "works" + add_foreign_key "works_concepts", "concepts" + add_foreign_key "works_concepts", "works" + add_foreign_key "works_ids", "works" + add_foreign_key "works_locations", "sources" + add_foreign_key "works_locations", "works" + add_foreign_key "works_meshes", "works" + add_foreign_key "works_open_accesses", "works" + add_foreign_key "works_primary_locations", "sources" + add_foreign_key "works_primary_locations", "works" + add_foreign_key "works_topics", "topics" + add_foreign_key "works_topics", "works" end From 76f6e2e45336462517a8896214f49d2b54b28e41 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Mon, 30 Sep 2024 19:28:09 +0000 Subject: [PATCH 07/44] Add model tests --- rails/spec/models/author_spec.rb | 4 +- .../models/authors_counts_by_year_spec.rb | 8 +-- rails/spec/models/concept_spec.rb | 16 ++++++ .../models/concepts_counts_by_year_spec.rb | 9 ++++ rails/spec/models/concepts_ids.rb | 9 ++++ .../models/concepts_related_concepts_spec.rb | 10 ++++ rails/spec/models/institution_spec.rb | 2 + ...stitutions_associated_institutions_spec.rb | 10 ++++ .../institutions_counts_by_year_spec.rb | 9 ++++ rails/spec/models/institutions_geo_spec.rb | 9 ++++ rails/spec/models/institutions_ids_spec.rb | 9 ++++ rails/spec/models/user_spec.rb | 54 +++++++++---------- rails/spec/models/venue_spec.rb | 12 +++++ .../spec/models/venues_counts_by_year_spec.rb | 9 ++++ rails/spec/models/venues_ids_spec.rb | 9 ++++ rails/spec/models/work_spec.rb | 8 ++- rails/spec/models/works_biblio_spec.rb | 9 ++++ rails/spec/models/works_concept_spec.rb | 10 ++++ rails/spec/models/works_ids_spec.rb | 9 ++++ rails/spec/models/works_mesh_spec.rb | 9 ++++ rails/spec/models/works_open_access_spec.rb | 9 ++++ 21 files changed, 192 insertions(+), 41 deletions(-) create mode 100644 rails/spec/models/concept_spec.rb create mode 100644 rails/spec/models/concepts_counts_by_year_spec.rb create mode 100644 rails/spec/models/concepts_ids.rb create mode 100644 rails/spec/models/concepts_related_concepts_spec.rb create mode 100644 rails/spec/models/institutions_associated_institutions_spec.rb create mode 100644 rails/spec/models/institutions_counts_by_year_spec.rb create mode 100644 rails/spec/models/institutions_geo_spec.rb create mode 100644 rails/spec/models/institutions_ids_spec.rb create mode 100644 rails/spec/models/venue_spec.rb create mode 100644 rails/spec/models/venues_counts_by_year_spec.rb create mode 100644 rails/spec/models/venues_ids_spec.rb create mode 100644 rails/spec/models/works_biblio_spec.rb create mode 100644 rails/spec/models/works_concept_spec.rb create mode 100644 rails/spec/models/works_ids_spec.rb create mode 100644 rails/spec/models/works_mesh_spec.rb create mode 100644 rails/spec/models/works_open_access_spec.rb diff --git a/rails/spec/models/author_spec.rb b/rails/spec/models/author_spec.rb index 74cd6f7..ec4124d 100644 --- a/rails/spec/models/author_spec.rb +++ b/rails/spec/models/author_spec.rb @@ -17,7 +17,7 @@ it { should have_one :authors_ids } it { should have_one :authors_counts_by_year } - # it { should have_many :authorship_connections } - # it { should have_many(:works).through(:authorship_connections) } + it { should have_many :works_authorships } + it { should have_many(:institutions).through(:works_authorships) } end end diff --git a/rails/spec/models/authors_counts_by_year_spec.rb b/rails/spec/models/authors_counts_by_year_spec.rb index 069171d..1ff484e 100644 --- a/rails/spec/models/authors_counts_by_year_spec.rb +++ b/rails/spec/models/authors_counts_by_year_spec.rb @@ -2,13 +2,7 @@ require 'rails_helper' -RSpec.describe AuthorsIds, type: :model do - describe 'validations' do - it { should allow_value(nil).for (:openalex) } - it { should allow_value(nil).for (:orcid) } - it { should allow_value(nil).for (:wikipedia) } - it { should allow_value(nil).for (:mag) } - end +RSpec.describe AuthorsCountsByYear, type: :model do describe 'relationships' do it { should belong_to :author } end diff --git a/rails/spec/models/concept_spec.rb b/rails/spec/models/concept_spec.rb new file mode 100644 index 0000000..bff635a --- /dev/null +++ b/rails/spec/models/concept_spec.rb @@ -0,0 +1,16 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe Concept, type: :model do + + describe 'relationships' do + it { should have_many :works_concepts } + it { should have_many(:works).through(:works_concepts) } + it { should have_one :concepts_counts_by_year } + it { should have_one :concepts_ids } + + it { should have_many(:concepts_related_concepts) } + it { should have_many(:related_concepts).through(:concepts_related_concepts) } + end +end diff --git a/rails/spec/models/concepts_counts_by_year_spec.rb b/rails/spec/models/concepts_counts_by_year_spec.rb new file mode 100644 index 0000000..d52eded --- /dev/null +++ b/rails/spec/models/concepts_counts_by_year_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe ConceptsCountsByYear, type: :model do + describe 'relationships' do + it { should belong_to :concept } + end +end \ No newline at end of file diff --git a/rails/spec/models/concepts_ids.rb b/rails/spec/models/concepts_ids.rb new file mode 100644 index 0000000..5f06bbb --- /dev/null +++ b/rails/spec/models/concepts_ids.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe ConceptsIds, type: :model do + describe 'relationships' do + it { should belong_to :concept } + end +end \ No newline at end of file diff --git a/rails/spec/models/concepts_related_concepts_spec.rb b/rails/spec/models/concepts_related_concepts_spec.rb new file mode 100644 index 0000000..1382d56 --- /dev/null +++ b/rails/spec/models/concepts_related_concepts_spec.rb @@ -0,0 +1,10 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe ConceptsRelatedConcepts, type: :model do + describe 'relationships' do + it { should belong_to :concept } + it { should belong_to :related_concept } + end +end diff --git a/rails/spec/models/institution_spec.rb b/rails/spec/models/institution_spec.rb index 865fc3f..c78e1f0 100644 --- a/rails/spec/models/institution_spec.rb +++ b/rails/spec/models/institution_spec.rb @@ -6,5 +6,7 @@ describe 'relationships' do it { should have_one :institutions_counts_by_year } it { should have_one :institutions_ids } + it { should have_one :institutions_geo } + it { should have_many(:associated_institutions).through(:institutions_associated_institutions) } end end \ No newline at end of file diff --git a/rails/spec/models/institutions_associated_institutions_spec.rb b/rails/spec/models/institutions_associated_institutions_spec.rb new file mode 100644 index 0000000..b78d9a1 --- /dev/null +++ b/rails/spec/models/institutions_associated_institutions_spec.rb @@ -0,0 +1,10 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe InstitutionsAssociatedInstitutions, type: :model do + describe 'relationships' do + it { should belong_to :institution } + it { should belong_to :associated_institution } + end +end diff --git a/rails/spec/models/institutions_counts_by_year_spec.rb b/rails/spec/models/institutions_counts_by_year_spec.rb new file mode 100644 index 0000000..506f7f3 --- /dev/null +++ b/rails/spec/models/institutions_counts_by_year_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe InstitutionsCountsByYear, type: :model do + describe 'relationships' do + it { should belong_to :institution } + end +end \ No newline at end of file diff --git a/rails/spec/models/institutions_geo_spec.rb b/rails/spec/models/institutions_geo_spec.rb new file mode 100644 index 0000000..cb2543d --- /dev/null +++ b/rails/spec/models/institutions_geo_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe InstitutionsGeo, type: :model do + describe 'relationships' do + it { should belong_to :institution } + end +end \ No newline at end of file diff --git a/rails/spec/models/institutions_ids_spec.rb b/rails/spec/models/institutions_ids_spec.rb new file mode 100644 index 0000000..80589ea --- /dev/null +++ b/rails/spec/models/institutions_ids_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe InstitutionsIds, type: :model do + describe 'relationships' do + it { should belong_to :institution } + end +end \ No newline at end of file diff --git a/rails/spec/models/user_spec.rb b/rails/spec/models/user_spec.rb index f4f506b..c221a4e 100644 --- a/rails/spec/models/user_spec.rb +++ b/rails/spec/models/user_spec.rb @@ -1,36 +1,36 @@ -require 'rails_helper' +# require 'rails_helper' -RSpec.describe User, type: :model do - describe 'validations' do - it { should validate_presence_of(:email) } - end +# RSpec.describe User, type: :model do +# describe 'validations' do +# it { should validate_presence_of(:email) } +# end - describe 'relationships' do - it { should have_many(:investigations) } - end +# describe 'relationships' do +# it { should have_many(:investigations) } +# end - describe 'methods' do - it 'has a graphql id' do - user = FactoryBot.create(:user) +# describe 'methods' do +# it 'has a graphql id' do +# user = FactoryBot.create(:user) - expect(user.gql_id).to be_a String - end +# expect(user.gql_id).to be_a String +# end - it 'can be found be graphql id' do - user = FactoryBot.create(:user) +# it 'can be found be graphql id' do +# user = FactoryBot.create(:user) - gql_id = user.gql_id +# gql_id = user.gql_id - expect(User.find_by_gql_id(gql_id)).to eq(user) - end +# expect(User.find_by_gql_id(gql_id)).to eq(user) +# end - it 'can find multiple users with multiple graphql ids' do - user_1 = FactoryBot.create(:user) - user_2 = FactoryBot.create(:user) +# it 'can find multiple users with multiple graphql ids' do +# user_1 = FactoryBot.create(:user) +# user_2 = FactoryBot.create(:user) - expect(User.find_by_gql_ids([user_1.gql_id, user_2.gql_id])).to eq( - [user_1, user_2] - ) - end - end -end +# expect(User.find_by_gql_ids([user_1.gql_id, user_2.gql_id])).to eq( +# [user_1, user_2] +# ) +# end +# end +# end diff --git a/rails/spec/models/venue_spec.rb b/rails/spec/models/venue_spec.rb new file mode 100644 index 0000000..6ae5119 --- /dev/null +++ b/rails/spec/models/venue_spec.rb @@ -0,0 +1,12 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe Venue, type: :model do + describe 'relationships' do + # it { should have_many :works_alternate_host_venues } + # it { should have_many(:works).through(:works_alternate_host_venues) } + it { should have_one :venues_counts_by_year } + it { should have_one :venues_ids } + end +end diff --git a/rails/spec/models/venues_counts_by_year_spec.rb b/rails/spec/models/venues_counts_by_year_spec.rb new file mode 100644 index 0000000..fb7b7b9 --- /dev/null +++ b/rails/spec/models/venues_counts_by_year_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe VenuesCountsByYear, type: :model do + describe 'relationships' do + it { should belong_to :venue } + end +end \ No newline at end of file diff --git a/rails/spec/models/venues_ids_spec.rb b/rails/spec/models/venues_ids_spec.rb new file mode 100644 index 0000000..b43a68e --- /dev/null +++ b/rails/spec/models/venues_ids_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe VenuesIds, type: :model do + describe 'relationships' do + it { should belong_to :venue } + end +end \ No newline at end of file diff --git a/rails/spec/models/work_spec.rb b/rails/spec/models/work_spec.rb index d9f7094..49ef79b 100644 --- a/rails/spec/models/work_spec.rb +++ b/rails/spec/models/work_spec.rb @@ -3,18 +3,16 @@ require 'rails_helper' RSpec.describe Work, type: :model do - describe 'validations' do - # it { should validate_presence_of(:doi) } - # it { should validate_presence_of(:title) } - end - describe 'relationships' do it { should have_one :works_biblio } it { should have_one :works_ids } it { should have_one :works_open_access } + it { should have_one :works_mesh } it { should have_many :works_related_works } it { should have_many(:related_works).through(:works_related_works) } it { should have_many :works_referenced_works } it { should have_many(:referenced_works).through(:works_referenced_works) } + it { should have_many :works_concepts } + it { should have_many(:concepts).through(:works_concepts) } end end diff --git a/rails/spec/models/works_biblio_spec.rb b/rails/spec/models/works_biblio_spec.rb new file mode 100644 index 0000000..5aee223 --- /dev/null +++ b/rails/spec/models/works_biblio_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe WorksBiblio, type: :model do + describe 'relationships' do + it { should belong_to :work } + end +end \ No newline at end of file diff --git a/rails/spec/models/works_concept_spec.rb b/rails/spec/models/works_concept_spec.rb new file mode 100644 index 0000000..15d9d64 --- /dev/null +++ b/rails/spec/models/works_concept_spec.rb @@ -0,0 +1,10 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe WorksConcept, type: :model do + describe 'relationships' do + it { should belong_to :work } + it { should belong_to :concept } + end +end \ No newline at end of file diff --git a/rails/spec/models/works_ids_spec.rb b/rails/spec/models/works_ids_spec.rb new file mode 100644 index 0000000..1b02b54 --- /dev/null +++ b/rails/spec/models/works_ids_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe WorksIds, type: :model do + describe 'relationships' do + it { should belong_to :work } + end +end \ No newline at end of file diff --git a/rails/spec/models/works_mesh_spec.rb b/rails/spec/models/works_mesh_spec.rb new file mode 100644 index 0000000..27f71b1 --- /dev/null +++ b/rails/spec/models/works_mesh_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe WorksMesh, type: :model do + describe 'relationships' do + it { should belong_to :work } + end +end \ No newline at end of file diff --git a/rails/spec/models/works_open_access_spec.rb b/rails/spec/models/works_open_access_spec.rb new file mode 100644 index 0000000..dd425b7 --- /dev/null +++ b/rails/spec/models/works_open_access_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe WorksOpenAccess, type: :model do + describe 'relationships' do + it { should belong_to :work } + end +end \ No newline at end of file From 142ceeaa98ddd50cb4895a72cb50636b9f880298 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Mon, 30 Sep 2024 19:34:07 +0000 Subject: [PATCH 08/44] Add concepts_ancestors --- rails/app/models/concepts_ancestors.rb | 8 ++++++++ rails/spec/models/concepts_ancestors_spec.rb | 10 ++++++++++ 2 files changed, 18 insertions(+) create mode 100644 rails/app/models/concepts_ancestors.rb create mode 100644 rails/spec/models/concepts_ancestors_spec.rb diff --git a/rails/app/models/concepts_ancestors.rb b/rails/app/models/concepts_ancestors.rb new file mode 100644 index 0000000..b21a9b0 --- /dev/null +++ b/rails/app/models/concepts_ancestors.rb @@ -0,0 +1,8 @@ +# frozen_string_literal: true + +class ConceptsAncestors < ApplicationRecord + + belongs_to :concept, foreign_key: 'concept_id', class_name: 'Concept' + belongs_to :ancestor, foreign_key: 'ancestor_id', class_name: 'Concept' + +end \ No newline at end of file diff --git a/rails/spec/models/concepts_ancestors_spec.rb b/rails/spec/models/concepts_ancestors_spec.rb new file mode 100644 index 0000000..a817082 --- /dev/null +++ b/rails/spec/models/concepts_ancestors_spec.rb @@ -0,0 +1,10 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe ConceptsAncestors, type: :model do + describe 'relationships' do + it { should belong_to :concept } + it { should belong_to :ancestor } + end +end From dc5acecdf5e4b9760dd4e99139608801caf166a6 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 2 Oct 2024 16:28:52 +0000 Subject: [PATCH 09/44] Add load institutions, institutions_geos, institutions_ids rake tasks --- rails/lib/tasks/load_institutions.rake | 30 ++++++++++++++++++++++ rails/lib/tasks/load_institutions_geo.rake | 27 +++++++++++++++++++ rails/lib/tasks/load_institutions_ids.rake | 26 +++++++++++++++++++ 3 files changed, 83 insertions(+) create mode 100644 rails/lib/tasks/load_institutions.rake create mode 100644 rails/lib/tasks/load_institutions_geo.rake create mode 100644 rails/lib/tasks/load_institutions_ids.rake diff --git a/rails/lib/tasks/load_institutions.rake b/rails/lib/tasks/load_institutions.rake new file mode 100644 index 0000000..939e7a7 --- /dev/null +++ b/rails/lib/tasks/load_institutions.rake @@ -0,0 +1,30 @@ +require 'rake' +require "zlib" +require 'csv' + +namespace :data_import do + desc "Load Institutions from gzipped csv to db" + task :load_institutions => :environment do + + Zlib::GzipReader.open('/opt/bookworm/csv-files/institutions.csv.gz') do |gzip| + csv = CSV.new(gzip) + csv.drop(1).each_with_index do |row, index| # drop(1) handles the header row + Institution.create( + openalex_id: row[0].split("/").last, + ror: row[1], + display_name: row[2], + country_code: row[3], + institution_type: row[4], + homepage_url: row[5], + image_url: row[6], + image_thumbnail_url: row[7], + display_name_acronyms: row[8], + display_name_alternatives: row[9], + works_count: row[10], + cited_by_count: row[11], + works_api_url: row[12] + ) + end + end + end +end diff --git a/rails/lib/tasks/load_institutions_geo.rake b/rails/lib/tasks/load_institutions_geo.rake new file mode 100644 index 0000000..2d21831 --- /dev/null +++ b/rails/lib/tasks/load_institutions_geo.rake @@ -0,0 +1,27 @@ +require 'rake' +require "zlib" +require 'csv' + +namespace :data_import do + desc "Load InstitutionsGeo from gzipped csv to db" + task :load_institutions_geo => :environment do + + Zlib::GzipReader.open('/opt/bookworm/csv-files/institutions_geo.csv.gz') do |gzip| + csv = CSV.new(gzip) + csv.drop(1).each_with_index do |row, index| # drop(1) handles the header row + institution = Institution.find_by(openalex_id: row[0].split("/").last) + + InstitutionsGeo.create( + institution_id: institution.id, + city: row[1], + geonames_city_id: row[2], + region: row[3], + country_code: row[4], + country: row[5], + latitude: row[6], + longitude: row[7] + ) + end + end + end +end diff --git a/rails/lib/tasks/load_institutions_ids.rake b/rails/lib/tasks/load_institutions_ids.rake new file mode 100644 index 0000000..20cadb5 --- /dev/null +++ b/rails/lib/tasks/load_institutions_ids.rake @@ -0,0 +1,26 @@ +require 'rake' +require "zlib" +require 'csv' + +namespace :data_import do + desc "Load InstitutionsIds from gzipped csv to db" + task :load_institutions_ids => :environment do + + Zlib::GzipReader.open('/opt/bookworm/csv-files/institutions_ids.csv.gz') do |gzip| + csv = CSV.new(gzip) + csv.drop(1).each_with_index do |row, index| # drop(1) handles the header row + institution = Institution.find_by(openalex_id: row[0].split("/").last) + + InstitutionsIds.create( + institution_id: institution.id, + openalex: row[0].split("/").last, + ror: row[2], + grid: row[3], + wikipedia: row[4], + wikidata: row[5], + mag: row[6] + ) + end + end + end +end From 014f429e1f1c8bcc333a19b1249a2253f261b523 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 2 Oct 2024 16:29:33 +0000 Subject: [PATCH 10/44] change migrations to use bigint fields --- ...opics.rb => 20240628174721_create_topics.rb} | 10 ++++++---- .../db/migrate/20240628174722_create_authors.rb | 6 ++---- ...0628174723_create_authors_counts_by_years.rb | 8 ++++---- .../20240628174724_create_authors_ids.rb | 4 +++- .../migrate/20240628174726_create_concepts.rb | 6 +++--- ...628174728_create_concepts_counts_by_years.rb | 8 ++++---- .../20240628174729_create_concepts_ids.rb | 2 +- .../20240628174731_create_institutions.rb | 7 ++++--- ...74733_create_institutions_counts_by_years.rb | 7 ++++--- .../20240628174735_create_institutions_ids.rb | 2 +- .../migrate/20240628174736_create_publishers.rb | 6 +++--- ...8174737_create_publishers_counts_by_years.rb | 8 ++++---- .../db/migrate/20240628174739_create_sources.rb | 4 ++-- ...0628174740_create_sources_counts_by_years.rb | 8 ++++---- .../20240628174741_create_sources_ids.rb | 2 +- rails/db/migrate/20240628174742_create_works.rb | 4 ++-- .../migrate/20240628174750_create_works_ids.rb | 2 +- .../db/migrate/20240628174755_create_venues.rb | 17 ----------------- ...40628174756_create_venues_counts_by_years.rb | 11 ----------- .../migrate/20240628174757_create_venues_ids.rb | 12 ------------ 20 files changed, 49 insertions(+), 85 deletions(-) rename rails/db/migrate/{20240628174725_create_topics.rb => 20240628174721_create_topics.rb} (69%) delete mode 100644 rails/db/migrate/20240628174755_create_venues.rb delete mode 100644 rails/db/migrate/20240628174756_create_venues_counts_by_years.rb delete mode 100644 rails/db/migrate/20240628174757_create_venues_ids.rb diff --git a/rails/db/migrate/20240628174725_create_topics.rb b/rails/db/migrate/20240628174721_create_topics.rb similarity index 69% rename from rails/db/migrate/20240628174725_create_topics.rb rename to rails/db/migrate/20240628174721_create_topics.rb index 7cba1fd..3434d05 100644 --- a/rails/db/migrate/20240628174725_create_topics.rb +++ b/rails/db/migrate/20240628174721_create_topics.rb @@ -9,12 +9,14 @@ def change t.string :domain_id t.string :domain_display_name t.string :description - t.string :keywords + t.string :keywords, array: true, default: [] t.string :works_api_url t.string :wikipedia_id - t.integer :works_count - t.integer :cited_by_count - t.timestamps + t.bigint :works_count + t.bigint :cited_by_count + + # siblings??? not documented but probably relationships of topics? + end end end diff --git a/rails/db/migrate/20240628174722_create_authors.rb b/rails/db/migrate/20240628174722_create_authors.rb index d1ea304..4bd5b5e 100644 --- a/rails/db/migrate/20240628174722_create_authors.rb +++ b/rails/db/migrate/20240628174722_create_authors.rb @@ -4,12 +4,10 @@ def change t.string :orcid t.string :display_name t.jsonb :display_name_alternatives - t.integer :works_count - t.integer :cited_by_count + t.bigint :works_count + t.bigint :cited_by_count t.string :last_known_institution t.string :works_api_url - - t.timestamps end end end diff --git a/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb b/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb index ba68652..e05f40d 100644 --- a/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb +++ b/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb @@ -2,10 +2,10 @@ class CreateAuthorsCountsByYears < ActiveRecord::Migration[7.1] def change create_table :authors_counts_by_years do |t| t.references :author, null: false, foreign_key: true - t.integer :year, null: false - t.integer :works_count - t.integer :cited_by_count - t.integer :oa_works_count + t.bigint :year, null: false + t.bigint :works_count + t.bigint :cited_by_count + t.bigint :oa_works_count t.timestamps end diff --git a/rails/db/migrate/20240628174724_create_authors_ids.rb b/rails/db/migrate/20240628174724_create_authors_ids.rb index 9a9bb61..9632fcc 100644 --- a/rails/db/migrate/20240628174724_create_authors_ids.rb +++ b/rails/db/migrate/20240628174724_create_authors_ids.rb @@ -4,8 +4,10 @@ def change t.references :author, null: false, foreign_key: true t.string :openalex t.string :orcid + t.string :scopus + t.string :twitter t.string :wikipedia - t.integer :mag + t.bigint :mag t.timestamps end diff --git a/rails/db/migrate/20240628174726_create_concepts.rb b/rails/db/migrate/20240628174726_create_concepts.rb index f2b6433..73200e1 100644 --- a/rails/db/migrate/20240628174726_create_concepts.rb +++ b/rails/db/migrate/20240628174726_create_concepts.rb @@ -3,10 +3,10 @@ def change create_table :concepts do |t| t.string :wikidata t.string :display_name - t.integer :level + t.bigint :level t.string :description - t.integer :works_count - t.integer :cited_by_count + t.bigint :works_count + t.bigint :cited_by_count t.string :image_url t.string :image_thumbnail_url t.string :works_api_url diff --git a/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb b/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb index 2dc7364..fc18132 100644 --- a/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb +++ b/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb @@ -2,10 +2,10 @@ class CreateConceptsCountsByYears < ActiveRecord::Migration[7.1] def change create_table :concepts_counts_by_years do |t| t.references :concept, null: false, foreign_key: true - t.integer :year, null: false - t.integer :works_count - t.integer :cited_by_count - t.integer :oa_works_count + t.bigint :year, null: false + t.bigint :works_count + t.bigint :cited_by_count + t.bigint :oa_works_count end end end diff --git a/rails/db/migrate/20240628174729_create_concepts_ids.rb b/rails/db/migrate/20240628174729_create_concepts_ids.rb index 0a201f4..3b350a5 100644 --- a/rails/db/migrate/20240628174729_create_concepts_ids.rb +++ b/rails/db/migrate/20240628174729_create_concepts_ids.rb @@ -7,7 +7,7 @@ def change t.string :wikipedia t.jsonb :umls_aui t.jsonb :umls_cui - t.integer :mag + t.bigint :mag end end end diff --git a/rails/db/migrate/20240628174731_create_institutions.rb b/rails/db/migrate/20240628174731_create_institutions.rb index f2f55ce..8ac8288 100644 --- a/rails/db/migrate/20240628174731_create_institutions.rb +++ b/rails/db/migrate/20240628174731_create_institutions.rb @@ -1,17 +1,18 @@ class CreateInstitutions < ActiveRecord::Migration[7.1] def change create_table :institutions do |t| + t.string :openalex_id t.string :ror t.string :display_name t.string :country_code - t.string :type + t.string :institution_type t.string :homepage_url t.string :image_url t.string :image_thumbnail_url t.jsonb :display_name_acronyms t.jsonb :display_name_alternatives - t.integer :works_count - t.integer :cited_by_count + t.bigint :works_count + t.bigint :cited_by_count t.string :works_api_url end diff --git a/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb b/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb index ed56ca7..e57fe0e 100644 --- a/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb +++ b/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb @@ -2,9 +2,10 @@ class CreateInstitutionsCountsByYears < ActiveRecord::Migration[7.1] def change create_table :institutions_counts_by_years do |t| t.references :institution, null: false, foreign_key: true - t.integer :year - t.integer :works_count - t.integer :oa_works_count + t.bigint :year + t.bigint :works_count + t.bigint :cited_by_count + t.bigint :oa_works_count end end diff --git a/rails/db/migrate/20240628174735_create_institutions_ids.rb b/rails/db/migrate/20240628174735_create_institutions_ids.rb index 67cf257..99fa4b6 100644 --- a/rails/db/migrate/20240628174735_create_institutions_ids.rb +++ b/rails/db/migrate/20240628174735_create_institutions_ids.rb @@ -7,7 +7,7 @@ def change t.string :grid t.string :wikipedia t.string :wikidata - t.integer :mag + t.bigint :mag end end diff --git a/rails/db/migrate/20240628174736_create_publishers.rb b/rails/db/migrate/20240628174736_create_publishers.rb index fcde5e3..33bfefd 100644 --- a/rails/db/migrate/20240628174736_create_publishers.rb +++ b/rails/db/migrate/20240628174736_create_publishers.rb @@ -4,10 +4,10 @@ def change t.string :display_name t.jsonb :alternate_titles t.jsonb :country_codes - t.integer :hierarchy_level + t.bigint :hierarchy_level t.string :parent_publisher - t.integer :works_count - t.integer :cited_by_count + t.bigint :works_count + t.bigint :cited_by_count t.string :sources_api_url end diff --git a/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb b/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb index b064cfe..d3b2930 100644 --- a/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb +++ b/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb @@ -2,10 +2,10 @@ class CreatePublishersCountsByYears < ActiveRecord::Migration[7.1] def change create_table :publishers_counts_by_years do |t| t.references :publisher, null: false, foreign_key: true - t.integer :year - t.integer :works_count - t.integer :cited_by_count - t.integer :oa_works_count + t.bigint :year + t.bigint :works_count + t.bigint :cited_by_count + t.bigint :oa_works_count end end diff --git a/rails/db/migrate/20240628174739_create_sources.rb b/rails/db/migrate/20240628174739_create_sources.rb index 98a9a02..8712741 100644 --- a/rails/db/migrate/20240628174739_create_sources.rb +++ b/rails/db/migrate/20240628174739_create_sources.rb @@ -5,8 +5,8 @@ def change t.jsonb :issn t.string :display_name t.string :publisher - t.integer :works_count - t.integer :cited_by_count + t.bigint :works_count + t.bigint :cited_by_count t.boolean :is_oa t.boolean :is_in_doaj t.string :homepage_url diff --git a/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb b/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb index 060e27e..2827710 100644 --- a/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb +++ b/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb @@ -2,10 +2,10 @@ class CreateSourcesCountsByYears < ActiveRecord::Migration[7.1] def change create_table :sources_counts_by_years do |t| t.references :source, null: false, foreign_key: true - t.integer :year - t.integer :works_count - t.integer :cited_by_count - t.integer :oa_works_count + t.bigint :year + t.bigint :works_count + t.bigint :cited_by_count + t.bigint :oa_works_count end end diff --git a/rails/db/migrate/20240628174741_create_sources_ids.rb b/rails/db/migrate/20240628174741_create_sources_ids.rb index 08b651f..4c2cf6d 100644 --- a/rails/db/migrate/20240628174741_create_sources_ids.rb +++ b/rails/db/migrate/20240628174741_create_sources_ids.rb @@ -5,7 +5,7 @@ def change t.string :openalex t.string :issn_l t.jsonb :issn - t.integer :mag + t.bigint :mag t.string :wikidata t.string :fatcat diff --git a/rails/db/migrate/20240628174742_create_works.rb b/rails/db/migrate/20240628174742_create_works.rb index 625da67..9c8d548 100644 --- a/rails/db/migrate/20240628174742_create_works.rb +++ b/rails/db/migrate/20240628174742_create_works.rb @@ -6,10 +6,10 @@ def change t.string :doi t.string :title t.string :display_name - t.integer :publication_year + t.bigint :publication_year t.string :publication_date t.string :type - t.integer :cited_by_count + t.bigint :cited_by_count t.boolean :is_retracted t.boolean :is_paratext t.string :cited_by_api_url diff --git a/rails/db/migrate/20240628174750_create_works_ids.rb b/rails/db/migrate/20240628174750_create_works_ids.rb index bcd82c9..a02f9fb 100644 --- a/rails/db/migrate/20240628174750_create_works_ids.rb +++ b/rails/db/migrate/20240628174750_create_works_ids.rb @@ -4,7 +4,7 @@ def change t.references :work, null: false, foreign_key: true t.string :openalex t.string :doi - t.integer :mag + t.bigint :mag t.string :pmid t.string :pmcid diff --git a/rails/db/migrate/20240628174755_create_venues.rb b/rails/db/migrate/20240628174755_create_venues.rb deleted file mode 100644 index af6bf7f..0000000 --- a/rails/db/migrate/20240628174755_create_venues.rb +++ /dev/null @@ -1,17 +0,0 @@ -class CreateVenues < ActiveRecord::Migration[7.1] - def change - create_table :venues do |t| - t.string :issn_l - t.string :issn - t.string :display_name - t.string :publisher - t.integer :works_count - t.integer :cited_by_count - t.boolean :is_oa - t.boolean :is_in_doaj - t.string :homepage_url - t.string :works_api_url - - end - end -end diff --git a/rails/db/migrate/20240628174756_create_venues_counts_by_years.rb b/rails/db/migrate/20240628174756_create_venues_counts_by_years.rb deleted file mode 100644 index e7100fa..0000000 --- a/rails/db/migrate/20240628174756_create_venues_counts_by_years.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreateVenuesCountsByYears < ActiveRecord::Migration[7.1] - def change - create_table :venues_counts_by_years do |t| - t.references :venue, null: false, foreign_key: true - t.integer :year - t.integer :works_count - t.integer :cited_by_count - - end - end -end diff --git a/rails/db/migrate/20240628174757_create_venues_ids.rb b/rails/db/migrate/20240628174757_create_venues_ids.rb deleted file mode 100644 index 2630d34..0000000 --- a/rails/db/migrate/20240628174757_create_venues_ids.rb +++ /dev/null @@ -1,12 +0,0 @@ -class CreateVenuesIds < ActiveRecord::Migration[7.1] - def change - create_table :venues_ids do |t| - t.references :venue, null: false, foreign_key: true - t.string :openalex - t.string :issn_l - t.string :issn - t.integer :mag - - end - end -end From 58979627275492a9cb419c45821a2c39893066d5 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 3 Oct 2024 19:55:42 +0000 Subject: [PATCH 11/44] update models for data import --- rails/app/models/author.rb | 2 +- rails/app/models/institution.rb | 6 +++--- rails/app/models/venue.rb | 8 -------- rails/app/models/venues_counts_by_year.rb | 5 ----- rails/app/models/venues_ids.rb | 5 ----- rails/app/models/work.rb | 3 ++- 6 files changed, 6 insertions(+), 23 deletions(-) delete mode 100644 rails/app/models/venue.rb delete mode 100644 rails/app/models/venues_counts_by_year.rb delete mode 100644 rails/app/models/venues_ids.rb diff --git a/rails/app/models/author.rb b/rails/app/models/author.rb index b2a5ece..c8f1ae9 100644 --- a/rails/app/models/author.rb +++ b/rails/app/models/author.rb @@ -2,7 +2,7 @@ class Author < ApplicationRecord has_one :authors_ids - has_one :authors_counts_by_year + has_many :authors_counts_by_year has_many :works_authorships has_many :institutions, through: :works_authorships end diff --git a/rails/app/models/institution.rb b/rails/app/models/institution.rb index 6f396f8..76871b3 100644 --- a/rails/app/models/institution.rb +++ b/rails/app/models/institution.rb @@ -1,7 +1,7 @@ # frozen_string_literal: true -class Institution < ApplicationRecord - has_one :institutions_counts_by_year +class Institution < ApplicationRecord + has_many :institutions_counts_by_year has_one :institutions_geo has_one :institutions_ids @@ -9,5 +9,5 @@ class Institution < ApplicationRecord foreign_key: :associated_institution_id, class_name: 'InstitutionsAssociatedInstitutions' - has_many :associated_institutions, through: :institutions_associated_institutions, source: :associated_institution + has_many :associated_institutions, through: :institutions_associated_institutions, source: :institution end diff --git a/rails/app/models/venue.rb b/rails/app/models/venue.rb deleted file mode 100644 index 44584d1..0000000 --- a/rails/app/models/venue.rb +++ /dev/null @@ -1,8 +0,0 @@ -# frozen_string_literal: true - -class Venue < ApplicationRecord - has_one :venues_counts_by_year - has_one :venues_ids - has_many :works - has_many :works_alternate_host_venues -end diff --git a/rails/app/models/venues_counts_by_year.rb b/rails/app/models/venues_counts_by_year.rb deleted file mode 100644 index 4a1303b..0000000 --- a/rails/app/models/venues_counts_by_year.rb +++ /dev/null @@ -1,5 +0,0 @@ -# frozen_string_literal: true - -class VenuesCountsByYear < ApplicationRecord - belongs_to :venue -end diff --git a/rails/app/models/venues_ids.rb b/rails/app/models/venues_ids.rb deleted file mode 100644 index bb32b95..0000000 --- a/rails/app/models/venues_ids.rb +++ /dev/null @@ -1,5 +0,0 @@ -# frozen_string_literal: true - -class VenuesIds < ApplicationRecord - belongs_to :venue -end diff --git a/rails/app/models/work.rb b/rails/app/models/work.rb index ed53faa..760494b 100644 --- a/rails/app/models/work.rb +++ b/rails/app/models/work.rb @@ -6,7 +6,8 @@ class Work < ApplicationRecord has_many :authors, through: :works_authorships has_many :institutions, through: :works_authorships - has_one :works_biblio + # these might need to be has_many + has_one :works_biblio has_one :works_ids has_one :works_open_access has_one :works_mesh From b5475841a613cd781991367d975944e3dfa7ebcf Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Fri, 4 Oct 2024 15:36:21 +0000 Subject: [PATCH 12/44] start reworking graphql, institutions --- .../app/graphql/mutations/add_author_works.rb | 85 -------------- rails/app/graphql/mutations/add_citations.rb | 109 ------------------ rails/app/graphql/mutations/add_references.rb | 103 ----------------- .../graphql/mutations/create_author_node.rb | 76 ------------ .../graphql/mutations/create_investigation.rb | 20 ---- .../app/graphql/mutations/create_note_node.rb | 30 ----- .../app/graphql/mutations/create_work_node.rb | 83 ------------- .../app/graphql/mutations/delete_note_node.rb | 30 ----- .../app/graphql/mutations/mutation_result.rb | 9 -- .../app/graphql/mutations/update_work_node.rb | 24 ---- rails/app/graphql/types/author_node_type.rb | 16 --- rails/app/graphql/types/author_type.rb | 16 --- .../types/authorship_connection_type.rb | 17 --- .../app/graphql/types/authorship_edge_type.rb | 35 ------ rails/app/graphql/types/connection_type.rb | 17 --- rails/app/graphql/types/institution_type.rb | 41 +++++++ .../types/institutions_counts_by_year_type.rb | 17 +++ .../graphql/types/institutions_geo_type.rb | 20 ++++ .../graphql/types/institutions_ids_type.rb | 20 ++++ rails/app/graphql/types/investigation_type.rb | 50 -------- rails/app/graphql/types/mutation_type.rb | 22 ++-- rails/app/graphql/types/note_node_type.rb | 12 -- rails/app/graphql/types/query_type.rb | 44 ++----- rails/app/graphql/types/work_edge_type.rb | 44 ------- rails/app/graphql/types/work_node_type.rb | 16 --- rails/app/graphql/types/work_type.rb | 35 ------ 26 files changed, 120 insertions(+), 871 deletions(-) delete mode 100644 rails/app/graphql/mutations/add_author_works.rb delete mode 100644 rails/app/graphql/mutations/add_citations.rb delete mode 100644 rails/app/graphql/mutations/add_references.rb delete mode 100644 rails/app/graphql/mutations/create_author_node.rb delete mode 100644 rails/app/graphql/mutations/create_investigation.rb delete mode 100644 rails/app/graphql/mutations/create_note_node.rb delete mode 100644 rails/app/graphql/mutations/create_work_node.rb delete mode 100644 rails/app/graphql/mutations/delete_note_node.rb delete mode 100644 rails/app/graphql/mutations/mutation_result.rb delete mode 100644 rails/app/graphql/mutations/update_work_node.rb delete mode 100644 rails/app/graphql/types/author_node_type.rb delete mode 100644 rails/app/graphql/types/author_type.rb delete mode 100644 rails/app/graphql/types/authorship_connection_type.rb delete mode 100644 rails/app/graphql/types/authorship_edge_type.rb delete mode 100644 rails/app/graphql/types/connection_type.rb create mode 100644 rails/app/graphql/types/institution_type.rb create mode 100644 rails/app/graphql/types/institutions_counts_by_year_type.rb create mode 100644 rails/app/graphql/types/institutions_geo_type.rb create mode 100644 rails/app/graphql/types/institutions_ids_type.rb delete mode 100644 rails/app/graphql/types/investigation_type.rb delete mode 100644 rails/app/graphql/types/note_node_type.rb delete mode 100644 rails/app/graphql/types/work_edge_type.rb delete mode 100644 rails/app/graphql/types/work_node_type.rb delete mode 100644 rails/app/graphql/types/work_type.rb diff --git a/rails/app/graphql/mutations/add_author_works.rb b/rails/app/graphql/mutations/add_author_works.rb deleted file mode 100644 index 1675a58..0000000 --- a/rails/app/graphql/mutations/add_author_works.rb +++ /dev/null @@ -1,85 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class AddAuthorWorks < BaseMutation - argument :openalex_id, String, required: true - argument :investigation_id, String, required: true - - type [Types::WorkNodeType] - - def resolve(**attributes) - authorize_user - - author = Author.find_or_create_by(openalex_id: attributes[:openalex_id]) - - investigation = Investigation.find(attributes[:investigation_id]) - - author_works = OpenalexFacade.get_author_works(attributes[:openalex_id]) - - author_node = - AuthorNode.find_by( - investigation_id: investigation.id, - author_id: author.id - ) - - work_nodes = [] - works = [] - - author_works.each_with_index do |openalex_work, index| - work = - Work.find_or_create_by( - doi: openalex_work.doi, - title: openalex_work.title, - openalex_id: openalex_work.openalex_id, - language: openalex_work.language, - publication_year: openalex_work.publication_year, - keywords: openalex_work.keywords, - topics: openalex_work.topics, - is_open_access: openalex_work.is_open_access, - open_access_url: openalex_work.open_access_url - ) - - circle_coordinates = - circle_point( - center_x = author_node.x_coordinate, - center_y = author_node.y_coordinate, - radius = 500, - degrees = index * author_works.length - ) - - work_node = - WorkNode.find_or_create_by( - investigation_id: investigation.id, - work_id: work.id - ) - - work_node.x_coordinate = - circle_coordinates.first unless work_node.x_coordinate.present? - - work_node.y_coordinate = - circle_coordinates.last unless work_node.y_coordinate.present? - - work_node.visible = true - - work_node.save - - authorship_connection = - AuthorshipConnection.find_or_create_by( - author_id: author.id, - work_id: work.id - ) - - authorship_edge = - AuthorshipEdge.find_or_create_by( - authorship_connection_id: authorship_connection.id, - investigation_id: investigation.id - ) - - works << work - work_nodes << work_node - end - - work_nodes - end - end -end diff --git a/rails/app/graphql/mutations/add_citations.rb b/rails/app/graphql/mutations/add_citations.rb deleted file mode 100644 index db2f6a7..0000000 --- a/rails/app/graphql/mutations/add_citations.rb +++ /dev/null @@ -1,109 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class AddCitations < BaseMutation - argument :openalex_id, String, required: true - argument :investigation_id, String, required: true - - type [Types::WorkNodeType] - - def resolve(**attributes) - authorize_user - - investigation = Investigation.find(attributes[:investigation_id]) - - root_work = Work.find_by(openalex_id: attributes[:openalex_id]) - - root_node = - root_work.work_nodes.find_by( - investigation_id: attributes[:investigation_id] - ) - - openalex_citations = - OpenalexFacade.get_paper_citations(attributes[:openalex_id]) - - created_citations = [] - openalex_citations.each do |citation| - created_citation = - Work.find_or_create_by( - doi: citation.doi, - title: citation.title, - language: citation.language, - openalex_id: citation.openalex_id, - publication_year: citation.publication_year, - keywords: citation.keywords, - topics: citation.topics, - is_open_access: citation.is_open_access, - open_access_url: citation.open_access_url, - abstract: citation.abstract - ) - - created_citations << created_citation - - citation.authors.each do |author_hash| - author = - Author.find_or_create_by( - name: author_hash[:name], - openalex_id: author_hash[:openalex_id], - orcid: author_hash[:orcid] - ) - - AuthorshipConnection.find_or_create_by( - author_id: author.id, - work_id: created_citation.id - ) - end - end - - created_citations.map do |citation| - connection = - Connection.find_or_create_by( - citation_id: citation.id, - reference_id: root_work.id - ) - - WorkEdge.find_or_create_by( - connection_id: connection.id, - investigation_id: investigation.id - ) - end - - work_nodes = [] - created_citations.each_with_index do |citation, index| - work_node = - WorkNode.find_or_create_by( - investigation_id: investigation.id.to_s, - work_id: citation.id - ) - - # use root_node.x_coordinate and root_node.y_coordinate as centering - # created_citations.count and something with degrees to get the spacing? - # what should the radius be? - - # circlePoint(0, 0, 1000, 200 + i * (150 / references.length - 1)) - - circle_coordinates = - circle_point( - center_x = root_node.x_coordinate, - center_y = root_node.y_coordinate, - radius = 1000, - degrees = 20 + index * (150 / created_citations.length) - ) - - work_node.x_coordinate = - circle_coordinates.first unless work_node.x_coordinate.present? - - work_node.y_coordinate = - circle_coordinates.last unless work_node.y_coordinate.present? - - work_node.visible = true - - work_node.save - - work_nodes << work_node - end - - work_nodes - end - end -end diff --git a/rails/app/graphql/mutations/add_references.rb b/rails/app/graphql/mutations/add_references.rb deleted file mode 100644 index a2b9b60..0000000 --- a/rails/app/graphql/mutations/add_references.rb +++ /dev/null @@ -1,103 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class AddReferences < BaseMutation - argument :openalex_id, String, required: true - argument :investigation_id, String, required: true - - type [Types::WorkNodeType] - - def resolve(**attributes) - authorize_user - - investigation = Investigation.find(attributes[:investigation_id]) - - root_work = Work.find_by(openalex_id: attributes[:openalex_id]) - - root_node = - root_work.work_nodes.find_by( - investigation_id: attributes[:investigation_id] - ) - - openalex_references = - OpenalexFacade.get_paper_references(attributes[:openalex_id]) - - created_references = [] - openalex_references.each do |reference| - created_reference = - Work.find_or_create_by( - doi: reference.doi, - title: reference.title, - openalex_id: reference.openalex_id, - language: reference.language, - publication_year: reference.publication_year, - keywords: reference.keywords, - topics: reference.topics, - is_open_access: reference.is_open_access, - open_access_url: reference.open_access_url, - abstract: reference.abstract - ) - - created_references << created_reference - - reference.authors.each do |author_hash| - author = - Author.find_or_create_by( - name: author_hash[:name], - openalex_id: author_hash[:openalex_id], - orcid: author_hash[:orcid] - ) - - AuthorshipConnection.find_or_create_by( - author_id: author.id, - work_id: created_reference.id - ) - end - end - - created_references.map do |reference| - connection = - Connection.find_or_create_by( - citation_id: root_work.id, - reference_id: reference.id - ) - - WorkEdge.find_or_create_by( - connection_id: connection.id, - investigation_id: investigation.id - ) - end - - work_nodes = [] - created_references.each_with_index do |reference, index| - work_node = - WorkNode.find_or_create_by( - investigation_id: investigation.id.to_s, - work_id: reference.id - ) - - circle_coordinates = - circle_point( - center_x = root_node.x_coordinate, - center_y = root_node.y_coordinate, - radius = 1000, - degrees = 200 + index * (150 / created_references.length) - ) - - work_node.x_coordinate = - circle_coordinates.first unless work_node.x_coordinate.present? - - work_node.y_coordinate = - circle_coordinates.last unless work_node.y_coordinate.present? - - work_node.visible = true - - work_node.save - - work_nodes << work_node - end - - work_nodes - end - end -end diff --git a/rails/app/graphql/mutations/create_author_node.rb b/rails/app/graphql/mutations/create_author_node.rb deleted file mode 100644 index ef051e9..0000000 --- a/rails/app/graphql/mutations/create_author_node.rb +++ /dev/null @@ -1,76 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class CreateAuthorNode < BaseMutation - argument :author_openalex_id, String, required: true - argument :work_openalex_id, String, required: true - argument :investigation_id, String, required: true - - type Types::AuthorNodeType - - def resolve(**attributes) - authorize_user - - investigation = Investigation.find(attributes[:investigation_id]) - - root_work = Work.find_by(openalex_id: attributes[:work_openalex_id]) - - root_work_node = - root_work.work_nodes.find_by( - investigation_id: attributes[:investigation_id] - ) - - openalex_author = - OpenalexFacade.get_author_details(attributes[:author_openalex_id]) - - author = - Author.find_or_create_by( - name: openalex_author.display_name, - orcid: openalex_author.orcid, - openalex_id: openalex_author.openalex_id - ) - - author.h_index = openalex_author.h_index - author.i10_index = openalex_author.i10_index - author.cited_by_count = openalex_author.cited_by_count - author.works_count = openalex_author.works_count - - author.save - - authorship_connection = - AuthorshipConnection.find_or_create_by( - author_id: author.id, - work_id: root_work.id - ) - - author_node = - AuthorNode.find_or_create_by( - author_id: author.id, - investigation_id: investigation.id - ) - - AuthorshipEdge.find_or_create_by( - authorship_connection_id: authorship_connection.id, - investigation_id: investigation.id - ) - - circle_coordinates = - circle_point( - center_x = root_work_node.x_coordinate, - center_y = root_work_node.y_coordinate, - radius = 300, - degrees = rand(0..360) # probably fix to more specific options on left/right of root node - ) - - author_node.x_coordinate = - circle_coordinates.first if author_node.x_coordinate.nil? - - author_node.y_coordinate = - circle_coordinates.last if author_node.y_coordinate.nil? - - author_node.save - - author_node.persisted? ? author_node : "uhoh" - end - end -end diff --git a/rails/app/graphql/mutations/create_investigation.rb b/rails/app/graphql/mutations/create_investigation.rb deleted file mode 100644 index 0345c1e..0000000 --- a/rails/app/graphql/mutations/create_investigation.rb +++ /dev/null @@ -1,20 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class CreateInvestigation < BaseMutation - argument :name, String, required: true - - type Types::InvestigationType - - def resolve(**attributes) - authorize_user - - user = context[:current_user] - - investigation = - user.investigations.create!(attributes.merge({ user_id: user.id })) - - investigation.persisted? ? investigation : 'uhoh' - end - end -end diff --git a/rails/app/graphql/mutations/create_note_node.rb b/rails/app/graphql/mutations/create_note_node.rb deleted file mode 100644 index f2a276b..0000000 --- a/rails/app/graphql/mutations/create_note_node.rb +++ /dev/null @@ -1,30 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class CreateNoteNode < BaseMutation - argument :body_text, String - argument :investigation_id, String - - type 'Types::NoteNodeType' - - def resolve(**attributes) - authorize_user - - user = context[:current_user] - - note_node = - NoteNode.create( - investigation_id: attributes[:investigation_id], - body_text: attributes[:body_text] - ) - - note_node.x_coordinate = rand(1000) unless note_node.x_coordinate.present? - note_node.y_coordinate = rand(1000) unless note_node.y_coordinate.present? - note_node.visible = true - - note_node.save - - note_node.persisted? ? note_node : 'uhoh' - end - end -end diff --git a/rails/app/graphql/mutations/create_work_node.rb b/rails/app/graphql/mutations/create_work_node.rb deleted file mode 100644 index 42b1595..0000000 --- a/rails/app/graphql/mutations/create_work_node.rb +++ /dev/null @@ -1,83 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class CreateWorkNode < BaseMutation - argument :doi, String, required: true - argument :investigation_id, String, required: true - - type 'Types::WorkNodeType' - - def resolve(**attributes) - authorize_user - - investigation = Investigation.find(attributes[:investigation_id]) - - openalex_work = OpenalexFacade.get_paper_details(attributes[:doi]) - - authors_list = [] - openalex_work.authors.each do |author| - author_hash = {} - - author[:name].present? ? - author_hash['name'] = author[:name] : - 'Name missing' - - author[:openalex_id].present? ? - author_hash['openalex_id'] = author[:openalex_id].split('/').last : - 'OpenAlex ID not found' - - author[:orcid].present? ? - author_hash['orcid'] = author[:orcid].split('/').last : - 'Orcid not found' - - authors_list << author_hash - end - - authors = [] - - # TODO - fix below - authors_list.each do |author_hash| - authors << Author.find_or_create_by( - name: author_hash['name'], - openalex_id: author_hash['openalex_id'], - orcid: author_hash['orcid'] - ) - end - - work = - Work.find_or_create_by( - doi: openalex_work.doi, - title: openalex_work.title, - openalex_id: openalex_work.openalex_id, - language: openalex_work.language, - publication_year: openalex_work.publication_year, - keywords: openalex_work.keywords, - topics: openalex_work.topics, - is_open_access: openalex_work.is_open_access, - open_access_url: openalex_work.open_access_url, - abstract: openalex_work.abstract - ) - - work_node = - WorkNode.find_or_create_by( - investigation_id: investigation.id.to_s, - work_id: work.id - ) - - work_node.x_coordinate = rand(1000) unless work_node.x_coordinate.present? - work_node.y_coordinate = rand(1000) unless work_node.y_coordinate.present? - work_node.visible = true - - work_node.save - - authors.map do |author| - AuthorshipConnection.find_or_create_by( - author_id: author.id, - work_id: work.id - ) - end - - work_node.persisted? ? work_node : 'no' - end - end -end diff --git a/rails/app/graphql/mutations/delete_note_node.rb b/rails/app/graphql/mutations/delete_note_node.rb deleted file mode 100644 index 4f56305..0000000 --- a/rails/app/graphql/mutations/delete_note_node.rb +++ /dev/null @@ -1,30 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class DeleteNoteNode < BaseMutation - argument :investigation_id, String, required: true - argument :note_node_id, String, required: true # should probably be ID type - - type Types::NoteNodeType - - def resolve(**attributes) - authorize_user - - note = NoteNode.find(attributes[:note_node_id]) - - if note.investigation.user != context[:current_user] - 'Unauthorized' - else - note.delete - - MutationResult.call( - obj: { - object: note - }, - success: true, - errors: 'uhoh' - ) - end - end - end -end diff --git a/rails/app/graphql/mutations/mutation_result.rb b/rails/app/graphql/mutations/mutation_result.rb deleted file mode 100644 index 9470b48..0000000 --- a/rails/app/graphql/mutations/mutation_result.rb +++ /dev/null @@ -1,9 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class MutationResult - def self.call(obj: {}, success: true, errors: []) - obj.merge(success: success, errors: errors) - end - end -end diff --git a/rails/app/graphql/mutations/update_work_node.rb b/rails/app/graphql/mutations/update_work_node.rb deleted file mode 100644 index af9f3c3..0000000 --- a/rails/app/graphql/mutations/update_work_node.rb +++ /dev/null @@ -1,24 +0,0 @@ -# frozen_string_literal: true - -module Mutations - class UpdateWorkNode < BaseMutation - argument :work_node_id, String, required: true - argument :x_coordinate, Integer, required: false - argument :y_coordinate, Integer, required: false - argument :visible, Boolean, required: false - - type Types::WorkNodeType - - def resolve(**attributes) - authorize_user - - work_node = WorkNode.find(attributes[:work_node_id]) - - update_attributes = attributes.except(:work_node_id) - - work_node.update(update_attributes) - - work_node - end - end -end diff --git a/rails/app/graphql/types/author_node_type.rb b/rails/app/graphql/types/author_node_type.rb deleted file mode 100644 index d14913d..0000000 --- a/rails/app/graphql/types/author_node_type.rb +++ /dev/null @@ -1,16 +0,0 @@ -# frozen_string_literal: true - -module Types - class AuthorNodeType < Types::BaseObject - field :id, Integer - field :x_coordinate, Integer - field :y_coordinate, Integer - field :visible, Boolean, null: false - - field :author, 'Types::AuthorType' - - def author - object.author - end - end -end diff --git a/rails/app/graphql/types/author_type.rb b/rails/app/graphql/types/author_type.rb deleted file mode 100644 index 08214a8..0000000 --- a/rails/app/graphql/types/author_type.rb +++ /dev/null @@ -1,16 +0,0 @@ -# frozen_string_literal: true - -module Types - class AuthorType < Types::BaseObject - field :id, ID, null: false - field :name, String - field :orcid, String - field :openalex_id, String - field :h_index, Integer - field :i10_index, Integer - field :cited_by_count, Integer - field :works_count, Integer - field :created_at, GraphQL::Types::ISO8601DateTime, null: false - field :updated_at, GraphQL::Types::ISO8601DateTime, null: false - end -end diff --git a/rails/app/graphql/types/authorship_connection_type.rb b/rails/app/graphql/types/authorship_connection_type.rb deleted file mode 100644 index c471b9a..0000000 --- a/rails/app/graphql/types/authorship_connection_type.rb +++ /dev/null @@ -1,17 +0,0 @@ -# frozen_string_literal: true - -module Types - class AuthorshipConnectionType < BaseObject - field :id, ID, null: false - field :author, Types::AuthorType - field :work, Types::WorkType - - def author - object.author - end - - def work - object.work - end - end -end diff --git a/rails/app/graphql/types/authorship_edge_type.rb b/rails/app/graphql/types/authorship_edge_type.rb deleted file mode 100644 index c7fa067..0000000 --- a/rails/app/graphql/types/authorship_edge_type.rb +++ /dev/null @@ -1,35 +0,0 @@ -# frozen_string_literal: true - -module Types - class AuthorshipEdgeType < BaseObject - field :id, ID, null: false - field :visible, Boolean, null: false - - field :investigation, Types::InvestigationType - field :authorship_connection, Types::AuthorshipConnectionType - field :author_node, Types::AuthorNodeType - field :work_node, Types::WorkNodeType - - def investigation - object.investigation - end - - def authorship_connection - object.authorship_connection - end - - def author_node - AuthorNode.find_by( - investigation_id: object.investigation.id, - author_id: object.authorship_connection.author.id - ) - end - - def work_node - WorkNode.find_by( - investigation_id: object.investigation.id, - work_id: object.authorship_connection.work.id - ) - end - end -end diff --git a/rails/app/graphql/types/connection_type.rb b/rails/app/graphql/types/connection_type.rb deleted file mode 100644 index c563970..0000000 --- a/rails/app/graphql/types/connection_type.rb +++ /dev/null @@ -1,17 +0,0 @@ -# frozen_string_literal: true - -module Types - class ConnectionType < BaseObject - field :id, ID, null: false - field :reference, Types::WorkType - field :citation, Types::WorkType - - def reference - object.reference - end - - def citation - object.citation - end - end -end diff --git a/rails/app/graphql/types/institution_type.rb b/rails/app/graphql/types/institution_type.rb new file mode 100644 index 0000000..bc546ce --- /dev/null +++ b/rails/app/graphql/types/institution_type.rb @@ -0,0 +1,41 @@ +# frozen_string_literal: true + +module Types + class InstitutionType < Types::BaseObject + field :id, ID, null: false + field :openalex_id, String + field :ror, String + field :display_name, String + field :country_code, String + field :institution_type, String + field :homepage_url, String + field :image_url, String + field :image_thumbnail_url, String + field :display_name_acronyms, String + field :display_name_alternatives, String + field :works_count, Integer + field :cited_by_count, Integer + field :works_api_url, String + + field :institutions_ids, Types::InstitutionsIdsType + field :institutions_geo, Types::InstitutionsGeoType + field :institutions_counts_by_year, [Types::InstitutionsCountsByYearType] + field :associated_institutions, [Types::InstitutionType] + + def institutions_ids + object.institutions_ids + end + + def institutions_geo + object.institutions_geo + end + + def institutions_counts_by_year + object.institutions_counts_by_year + end + + def associated_institutions + object.associated_institutions + end + end +end diff --git a/rails/app/graphql/types/institutions_counts_by_year_type.rb b/rails/app/graphql/types/institutions_counts_by_year_type.rb new file mode 100644 index 0000000..e6077c6 --- /dev/null +++ b/rails/app/graphql/types/institutions_counts_by_year_type.rb @@ -0,0 +1,17 @@ +# frozen_string_literal: true + +module Types + class InstitutionsCountsByYearType < Types::BaseObject + field :id, ID, null: false + field :year, Integer + field :works_count, Integer + field :cited_by_count, Integer + field :oa_works_count, Integer + + field :institution, Types::InstitutionType + + def institution + object.institution + end + end +end diff --git a/rails/app/graphql/types/institutions_geo_type.rb b/rails/app/graphql/types/institutions_geo_type.rb new file mode 100644 index 0000000..7aab8e6 --- /dev/null +++ b/rails/app/graphql/types/institutions_geo_type.rb @@ -0,0 +1,20 @@ +# frozen_string_literal: true + +module Types + class InstitutionsGeoType < Types::BaseObject + field :id, ID, null: false + field :institution_id, Integer + field :city, String + field :region, String + field :country_code, String + field :country, String + field :latitude, Float + field :longitude, Float + + field :institution, Types::InstitutionType + + def institution + object.institution + end + end +end diff --git a/rails/app/graphql/types/institutions_ids_type.rb b/rails/app/graphql/types/institutions_ids_type.rb new file mode 100644 index 0000000..780179e --- /dev/null +++ b/rails/app/graphql/types/institutions_ids_type.rb @@ -0,0 +1,20 @@ +# frozen_string_literal: true + +module Types + class InstitutionsIdsType < Types::BaseObject + field :id, ID, null: false + field :institution_id, Integer + field :openalex, String + field :ror, String + field :grid, String + field :wikipedia, String + field :wikidata, String + field :mag, Integer + + field :institution, Types::InstitutionType + + def institution + object.institution + end + end +end diff --git a/rails/app/graphql/types/investigation_type.rb b/rails/app/graphql/types/investigation_type.rb deleted file mode 100644 index 943d267..0000000 --- a/rails/app/graphql/types/investigation_type.rb +++ /dev/null @@ -1,50 +0,0 @@ -# frozen_string_literal: true - -module Types - class InvestigationType < Types::BaseObject - field :id, ID, null: false - field :user_id, Integer - field :name, String - field :created_at, GraphQL::Types::ISO8601DateTime, null: false - field :updated_at, GraphQL::Types::ISO8601DateTime, null: false - - field :note_nodes, [Types::NoteNodeType], null: true - field :author_nodes, [Types::AuthorNodeType], null: true - field :work_nodes, [Types::WorkNodeType], null: true - - field :work_edges, [Types::WorkEdgeType], null: true - field :authorship_edges, [Types::AuthorshipEdgeType], null: true - - def note_nodes - object.note_nodes - end - - def author_nodes - object.author_nodes - end - - def work_nodes - object.work_nodes - end - - def work_edges - object.work_edges - end - - def authorship_edges - object.authorship_edges - end - - # def citation_edges - # object.citation_edges - # end - - # def reference_edges - # object.reference_edges - # end - - # def authorship_edges - # object.authorship_edges - # end - end -end diff --git a/rails/app/graphql/types/mutation_type.rb b/rails/app/graphql/types/mutation_type.rb index 1a761d5..523b451 100644 --- a/rails/app/graphql/types/mutation_type.rb +++ b/rails/app/graphql/types/mutation_type.rb @@ -3,20 +3,20 @@ module Types class MutationType < Types::BaseObject field :register_user, mutation: Mutations::RegisterUser - field :sign_in, mutation: Mutations::SignIn - # field :sign_out, mutation: Mutations::SignOut + # field :sign_in, mutation: Mutations::SignIn + # # field :sign_out, mutation: Mutations::SignOut - field :create_investigation, mutation: Mutations::CreateInvestigation + # field :create_investigation, mutation: Mutations::CreateInvestigation - field :create_work_node, mutation: Mutations::CreateWorkNode - field :update_work_node, mutation: Mutations::UpdateWorkNode - field :add_references, mutation: Mutations::AddReferences - field :add_citations, mutation: Mutations::AddCitations + # field :create_work_node, mutation: Mutations::CreateWorkNode + # field :update_work_node, mutation: Mutations::UpdateWorkNode + # field :add_references, mutation: Mutations::AddReferences + # field :add_citations, mutation: Mutations::AddCitations - field :create_author_node, mutation: Mutations::CreateAuthorNode - field :add_author_works, mutation: Mutations::AddAuthorWorks + # field :create_author_node, mutation: Mutations::CreateAuthorNode + # field :add_author_works, mutation: Mutations::AddAuthorWorks - field :create_note_node, mutation: Mutations::CreateNoteNode - field :delete_note_node, mutation: Mutations::DeleteNoteNode + # field :create_note_node, mutation: Mutations::CreateNoteNode + # field :delete_note_node, mutation: Mutations::DeleteNoteNode end end diff --git a/rails/app/graphql/types/note_node_type.rb b/rails/app/graphql/types/note_node_type.rb deleted file mode 100644 index d7168d1..0000000 --- a/rails/app/graphql/types/note_node_type.rb +++ /dev/null @@ -1,12 +0,0 @@ -# frozen_string_literal: true - -module Types - class NoteNodeType < Types::BaseObject - field :id, Integer - field :x_coordinate, Integer - field :y_coordinate, Integer - field :visible, Boolean, null: false - - field :body_text, String - end -end diff --git a/rails/app/graphql/types/query_type.rb b/rails/app/graphql/types/query_type.rb index 24a9d5e..f0b0fbf 100644 --- a/rails/app/graphql/types/query_type.rb +++ b/rails/app/graphql/types/query_type.rb @@ -27,44 +27,22 @@ def nodes(ids:) # Add root-level fields here. # They will be entry points for queries on your schema. - field :works, - [Types::WorkType], + field :institutions, + [Types::InstitutionType], null: true, - description: 'Fetches all the works' - def works - Work.all + description: 'Fetch all institutions' + def institutions + Institution.all end - field :work, - Types::WorkType, + field :institution, + Types::InstitutionType, null: true, - description: 'Fetches a work by ID' do - argument :id, ID, required: true + description: 'Fetches an institution by ID' do + argument :id, ID, required: true end - def work(id:) - Work.find_by(id: id) - end - - field :investigations, - [Types::InvestigationType], - null: true, - description: 'Fetches all investigations' - def investigations - if context[:current_user].present? - Investigation.where(user_id: context[:current_user].id) - else - [] - end - end - - field :investigation, - Types::InvestigationType, - null: true, - description: 'Fetches an Investigation by ID' do - argument :id, ID, required: true - end - def investigation(id:) - Investigation.find_by(id: id) + def institution(id:) + Institution.find(id) end end end diff --git a/rails/app/graphql/types/work_edge_type.rb b/rails/app/graphql/types/work_edge_type.rb deleted file mode 100644 index 0f16552..0000000 --- a/rails/app/graphql/types/work_edge_type.rb +++ /dev/null @@ -1,44 +0,0 @@ -# frozen_string_literal: true - -module Types - class WorkEdgeType < BaseObject - field :id, ID, null: false - field :visible, Boolean, null: false - field :investigation, Types::InvestigationType - field :connection, Types::ConnectionType - field :citation, Types::WorkType - field :reference, Types::WorkType - field :citation_node, Types::WorkNodeType - field :reference_node, Types::WorkNodeType - - def connection - object.connection - end - - def investigation - object.investigation - end - - def citation - object.connection.citation - end - - def reference - object.connection.reference - end - - def citation_node - WorkNode.find_by( - investigation_id: object.investigation_id, - work_id: object.connection.citation.id - ) - end - - def reference_node - WorkNode.find_by( - investigation_id: object.investigation_id, - work_id: object.connection.reference.id - ) - end - end -end diff --git a/rails/app/graphql/types/work_node_type.rb b/rails/app/graphql/types/work_node_type.rb deleted file mode 100644 index 5f9f9fc..0000000 --- a/rails/app/graphql/types/work_node_type.rb +++ /dev/null @@ -1,16 +0,0 @@ -# frozen_string_literal: true - -module Types - class WorkNodeType < Types::BaseObject - field :id, Integer - field :x_coordinate, Integer - field :y_coordinate, Integer - field :visible, Boolean, null: false - - field :work, Types::WorkType - - def work - object.work - end - end -end diff --git a/rails/app/graphql/types/work_type.rb b/rails/app/graphql/types/work_type.rb deleted file mode 100644 index e9691fd..0000000 --- a/rails/app/graphql/types/work_type.rb +++ /dev/null @@ -1,35 +0,0 @@ -# frozen_string_literal: true - -module Types - class WorkType < Types::BaseObject - field :id, ID, null: false - field :doi, String - field :title, String - field :openalex_id, String - field :language, String - field :publication_year, String - field :keywords, [String] - field :topics, [String] - field :is_open_access, Boolean - field :open_access_url, String - field :created_at, GraphQL::Types::ISO8601DateTime, null: false - field :updated_at, GraphQL::Types::ISO8601DateTime, null: false - field :abstract, String - - field :authors, [Types::AuthorType] - field :citations, [Types::WorkType] - field :references, [Types::WorkType] - - def authors - object.authors - end - - def citations - object.citations - end - - def references - object.references - end - end -end From 5b08a644bfd5b54d64f4a1a500a4c8e4d8d4c32d Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Fri, 4 Oct 2024 16:21:50 +0000 Subject: [PATCH 13/44] start to rework model tests --- rails/spec/models/author_spec.rb | 2 +- rails/spec/models/authors_counts_by_year_spec.rb | 2 +- rails/spec/models/authors_ids_spec.rb | 2 +- rails/spec/models/concept_spec.rb | 5 +++-- rails/spec/models/concepts_counts_by_year_spec.rb | 2 +- rails/spec/models/concepts_ids.rb | 2 +- rails/spec/models/institution_spec.rb | 10 +++++++--- .../spec/models/institutions_counts_by_year_spec.rb | 2 +- rails/spec/models/institutions_geo_spec.rb | 2 +- rails/spec/models/institutions_ids_spec.rb | 2 +- rails/spec/models/publisher_spec.rb | 10 ++++++++++ rails/spec/models/publishers_counts_by_year_spec.rb | 9 +++++++++ ...counts_by_year_spec.rb => publishers_ids_spec.rb} | 6 +++--- rails/spec/models/venue_spec.rb | 12 ------------ rails/spec/models/venues_ids_spec.rb | 9 --------- rails/spec/models/works_biblio_spec.rb | 2 +- rails/spec/models/works_concept_spec.rb | 2 +- rails/spec/models/works_ids_spec.rb | 2 +- rails/spec/models/works_mesh_spec.rb | 2 +- rails/spec/models/works_open_access_spec.rb | 2 +- 20 files changed, 45 insertions(+), 42 deletions(-) create mode 100644 rails/spec/models/publisher_spec.rb create mode 100644 rails/spec/models/publishers_counts_by_year_spec.rb rename rails/spec/models/{venues_counts_by_year_spec.rb => publishers_ids_spec.rb} (50%) delete mode 100644 rails/spec/models/venue_spec.rb delete mode 100644 rails/spec/models/venues_ids_spec.rb diff --git a/rails/spec/models/author_spec.rb b/rails/spec/models/author_spec.rb index ec4124d..17526ef 100644 --- a/rails/spec/models/author_spec.rb +++ b/rails/spec/models/author_spec.rb @@ -15,7 +15,7 @@ describe 'relationships' do # it { should have_many :author_nodes } it { should have_one :authors_ids } - it { should have_one :authors_counts_by_year } + it { should have_many :authors_counts_by_year } it { should have_many :works_authorships } it { should have_many(:institutions).through(:works_authorships) } diff --git a/rails/spec/models/authors_counts_by_year_spec.rb b/rails/spec/models/authors_counts_by_year_spec.rb index 1ff484e..ece737e 100644 --- a/rails/spec/models/authors_counts_by_year_spec.rb +++ b/rails/spec/models/authors_counts_by_year_spec.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :author } end -end \ No newline at end of file +end diff --git a/rails/spec/models/authors_ids_spec.rb b/rails/spec/models/authors_ids_spec.rb index 069171d..3388663 100644 --- a/rails/spec/models/authors_ids_spec.rb +++ b/rails/spec/models/authors_ids_spec.rb @@ -12,4 +12,4 @@ describe 'relationships' do it { should belong_to :author } end -end \ No newline at end of file +end diff --git a/rails/spec/models/concept_spec.rb b/rails/spec/models/concept_spec.rb index bff635a..6da7752 100644 --- a/rails/spec/models/concept_spec.rb +++ b/rails/spec/models/concept_spec.rb @@ -3,7 +3,6 @@ require 'rails_helper' RSpec.describe Concept, type: :model do - describe 'relationships' do it { should have_many :works_concepts } it { should have_many(:works).through(:works_concepts) } @@ -11,6 +10,8 @@ it { should have_one :concepts_ids } it { should have_many(:concepts_related_concepts) } - it { should have_many(:related_concepts).through(:concepts_related_concepts) } + it do + should have_many(:related_concepts).through(:concepts_related_concepts) + end end end diff --git a/rails/spec/models/concepts_counts_by_year_spec.rb b/rails/spec/models/concepts_counts_by_year_spec.rb index d52eded..8644aae 100644 --- a/rails/spec/models/concepts_counts_by_year_spec.rb +++ b/rails/spec/models/concepts_counts_by_year_spec.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :concept } end -end \ No newline at end of file +end diff --git a/rails/spec/models/concepts_ids.rb b/rails/spec/models/concepts_ids.rb index 5f06bbb..841c516 100644 --- a/rails/spec/models/concepts_ids.rb +++ b/rails/spec/models/concepts_ids.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :concept } end -end \ No newline at end of file +end diff --git a/rails/spec/models/institution_spec.rb b/rails/spec/models/institution_spec.rb index c78e1f0..ab9dde1 100644 --- a/rails/spec/models/institution_spec.rb +++ b/rails/spec/models/institution_spec.rb @@ -4,9 +4,13 @@ RSpec.describe Institution, type: :model do describe 'relationships' do - it { should have_one :institutions_counts_by_year } + it { should have_many :institutions_counts_by_year } it { should have_one :institutions_ids } it { should have_one :institutions_geo } - it { should have_many(:associated_institutions).through(:institutions_associated_institutions) } + it do + should have_many(:associated_institutions).through( + :institutions_associated_institutions + ) + end end -end \ No newline at end of file +end diff --git a/rails/spec/models/institutions_counts_by_year_spec.rb b/rails/spec/models/institutions_counts_by_year_spec.rb index 506f7f3..cf60ad4 100644 --- a/rails/spec/models/institutions_counts_by_year_spec.rb +++ b/rails/spec/models/institutions_counts_by_year_spec.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :institution } end -end \ No newline at end of file +end diff --git a/rails/spec/models/institutions_geo_spec.rb b/rails/spec/models/institutions_geo_spec.rb index cb2543d..9d4040b 100644 --- a/rails/spec/models/institutions_geo_spec.rb +++ b/rails/spec/models/institutions_geo_spec.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :institution } end -end \ No newline at end of file +end diff --git a/rails/spec/models/institutions_ids_spec.rb b/rails/spec/models/institutions_ids_spec.rb index 80589ea..d2bc4e0 100644 --- a/rails/spec/models/institutions_ids_spec.rb +++ b/rails/spec/models/institutions_ids_spec.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :institution } end -end \ No newline at end of file +end diff --git a/rails/spec/models/publisher_spec.rb b/rails/spec/models/publisher_spec.rb new file mode 100644 index 0000000..9f0e65c --- /dev/null +++ b/rails/spec/models/publisher_spec.rb @@ -0,0 +1,10 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe Publisher, type: :model do + describe 'relationships' do + it { should have_one :publishers_ids } + it { should have_many :publishers_counts_by_year } + end +end diff --git a/rails/spec/models/publishers_counts_by_year_spec.rb b/rails/spec/models/publishers_counts_by_year_spec.rb new file mode 100644 index 0000000..55145cf --- /dev/null +++ b/rails/spec/models/publishers_counts_by_year_spec.rb @@ -0,0 +1,9 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe PublishersCountsByYear, type: :model do + describe 'relationships' do + it { should belong_to :publisher } + end +end diff --git a/rails/spec/models/venues_counts_by_year_spec.rb b/rails/spec/models/publishers_ids_spec.rb similarity index 50% rename from rails/spec/models/venues_counts_by_year_spec.rb rename to rails/spec/models/publishers_ids_spec.rb index fb7b7b9..56e88b2 100644 --- a/rails/spec/models/venues_counts_by_year_spec.rb +++ b/rails/spec/models/publishers_ids_spec.rb @@ -2,8 +2,8 @@ require 'rails_helper' -RSpec.describe VenuesCountsByYear, type: :model do +RSpec.describe PublishersIds, type: :model do describe 'relationships' do - it { should belong_to :venue } + it { should belong_to :publisher } end -end \ No newline at end of file +end diff --git a/rails/spec/models/venue_spec.rb b/rails/spec/models/venue_spec.rb deleted file mode 100644 index 6ae5119..0000000 --- a/rails/spec/models/venue_spec.rb +++ /dev/null @@ -1,12 +0,0 @@ -# frozen_string_literal: true - -require 'rails_helper' - -RSpec.describe Venue, type: :model do - describe 'relationships' do - # it { should have_many :works_alternate_host_venues } - # it { should have_many(:works).through(:works_alternate_host_venues) } - it { should have_one :venues_counts_by_year } - it { should have_one :venues_ids } - end -end diff --git a/rails/spec/models/venues_ids_spec.rb b/rails/spec/models/venues_ids_spec.rb deleted file mode 100644 index b43a68e..0000000 --- a/rails/spec/models/venues_ids_spec.rb +++ /dev/null @@ -1,9 +0,0 @@ -# frozen_string_literal: true - -require 'rails_helper' - -RSpec.describe VenuesIds, type: :model do - describe 'relationships' do - it { should belong_to :venue } - end -end \ No newline at end of file diff --git a/rails/spec/models/works_biblio_spec.rb b/rails/spec/models/works_biblio_spec.rb index 5aee223..be7c495 100644 --- a/rails/spec/models/works_biblio_spec.rb +++ b/rails/spec/models/works_biblio_spec.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :work } end -end \ No newline at end of file +end diff --git a/rails/spec/models/works_concept_spec.rb b/rails/spec/models/works_concept_spec.rb index 15d9d64..da3e9a2 100644 --- a/rails/spec/models/works_concept_spec.rb +++ b/rails/spec/models/works_concept_spec.rb @@ -7,4 +7,4 @@ it { should belong_to :work } it { should belong_to :concept } end -end \ No newline at end of file +end diff --git a/rails/spec/models/works_ids_spec.rb b/rails/spec/models/works_ids_spec.rb index 1b02b54..0cc9152 100644 --- a/rails/spec/models/works_ids_spec.rb +++ b/rails/spec/models/works_ids_spec.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :work } end -end \ No newline at end of file +end diff --git a/rails/spec/models/works_mesh_spec.rb b/rails/spec/models/works_mesh_spec.rb index 27f71b1..4d35648 100644 --- a/rails/spec/models/works_mesh_spec.rb +++ b/rails/spec/models/works_mesh_spec.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :work } end -end \ No newline at end of file +end diff --git a/rails/spec/models/works_open_access_spec.rb b/rails/spec/models/works_open_access_spec.rb index dd425b7..4aa7023 100644 --- a/rails/spec/models/works_open_access_spec.rb +++ b/rails/spec/models/works_open_access_spec.rb @@ -6,4 +6,4 @@ describe 'relationships' do it { should belong_to :work } end -end \ No newline at end of file +end From 83bf2d9a8b304ebcc978f7a40cb95d97068c0ba1 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Fri, 4 Oct 2024 16:43:47 +0000 Subject: [PATCH 14/44] work on topics/works relationships --- rails/app/models/concept.rb | 4 +++- rails/app/models/concepts_ancestors.rb | 4 +--- rails/app/models/concepts_related_concepts.rb | 8 ++++---- rails/app/models/institution.rb | 6 ++++-- .../models/institutions_associated_institutions.rb | 12 +++++++----- rails/app/models/publisher.rb | 6 ++++++ rails/app/models/publishers_counts_by_year.rb | 5 +++++ rails/app/models/publishers_ids.rb | 5 +++++ rails/app/models/topic.rb | 6 ++++++ rails/app/models/work.rb | 10 +++++++--- rails/app/models/works_referenced_works.rb | 8 ++++---- rails/app/models/works_related_works.rb | 4 +--- rails/app/models/works_topic.rb | 6 ++++++ rails/spec/models/topics_spec.rb | 10 ++++++++++ rails/spec/models/work_spec.rb | 3 +++ rails/spec/models/works_topic_spec.rb | 10 ++++++++++ 16 files changed, 82 insertions(+), 25 deletions(-) create mode 100644 rails/app/models/publisher.rb create mode 100644 rails/app/models/publishers_counts_by_year.rb create mode 100644 rails/app/models/publishers_ids.rb create mode 100644 rails/app/models/topic.rb create mode 100644 rails/app/models/works_topic.rb create mode 100644 rails/spec/models/topics_spec.rb create mode 100644 rails/spec/models/works_topic_spec.rb diff --git a/rails/app/models/concept.rb b/rails/app/models/concept.rb index c081e3e..7204d45 100644 --- a/rails/app/models/concept.rb +++ b/rails/app/models/concept.rb @@ -10,5 +10,7 @@ class Concept < ApplicationRecord foreign_key: :related_concept_id, class_name: 'ConceptsRelatedConcepts' - has_many :related_concepts, through: :concepts_related_concepts, source: :related_concept + has_many :related_concepts, + through: :concepts_related_concepts, + source: :related_concept end diff --git a/rails/app/models/concepts_ancestors.rb b/rails/app/models/concepts_ancestors.rb index b21a9b0..e26ed9f 100644 --- a/rails/app/models/concepts_ancestors.rb +++ b/rails/app/models/concepts_ancestors.rb @@ -1,8 +1,6 @@ # frozen_string_literal: true class ConceptsAncestors < ApplicationRecord - belongs_to :concept, foreign_key: 'concept_id', class_name: 'Concept' belongs_to :ancestor, foreign_key: 'ancestor_id', class_name: 'Concept' - -end \ No newline at end of file +end diff --git a/rails/app/models/concepts_related_concepts.rb b/rails/app/models/concepts_related_concepts.rb index d2f9847..563e972 100644 --- a/rails/app/models/concepts_related_concepts.rb +++ b/rails/app/models/concepts_related_concepts.rb @@ -1,8 +1,8 @@ # frozen_string_literal: true class ConceptsRelatedConcepts < ApplicationRecord - belongs_to :concept, foreign_key: 'concept_id', class_name: 'Concept' - belongs_to :related_concept, foreign_key: 'related_concept_id', class_name: 'Concept' - -end \ No newline at end of file + belongs_to :related_concept, + foreign_key: 'related_concept_id', + class_name: 'Concept' +end diff --git a/rails/app/models/institution.rb b/rails/app/models/institution.rb index 76871b3..2cc42d1 100644 --- a/rails/app/models/institution.rb +++ b/rails/app/models/institution.rb @@ -1,6 +1,6 @@ # frozen_string_literal: true -class Institution < ApplicationRecord +class Institution < ApplicationRecord has_many :institutions_counts_by_year has_one :institutions_geo has_one :institutions_ids @@ -9,5 +9,7 @@ class Institution < ApplicationRecord foreign_key: :associated_institution_id, class_name: 'InstitutionsAssociatedInstitutions' - has_many :associated_institutions, through: :institutions_associated_institutions, source: :institution + has_many :associated_institutions, + through: :institutions_associated_institutions, + source: :institution end diff --git a/rails/app/models/institutions_associated_institutions.rb b/rails/app/models/institutions_associated_institutions.rb index 14b9e32..3bcd2d2 100644 --- a/rails/app/models/institutions_associated_institutions.rb +++ b/rails/app/models/institutions_associated_institutions.rb @@ -1,11 +1,13 @@ # frozen_string_literal: true class InstitutionsAssociatedInstitutions < ApplicationRecord - validates :institution_id, presence: true validates :associated_institution_id, presence: true - belongs_to :institution, foreign_key: 'institution_id', class_name: 'Institution' - belongs_to :associated_institution, foreign_key: 'associated_institution_id', class_name: 'Institution' - -end \ No newline at end of file + belongs_to :institution, + foreign_key: 'institution_id', + class_name: 'Institution' + belongs_to :associated_institution, + foreign_key: 'associated_institution_id', + class_name: 'Institution' +end diff --git a/rails/app/models/publisher.rb b/rails/app/models/publisher.rb new file mode 100644 index 0000000..d06a89c --- /dev/null +++ b/rails/app/models/publisher.rb @@ -0,0 +1,6 @@ +# frozen_string_literal: true + +class Publisher < ApplicationRecord + has_one :publishers_ids + has_many :publishers_counts_by_year +end diff --git a/rails/app/models/publishers_counts_by_year.rb b/rails/app/models/publishers_counts_by_year.rb new file mode 100644 index 0000000..624ddaa --- /dev/null +++ b/rails/app/models/publishers_counts_by_year.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class PublishersCountsByYear < ApplicationRecord + belongs_to :publisher +end diff --git a/rails/app/models/publishers_ids.rb b/rails/app/models/publishers_ids.rb new file mode 100644 index 0000000..d7b2867 --- /dev/null +++ b/rails/app/models/publishers_ids.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class PublishersIds < ApplicationRecord + belongs_to :publisher +end diff --git a/rails/app/models/topic.rb b/rails/app/models/topic.rb new file mode 100644 index 0000000..d967643 --- /dev/null +++ b/rails/app/models/topic.rb @@ -0,0 +1,6 @@ +# frozen_string_literal: true + +class Topic < ApplicationRecord + has_many :works_topics + has_many :works, through: :works_topics +end diff --git a/rails/app/models/work.rb b/rails/app/models/work.rb index 760494b..ef44cf5 100644 --- a/rails/app/models/work.rb +++ b/rails/app/models/work.rb @@ -1,13 +1,12 @@ # frozen_string_literal: true class Work < ApplicationRecord - has_many :works_authorships has_many :authors, through: :works_authorships has_many :institutions, through: :works_authorships # these might need to be has_many - has_one :works_biblio + has_one :works_biblio has_one :works_ids has_one :works_open_access has_one :works_mesh @@ -15,6 +14,9 @@ class Work < ApplicationRecord has_many :works_concepts has_many :concepts, through: :works_concepts + has_many :works_topics + has_many :topics, through: :works_topics + # reference_connections "names" the Connection join table for accessing through the reference association has_many :works_related_works, foreign_key: :related_work_id, @@ -28,5 +30,7 @@ class Work < ApplicationRecord class_name: 'WorksReferencedWorks' # source: :citation matches with the belong_to :citation identification in the Connection model - has_many :referenced_works, through: :works_referenced_works, source: :referenced_work + has_many :referenced_works, + through: :works_referenced_works, + source: :referenced_work end diff --git a/rails/app/models/works_referenced_works.rb b/rails/app/models/works_referenced_works.rb index 34a7079..977d41a 100644 --- a/rails/app/models/works_referenced_works.rb +++ b/rails/app/models/works_referenced_works.rb @@ -1,11 +1,11 @@ # frozen_string_literal: true class WorksReferencedWorks < ApplicationRecord - validates :work_id, presence: true validates :referenced_work_id, presence: true belongs_to :work, foreign_key: 'work_id', class_name: 'Work' - belongs_to :referenced_work, foreign_key: 'referenced_work_id', class_name: 'Work' - -end \ No newline at end of file + belongs_to :referenced_work, + foreign_key: 'referenced_work_id', + class_name: 'Work' +end diff --git a/rails/app/models/works_related_works.rb b/rails/app/models/works_related_works.rb index be90ea2..6258969 100644 --- a/rails/app/models/works_related_works.rb +++ b/rails/app/models/works_related_works.rb @@ -1,11 +1,9 @@ # frozen_string_literal: true class WorksRelatedWorks < ApplicationRecord - validates :work_id, presence: true validates :related_work_id, presence: true belongs_to :work, foreign_key: 'work_id', class_name: 'Work' belongs_to :related_work, foreign_key: 'related_work_id', class_name: 'Work' - -end \ No newline at end of file +end diff --git a/rails/app/models/works_topic.rb b/rails/app/models/works_topic.rb new file mode 100644 index 0000000..d6dd7b5 --- /dev/null +++ b/rails/app/models/works_topic.rb @@ -0,0 +1,6 @@ +# frozen_string_literal: true + +class WorksTopic < ApplicationRecord + belongs_to :work + belongs_to :topic +end diff --git a/rails/spec/models/topics_spec.rb b/rails/spec/models/topics_spec.rb new file mode 100644 index 0000000..56018e9 --- /dev/null +++ b/rails/spec/models/topics_spec.rb @@ -0,0 +1,10 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe Topic, type: :model do + describe 'relationships' do + it { should have_many :works_topics } + it { should have_many(:works).through(:works_topics) } + end +end diff --git a/rails/spec/models/work_spec.rb b/rails/spec/models/work_spec.rb index 49ef79b..a7fdffb 100644 --- a/rails/spec/models/work_spec.rb +++ b/rails/spec/models/work_spec.rb @@ -14,5 +14,8 @@ it { should have_many(:referenced_works).through(:works_referenced_works) } it { should have_many :works_concepts } it { should have_many(:concepts).through(:works_concepts) } + + it { should have_many(:works_topics) } + it { should have_many(:topics).through(:works_topics) } end end diff --git a/rails/spec/models/works_topic_spec.rb b/rails/spec/models/works_topic_spec.rb new file mode 100644 index 0000000..e88ccb2 --- /dev/null +++ b/rails/spec/models/works_topic_spec.rb @@ -0,0 +1,10 @@ +# frozen_string_literal: true + +require 'rails_helper' + +RSpec.describe WorksTopic, type: :model do + describe 'relationships' do + it { should belong_to :work } + it { should belong_to :topic } + end +end From 858368ff20505e6611b5a52d97f8eea4ed6ae031 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 16 Oct 2024 18:35:08 +0000 Subject: [PATCH 15/44] Add data_import rake tasks --- rails/lib/tasks/load_authors.rake | 38 +++++++++++++++ .../tasks/load_authors_counts_by_years.rake | 42 ++++++++++++++++ rails/lib/tasks/load_authors_ids.rake | 42 ++++++++++++++++ rails/lib/tasks/load_institutions.rake | 48 +++++++++++-------- ..._institutions_associated_institutions.rake | 45 +++++++++++++++++ .../load_institutions_counts_by_year.rake | 38 +++++++++++++++ rails/lib/tasks/load_institutions_geo.rake | 47 +++++++++++------- rails/lib/tasks/load_institutions_ids.rake | 39 ++++++++------- rails/lib/tasks/load_publishers.rake | 36 ++++++++++++++ .../tasks/load_publishers_counts_by_year.rake | 37 ++++++++++++++ rails/lib/tasks/load_publishers_ids.rake | 34 +++++++++++++ rails/lib/tasks/verbose.rake | 16 +++++++ 12 files changed, 408 insertions(+), 54 deletions(-) create mode 100644 rails/lib/tasks/load_authors.rake create mode 100644 rails/lib/tasks/load_authors_counts_by_years.rake create mode 100644 rails/lib/tasks/load_authors_ids.rake create mode 100644 rails/lib/tasks/load_institutions_associated_institutions.rake create mode 100644 rails/lib/tasks/load_institutions_counts_by_year.rake create mode 100644 rails/lib/tasks/load_publishers.rake create mode 100644 rails/lib/tasks/load_publishers_counts_by_year.rake create mode 100644 rails/lib/tasks/load_publishers_ids.rake create mode 100644 rails/lib/tasks/verbose.rake diff --git a/rails/lib/tasks/load_authors.rake b/rails/lib/tasks/load_authors.rake new file mode 100644 index 0000000..64f97eb --- /dev/null +++ b/rails/lib/tasks/load_authors.rake @@ -0,0 +1,38 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load Authors from gzipped csv to db' + task load_authors: :environment do + file_paths = Dir['/opt/bookworm/csv-files/authors/author_split*'] + + file_paths.each do |file_path| + authors = [] + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip) + csv + .drop(1) + .each_with_index do |row, index| # drop(1) handles the header row + authors << { + openalex_id: row[0].split('/').last, + orcid: row[1], + display_name: row[2], + display_name_alternatives: row[3], + works_count: row[4].to_i, + cited_by_count: row[5].to_i, + last_known_institution: row[6], + works_api_url: row[7] + } + + if authors.count >= 100 + Author.insert_all(authors) + + authors = [] + end + end + end + Author.insert_all(authors) + end + end +end diff --git a/rails/lib/tasks/load_authors_counts_by_years.rake b/rails/lib/tasks/load_authors_counts_by_years.rake new file mode 100644 index 0000000..0cd86b6 --- /dev/null +++ b/rails/lib/tasks/load_authors_counts_by_years.rake @@ -0,0 +1,42 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load AuthorsCountsByYear from gzipped csv to db' + task load_authors_counts_by_year: :environment do + file_paths = + Dir[ + '/opt/bookworm/csv-files/authors_counts_by_year/authors_counts_by_year_split*' + ] + + file_paths.each do |file_path| + authors_counts_by_year = [] + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip) + + csv.each_with_index do |row, index| # drop(1) handles the header row + author = Author.find_by(openalex_id: row[0].split('/').last) + + unless author.nil? + authors_counts_by_year << { + author_id: author.id, + year: row[1], + works_count: row[2], + cited_by_count: row[3], + oa_works_count: row[4] + } + end + + if authors_counts_by_year.count >= 1000 + AuthorsCountsByYear.insert_all(authors_counts_by_year) + + authors_counts_by_year = [] + end + end + end + + AuthorsCountsByYear.insert_all(authors_counts_by_year) + end + end +end diff --git a/rails/lib/tasks/load_authors_ids.rake b/rails/lib/tasks/load_authors_ids.rake new file mode 100644 index 0000000..9c788a4 --- /dev/null +++ b/rails/lib/tasks/load_authors_ids.rake @@ -0,0 +1,42 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load AuthorsIds from gzipped csv to db' + task load_authors_ids: :environment do + file_paths = Dir['/opt/bookworm/csv-files/authors_ids/authors_ids_split*'] + + file_paths.each do |file_path| + authors_ids = [] + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip) + csv + .drop(1) + .each_with_index do |row, index| # drop(1) handles the header row + author = Author.find_by(openalex_id: row[1].split('/').last) + + unless author.nil? + authors_ids << { + author_id: author.id, + openalex: row[1].split('/').last, + orcid: row[2], + scopus: row[3], + twitter: row[4], + wikipedia: row[5], + mag: row[6] + } + end + + if authors_ids.count >= 100 + AuthorsIds.insert_all(authors_ids) + + authors_ids = [] + end + end + end + + AuthorsIds.insert_all(authors_ids) + end + end +end diff --git a/rails/lib/tasks/load_institutions.rake b/rails/lib/tasks/load_institutions.rake index 939e7a7..c8f48c4 100644 --- a/rails/lib/tasks/load_institutions.rake +++ b/rails/lib/tasks/load_institutions.rake @@ -1,30 +1,36 @@ require 'rake' -require "zlib" +require 'zlib' require 'csv' namespace :data_import do - desc "Load Institutions from gzipped csv to db" - task :load_institutions => :environment do + desc 'Load Institutions from gzipped csv to db' + task load_institutions: :environment do + institutions = [] - Zlib::GzipReader.open('/opt/bookworm/csv-files/institutions.csv.gz') do |gzip| + Zlib::GzipReader.open( + '/opt/bookworm/csv-files/institutions.csv.gz' + ) do |gzip| csv = CSV.new(gzip) - csv.drop(1).each_with_index do |row, index| # drop(1) handles the header row - Institution.create( - openalex_id: row[0].split("/").last, - ror: row[1], - display_name: row[2], - country_code: row[3], - institution_type: row[4], - homepage_url: row[5], - image_url: row[6], - image_thumbnail_url: row[7], - display_name_acronyms: row[8], - display_name_alternatives: row[9], - works_count: row[10], - cited_by_count: row[11], - works_api_url: row[12] - ) - end + csv + .drop(1) + .each_with_index do |row, index| # drop(1) handles the header row + institutions << { + openalex_id: row[0].split('/').last, + ror: row[1], + display_name: row[2], + country_code: row[3], + institution_type: row[4], + homepage_url: row[5], + image_url: row[6], + image_thumbnail_url: row[7], + display_name_acronyms: row[8], + display_name_alternatives: row[9], + works_count: row[10], + cited_by_count: row[11], + works_api_url: row[12] + } + end end + Institution.insert_all(institutions) end end diff --git a/rails/lib/tasks/load_institutions_associated_institutions.rake b/rails/lib/tasks/load_institutions_associated_institutions.rake new file mode 100644 index 0000000..ee8e6ca --- /dev/null +++ b/rails/lib/tasks/load_institutions_associated_institutions.rake @@ -0,0 +1,45 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load InstitutionsAssociatedInstitutions from gzipped csv to db' + task load_institutions_associated_institutions: :environment do + institutions_associated_institutions = [] + + Zlib::GzipReader.open( + '/opt/bookworm/csv-files/institutions_associated_institutions.csv.gz' + ) do |gzip| + csv = CSV.new(gzip) + + csv + .drop(1) + .each_with_index do |row, index| # drop(1) handles the header row + institution = Institution.find_by(openalex_id: row[0].split('/').last) + + associated_institution = + Institution.find_by(openalex_id: row[1].split('/').last) + + unless institution.nil? || associated_institution.nil? + institutions_associated_institutions << { + institution_id: institution.id, + associated_institution_id: associated_institution.id, + relationship: row[2] + } + end + + if institutions_associated_institutions.count >= 100 + InstitutionsAssociatedInstitutions.insert_all( + institutions_associated_institutions + ) + + institutions_associated_institutions = [] + end + end + end + + InstitutionsAssociatedInstitutions.insert_all( + institutions_associated_institutions + ) + end +end diff --git a/rails/lib/tasks/load_institutions_counts_by_year.rake b/rails/lib/tasks/load_institutions_counts_by_year.rake new file mode 100644 index 0000000..275b520 --- /dev/null +++ b/rails/lib/tasks/load_institutions_counts_by_year.rake @@ -0,0 +1,38 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load InstitutionsCountsByYear from gzipped csv to db' + task load_institutions_counts_by_year: :environment do + institutions_counts_by_years = [] + + Zlib::GzipReader.open( + '/opt/bookworm/csv-files/institutions_counts_by_year.csv.gz' + ) do |gzip| + csv = CSV.new(gzip) + + csv + .drop(1) + .each_with_index do |row, index| # drop(1) handles the header row + institution = Institution.find_by(openalex_id: row[0].split('/').last) + + institutions_counts_by_years << { + institution_id: institution.id, + year: row[1], + works_count: row[2], + cited_by_count: row[3], + oa_works_count: row[4] + } + + if institutions_counts_by_years.count >= 100 + InstitutionsCountsByYear.insert_all(institutions_counts_by_years) + + institutions_counts_by_years = [] + end + end + end + + InstitutionsCountsByYear.insert_all(institutions_counts_by_years) + end +end diff --git a/rails/lib/tasks/load_institutions_geo.rake b/rails/lib/tasks/load_institutions_geo.rake index 2d21831..652bab0 100644 --- a/rails/lib/tasks/load_institutions_geo.rake +++ b/rails/lib/tasks/load_institutions_geo.rake @@ -1,27 +1,40 @@ require 'rake' -require "zlib" +require 'zlib' require 'csv' namespace :data_import do - desc "Load InstitutionsGeo from gzipped csv to db" - task :load_institutions_geo => :environment do + desc 'Load InstitutionsGeo from gzipped csv to db' + task load_institutions_geo: :environment do + institutions_geos = [] - Zlib::GzipReader.open('/opt/bookworm/csv-files/institutions_geo.csv.gz') do |gzip| + Zlib::GzipReader.open( + '/opt/bookworm/csv-files/institutions_geo.csv.gz' + ) do |gzip| csv = CSV.new(gzip) - csv.drop(1).each_with_index do |row, index| # drop(1) handles the header row - institution = Institution.find_by(openalex_id: row[0].split("/").last) + csv + .drop(1) + .each_with_index do |row, index| # drop(1) handles the header row + institution = Institution.find_by(openalex_id: row[0].split('/').last) - InstitutionsGeo.create( - institution_id: institution.id, - city: row[1], - geonames_city_id: row[2], - region: row[3], - country_code: row[4], - country: row[5], - latitude: row[6], - longitude: row[7] - ) - end + institutions_geos << { + institution_id: institution.id, + city: row[1], + geonames_city_id: row[2], + region: row[3], + country_code: row[4], + country: row[5], + latitude: row[6], + longitude: row[7] + } + + if institutions_geos.count >= 100 + InstitutionsGeo.insert_all(institutions_geos) + + institutions_geos = [] + end + end end + + InstitutionsGeo.insert_all(institutions_geos) end end diff --git a/rails/lib/tasks/load_institutions_ids.rake b/rails/lib/tasks/load_institutions_ids.rake index 20cadb5..727e472 100644 --- a/rails/lib/tasks/load_institutions_ids.rake +++ b/rails/lib/tasks/load_institutions_ids.rake @@ -1,26 +1,33 @@ require 'rake' -require "zlib" +require 'zlib' require 'csv' namespace :data_import do - desc "Load InstitutionsIds from gzipped csv to db" - task :load_institutions_ids => :environment do + desc 'Load InstitutionsIds from gzipped csv to db' + task load_institutions_ids: :environment do + institution_ids = [] - Zlib::GzipReader.open('/opt/bookworm/csv-files/institutions_ids.csv.gz') do |gzip| + Zlib::GzipReader.open( + '/opt/bookworm/csv-files/institutions_ids.csv.gz' + ) do |gzip| csv = CSV.new(gzip) - csv.drop(1).each_with_index do |row, index| # drop(1) handles the header row - institution = Institution.find_by(openalex_id: row[0].split("/").last) + csv + .drop(1) + .each_with_index do |row, index| # drop(1) handles the header row + institution = Institution.find_by(openalex_id: row[0].split('/').last) - InstitutionsIds.create( - institution_id: institution.id, - openalex: row[0].split("/").last, - ror: row[2], - grid: row[3], - wikipedia: row[4], - wikidata: row[5], - mag: row[6] - ) - end + institution_ids << { + institution_id: institution.id, + openalex: row[0].split('/').last, + ror: row[2], + grid: row[3], + wikipedia: row[4], + wikidata: row[5], + mag: row[6] + } + end end + + InstitutionsIds.insert_all(institution_ids) end end diff --git a/rails/lib/tasks/load_publishers.rake b/rails/lib/tasks/load_publishers.rake new file mode 100644 index 0000000..1c347f9 --- /dev/null +++ b/rails/lib/tasks/load_publishers.rake @@ -0,0 +1,36 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load Publishers from gzipped csv' + task load_publishers: :environment do + file_path = '/opt/bookworm/csv-files/publishers.csv.gz' + + Zlib::GzipReader.open(file_path) do |gzip| + publishers = [] + csv = CSV.new(gzip) + + csv.drop(1).each_with_index do |row, index| + publishers << { + openalex_id: row[0].split('/').last, + display_name: row[1], + alternate_titles: row[2], + country_codes: row[3], + hierarchy_level: row[4], + parent_publisher: row[5], + works_count: row[6], + cited_by_count: row[7], + sources_api_url: row[8], + } + + if publishers.count >= 500 + Publisher.insert_all(publishers) + + publishers = [] + end + end + Publisher.insert_all(publishers) + end + end +end \ No newline at end of file diff --git a/rails/lib/tasks/load_publishers_counts_by_year.rake b/rails/lib/tasks/load_publishers_counts_by_year.rake new file mode 100644 index 0000000..610b945 --- /dev/null +++ b/rails/lib/tasks/load_publishers_counts_by_year.rake @@ -0,0 +1,37 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load PublishersCountsByYear from gzipped csv to db' + task load_publishers_counts_by_year: :environment do + file_path = '/opt/bookworm/csv-files/publishers_counts_by_year.csv.gz' + + publishers_counts_by_years = [] + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip) + + csv.each_with_index do |row, index| + publisher = Publisher.find_by(openalex_id: row[0].split('/').last) + + unless publisher.nil? + publishers_counts_by_years << { + publisher_id: publisher.id, + year: row[1], + works_count: row[2], + cited_by_count: row[3], + oa_works_count: row[4] + } + end + + if publishers_counts_by_years.count >= 1000 + PublishersCountsByYear.insert_all(publishers_counts_by_years) + + publishers_counts_by_years = [] + end + end + end + + PublishersCountsByYear.insert_all(publishers_counts_by_years) + end +end \ No newline at end of file diff --git a/rails/lib/tasks/load_publishers_ids.rake b/rails/lib/tasks/load_publishers_ids.rake new file mode 100644 index 0000000..d2bd20c --- /dev/null +++ b/rails/lib/tasks/load_publishers_ids.rake @@ -0,0 +1,34 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load PublishersIds from gzipped csv to db' + task load_publishers_ids: :environment do + file_path = '/opt/bookworm/csv-files/publishers_ids.csv.gz' + publishers_ids = [] + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip) + + csv.each_with_index do |row, index| + publisher = Publisher.find_by(openalex_id: row[0].split('/').last) + + unless publisher.nil? + publishers_ids << { + publisher_id: publisher.id, + openalex: row[1].split('/').last, + ror: row[2], + wikidata: row[3] + } + end + + if publishers_ids.count >= 1000 + PublishersIds.insert_all(publishers_ids) + + publishers_ids = [] + end + end + end + PublishersIds.insert_all(publishers_ids) + end +end diff --git a/rails/lib/tasks/verbose.rake b/rails/lib/tasks/verbose.rake new file mode 100644 index 0000000..33ccd96 --- /dev/null +++ b/rails/lib/tasks/verbose.rake @@ -0,0 +1,16 @@ +desc 'Switch Rails logger to stdout (app level)' +task v: :environment do + init_logger +end + +desc 'Switch Rails logger to stdout (debug level)' +task vd: :environment do + init_logger + Rails.logger.level = 0 +end + +def init_logger + stdout_logger = Logger.new(STDOUT) + file_logger = Logger.new("#{Rails.env}.log") + ActiveSupport::BroadcastLogger.new(stdout_logger, file_logger) +end From a94386d869b443f1198686f776d0ded2761d9c95 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 16 Oct 2024 18:35:30 +0000 Subject: [PATCH 16/44] Add migrations --- .../migrate/20240628174721_create_topics.rb | 1 - .../migrate/20240628174722_create_authors.rb | 2 +- ...28174723_create_authors_counts_by_years.rb | 2 +- .../20240628174724_create_authors_ids.rb | 2 +- .../migrate/20240628174726_create_concepts.rb | 1 - .../20240628174731_create_institutions.rb | 1 - ...te_institutions_associated_institutions.rb | 1 - ...733_create_institutions_counts_by_years.rb | 1 - ...20240628174734_create_institutions_geos.rb | 1 - .../20240628174735_create_institutions_ids.rb | 1 - .../20240628174736_create_publishers.rb | 1 - ...74737_create_publishers_counts_by_years.rb | 1 - .../20240628174738_create_publishers_ids.rb | 1 - .../migrate/20240628174739_create_sources.rb | 1 - ...28174740_create_sources_counts_by_years.rb | 1 - .../20240628174741_create_sources_ids.rb | 1 - .../db/migrate/20240628174742_create_works.rb | 1 - ...28174743_create_works_primary_locations.rb | 1 - .../20240628174744_create_works_locations.rb | 1 - ...28174745_create_works_best_oa_locations.rb | 1 - .../20240628174748_create_works_topics.rb | 1 - .../20240628174749_create_works_concepts.rb | 3 +- .../20240628174750_create_works_ids.rb | 1 - .../20240628174751_create_works_meshes.rb | 1 - ...240628174752_create_works_open_accesses.rb | 1 - ...628174753_create_works_referenced_works.rb | 1 - ...or_institutions_associated_institutions.rb | 21 +++ ...41003155622_add_open_alex_id_to_authors.rb | 5 + ...623_change_openalex_id_type_for_authors.rb | 5 + ...624_add_openalex_id_indexing_to_authors.rb | 5 + ...03155625_add_open_alex_id_to_publishers.rb | 5 + ..._change_openalex_id_type_for_publishers.rb | 5 + ..._add_openalex_id_indexing_to_publishers.rb | 5 + rails/db/schema.rb | 134 +++++++----------- 34 files changed, 108 insertions(+), 108 deletions(-) create mode 100644 rails/db/migrate/20241003012114_change_id_types_for_institutions_associated_institutions.rb create mode 100644 rails/db/migrate/20241003155622_add_open_alex_id_to_authors.rb create mode 100644 rails/db/migrate/20241003155623_change_openalex_id_type_for_authors.rb create mode 100644 rails/db/migrate/20241003155624_add_openalex_id_indexing_to_authors.rb create mode 100644 rails/db/migrate/20241003155625_add_open_alex_id_to_publishers.rb create mode 100644 rails/db/migrate/20241003155626_change_openalex_id_type_for_publishers.rb create mode 100644 rails/db/migrate/20241003155627_add_openalex_id_indexing_to_publishers.rb diff --git a/rails/db/migrate/20240628174721_create_topics.rb b/rails/db/migrate/20240628174721_create_topics.rb index 3434d05..a4a863a 100644 --- a/rails/db/migrate/20240628174721_create_topics.rb +++ b/rails/db/migrate/20240628174721_create_topics.rb @@ -16,7 +16,6 @@ def change t.bigint :cited_by_count # siblings??? not documented but probably relationships of topics? - end end end diff --git a/rails/db/migrate/20240628174722_create_authors.rb b/rails/db/migrate/20240628174722_create_authors.rb index 4bd5b5e..8daa8b3 100644 --- a/rails/db/migrate/20240628174722_create_authors.rb +++ b/rails/db/migrate/20240628174722_create_authors.rb @@ -7,7 +7,7 @@ def change t.bigint :works_count t.bigint :cited_by_count t.string :last_known_institution - t.string :works_api_url + t.string :works_api_url end end end diff --git a/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb b/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb index e05f40d..a2f8dbc 100644 --- a/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb +++ b/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb @@ -5,7 +5,7 @@ def change t.bigint :year, null: false t.bigint :works_count t.bigint :cited_by_count - t.bigint :oa_works_count + t.bigint :oa_works_count t.timestamps end diff --git a/rails/db/migrate/20240628174724_create_authors_ids.rb b/rails/db/migrate/20240628174724_create_authors_ids.rb index 9632fcc..62c3bf3 100644 --- a/rails/db/migrate/20240628174724_create_authors_ids.rb +++ b/rails/db/migrate/20240628174724_create_authors_ids.rb @@ -7,7 +7,7 @@ def change t.string :scopus t.string :twitter t.string :wikipedia - t.bigint :mag + t.bigint :mag t.timestamps end diff --git a/rails/db/migrate/20240628174726_create_concepts.rb b/rails/db/migrate/20240628174726_create_concepts.rb index 73200e1..e1de0b6 100644 --- a/rails/db/migrate/20240628174726_create_concepts.rb +++ b/rails/db/migrate/20240628174726_create_concepts.rb @@ -10,7 +10,6 @@ def change t.string :image_url t.string :image_thumbnail_url t.string :works_api_url - end end end diff --git a/rails/db/migrate/20240628174731_create_institutions.rb b/rails/db/migrate/20240628174731_create_institutions.rb index 8ac8288..5de6342 100644 --- a/rails/db/migrate/20240628174731_create_institutions.rb +++ b/rails/db/migrate/20240628174731_create_institutions.rb @@ -14,7 +14,6 @@ def change t.bigint :works_count t.bigint :cited_by_count t.string :works_api_url - end end end diff --git a/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb b/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb index 53b6b00..6d08390 100644 --- a/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb +++ b/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb @@ -4,7 +4,6 @@ def change t.string :institution_id t.string :associated_institution_id t.string :relationship - end end end diff --git a/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb b/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb index e57fe0e..cff24e0 100644 --- a/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb +++ b/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb @@ -6,7 +6,6 @@ def change t.bigint :works_count t.bigint :cited_by_count t.bigint :oa_works_count - end end end diff --git a/rails/db/migrate/20240628174734_create_institutions_geos.rb b/rails/db/migrate/20240628174734_create_institutions_geos.rb index f354452..46b742d 100644 --- a/rails/db/migrate/20240628174734_create_institutions_geos.rb +++ b/rails/db/migrate/20240628174734_create_institutions_geos.rb @@ -9,7 +9,6 @@ def change t.string :country t.float :latitude t.float :longitude - end end end diff --git a/rails/db/migrate/20240628174735_create_institutions_ids.rb b/rails/db/migrate/20240628174735_create_institutions_ids.rb index 99fa4b6..24f1b67 100644 --- a/rails/db/migrate/20240628174735_create_institutions_ids.rb +++ b/rails/db/migrate/20240628174735_create_institutions_ids.rb @@ -8,7 +8,6 @@ def change t.string :wikipedia t.string :wikidata t.bigint :mag - end end end diff --git a/rails/db/migrate/20240628174736_create_publishers.rb b/rails/db/migrate/20240628174736_create_publishers.rb index 33bfefd..59a8a18 100644 --- a/rails/db/migrate/20240628174736_create_publishers.rb +++ b/rails/db/migrate/20240628174736_create_publishers.rb @@ -9,7 +9,6 @@ def change t.bigint :works_count t.bigint :cited_by_count t.string :sources_api_url - end end end diff --git a/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb b/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb index d3b2930..d98aaed 100644 --- a/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb +++ b/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb @@ -6,7 +6,6 @@ def change t.bigint :works_count t.bigint :cited_by_count t.bigint :oa_works_count - end end end diff --git a/rails/db/migrate/20240628174738_create_publishers_ids.rb b/rails/db/migrate/20240628174738_create_publishers_ids.rb index 7fb683f..be8ec72 100644 --- a/rails/db/migrate/20240628174738_create_publishers_ids.rb +++ b/rails/db/migrate/20240628174738_create_publishers_ids.rb @@ -5,7 +5,6 @@ def change t.string :openalex t.string :ror t.string :wikidata - end end end diff --git a/rails/db/migrate/20240628174739_create_sources.rb b/rails/db/migrate/20240628174739_create_sources.rb index 8712741..a338e4f 100644 --- a/rails/db/migrate/20240628174739_create_sources.rb +++ b/rails/db/migrate/20240628174739_create_sources.rb @@ -11,7 +11,6 @@ def change t.boolean :is_in_doaj t.string :homepage_url t.string :works_api_url - end end end diff --git a/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb b/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb index 2827710..707852d 100644 --- a/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb +++ b/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb @@ -6,7 +6,6 @@ def change t.bigint :works_count t.bigint :cited_by_count t.bigint :oa_works_count - end end end diff --git a/rails/db/migrate/20240628174741_create_sources_ids.rb b/rails/db/migrate/20240628174741_create_sources_ids.rb index 4c2cf6d..aadcc7f 100644 --- a/rails/db/migrate/20240628174741_create_sources_ids.rb +++ b/rails/db/migrate/20240628174741_create_sources_ids.rb @@ -8,7 +8,6 @@ def change t.bigint :mag t.string :wikidata t.string :fatcat - end end end diff --git a/rails/db/migrate/20240628174742_create_works.rb b/rails/db/migrate/20240628174742_create_works.rb index 9c8d548..9e16d28 100644 --- a/rails/db/migrate/20240628174742_create_works.rb +++ b/rails/db/migrate/20240628174742_create_works.rb @@ -15,7 +15,6 @@ def change t.string :cited_by_api_url t.jsonb :abstract_inverted_index t.string :language - end end end diff --git a/rails/db/migrate/20240628174743_create_works_primary_locations.rb b/rails/db/migrate/20240628174743_create_works_primary_locations.rb index 39a02b8..01ed5d7 100644 --- a/rails/db/migrate/20240628174743_create_works_primary_locations.rb +++ b/rails/db/migrate/20240628174743_create_works_primary_locations.rb @@ -10,7 +10,6 @@ def change t.boolean :is_oa t.string :version t.string :license - end end end diff --git a/rails/db/migrate/20240628174744_create_works_locations.rb b/rails/db/migrate/20240628174744_create_works_locations.rb index 587d4c5..b6ae9b4 100644 --- a/rails/db/migrate/20240628174744_create_works_locations.rb +++ b/rails/db/migrate/20240628174744_create_works_locations.rb @@ -10,7 +10,6 @@ def change t.boolean :is_oa t.string :version t.string :license - end end end diff --git a/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb b/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb index f8f190d..5e0f15e 100644 --- a/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb +++ b/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb @@ -10,7 +10,6 @@ def change t.boolean :is_oa t.string :version t.string :license - end end end diff --git a/rails/db/migrate/20240628174748_create_works_topics.rb b/rails/db/migrate/20240628174748_create_works_topics.rb index 63a00d1..a389611 100644 --- a/rails/db/migrate/20240628174748_create_works_topics.rb +++ b/rails/db/migrate/20240628174748_create_works_topics.rb @@ -4,7 +4,6 @@ def change t.references :work, null: false, foreign_key: true t.references :topic, null: false, foreign_key: true t.float :score - end end end diff --git a/rails/db/migrate/20240628174749_create_works_concepts.rb b/rails/db/migrate/20240628174749_create_works_concepts.rb index b2d3f5a..f1f0879 100644 --- a/rails/db/migrate/20240628174749_create_works_concepts.rb +++ b/rails/db/migrate/20240628174749_create_works_concepts.rb @@ -3,9 +3,8 @@ def change create_table :works_concepts do |t| t.references :work, null: false, foreign_key: true t.references :concept, null: false, foreign_key: true - - t.float :score + t.float :score end end end diff --git a/rails/db/migrate/20240628174750_create_works_ids.rb b/rails/db/migrate/20240628174750_create_works_ids.rb index a02f9fb..2f2c91a 100644 --- a/rails/db/migrate/20240628174750_create_works_ids.rb +++ b/rails/db/migrate/20240628174750_create_works_ids.rb @@ -7,7 +7,6 @@ def change t.bigint :mag t.string :pmid t.string :pmcid - end end end diff --git a/rails/db/migrate/20240628174751_create_works_meshes.rb b/rails/db/migrate/20240628174751_create_works_meshes.rb index a18b6cc..5d227b4 100644 --- a/rails/db/migrate/20240628174751_create_works_meshes.rb +++ b/rails/db/migrate/20240628174751_create_works_meshes.rb @@ -7,7 +7,6 @@ def change t.string :qualifier_ui t.string :qualifier_name t.boolean :is_major_topic - end end end diff --git a/rails/db/migrate/20240628174752_create_works_open_accesses.rb b/rails/db/migrate/20240628174752_create_works_open_accesses.rb index c030b59..78ed98d 100644 --- a/rails/db/migrate/20240628174752_create_works_open_accesses.rb +++ b/rails/db/migrate/20240628174752_create_works_open_accesses.rb @@ -6,7 +6,6 @@ def change t.string :oa_status t.string :oa_url t.boolean :any_repository_has_fulltext - end end end diff --git a/rails/db/migrate/20240628174753_create_works_referenced_works.rb b/rails/db/migrate/20240628174753_create_works_referenced_works.rb index 9e7c5ef..7d5c4b4 100644 --- a/rails/db/migrate/20240628174753_create_works_referenced_works.rb +++ b/rails/db/migrate/20240628174753_create_works_referenced_works.rb @@ -5,7 +5,6 @@ def change t.string :referenced_work_id # self-referential many-to-many - end end end diff --git a/rails/db/migrate/20241003012114_change_id_types_for_institutions_associated_institutions.rb b/rails/db/migrate/20241003012114_change_id_types_for_institutions_associated_institutions.rb new file mode 100644 index 0000000..cc9e9fb --- /dev/null +++ b/rails/db/migrate/20241003012114_change_id_types_for_institutions_associated_institutions.rb @@ -0,0 +1,21 @@ +class ChangeIdTypesForInstitutionsAssociatedInstitutions < ActiveRecord::Migration[ + 7.1 +] + def up + connection.execute( + ' + alter table institutions_associated_institutions + alter column institution_id + type integer using cast(institution_id as integer) + ' + ) + + connection.execute( + ' + alter table institutions_associated_institutions + alter column associated_institution_id + type integer using cast(associated_institution_id as integer) + ' + ) + end +end diff --git a/rails/db/migrate/20241003155622_add_open_alex_id_to_authors.rb b/rails/db/migrate/20241003155622_add_open_alex_id_to_authors.rb new file mode 100644 index 0000000..99b879e --- /dev/null +++ b/rails/db/migrate/20241003155622_add_open_alex_id_to_authors.rb @@ -0,0 +1,5 @@ +class AddOpenAlexIdToAuthors < ActiveRecord::Migration[7.1] + def change + add_column :authors, :openalex_id, :integer + end +end diff --git a/rails/db/migrate/20241003155623_change_openalex_id_type_for_authors.rb b/rails/db/migrate/20241003155623_change_openalex_id_type_for_authors.rb new file mode 100644 index 0000000..6414343 --- /dev/null +++ b/rails/db/migrate/20241003155623_change_openalex_id_type_for_authors.rb @@ -0,0 +1,5 @@ +class ChangeOpenalexIdTypeForAuthors < ActiveRecord::Migration[7.1] + def change + change_column(:authors, :openalex_id, :string) + end +end diff --git a/rails/db/migrate/20241003155624_add_openalex_id_indexing_to_authors.rb b/rails/db/migrate/20241003155624_add_openalex_id_indexing_to_authors.rb new file mode 100644 index 0000000..1182f7f --- /dev/null +++ b/rails/db/migrate/20241003155624_add_openalex_id_indexing_to_authors.rb @@ -0,0 +1,5 @@ +class AddOpenalexIdIndexingToAuthors < ActiveRecord::Migration[7.1] + def change + add_index :authors, :openalex_id + end +end diff --git a/rails/db/migrate/20241003155625_add_open_alex_id_to_publishers.rb b/rails/db/migrate/20241003155625_add_open_alex_id_to_publishers.rb new file mode 100644 index 0000000..4e66850 --- /dev/null +++ b/rails/db/migrate/20241003155625_add_open_alex_id_to_publishers.rb @@ -0,0 +1,5 @@ +class AddOpenAlexIdToPublishers < ActiveRecord::Migration[7.1] + def change + add_column :publishers, :openalex_id, :integer + end +end diff --git a/rails/db/migrate/20241003155626_change_openalex_id_type_for_publishers.rb b/rails/db/migrate/20241003155626_change_openalex_id_type_for_publishers.rb new file mode 100644 index 0000000..dbdd22b --- /dev/null +++ b/rails/db/migrate/20241003155626_change_openalex_id_type_for_publishers.rb @@ -0,0 +1,5 @@ +class ChangeOpenalexIdTypeForPublishers < ActiveRecord::Migration[7.1] + def change + change_column(:publishers, :openalex_id, :string) + end +end diff --git a/rails/db/migrate/20241003155627_add_openalex_id_indexing_to_publishers.rb b/rails/db/migrate/20241003155627_add_openalex_id_indexing_to_publishers.rb new file mode 100644 index 0000000..7ab0be0 --- /dev/null +++ b/rails/db/migrate/20241003155627_add_openalex_id_indexing_to_publishers.rb @@ -0,0 +1,5 @@ +class AddOpenalexIdIndexingToPublishers < ActiveRecord::Migration[7.1] + def change + add_index :publishers, :openalex_id + end +end diff --git a/rails/db/schema.rb b/rails/db/schema.rb index 1f31511..9df9ec9 100644 --- a/rails/db/schema.rb +++ b/rails/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema[7.1].define(version: 2024_06_28_174757) do +ActiveRecord::Schema[7.1].define(version: 2024_10_03_155627) do # These are extensions that must be enabled in order to support this database enable_extension "plpgsql" @@ -18,20 +18,20 @@ t.string "orcid" t.string "display_name" t.jsonb "display_name_alternatives" - t.integer "works_count" - t.integer "cited_by_count" + t.bigint "works_count" + t.bigint "cited_by_count" t.string "last_known_institution" t.string "works_api_url" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false + t.string "openalex_id" + t.index ["openalex_id"], name: "index_authors_on_openalex_id" end create_table "authors_counts_by_years", force: :cascade do |t| t.bigint "author_id", null: false - t.integer "year", null: false - t.integer "works_count" - t.integer "cited_by_count" - t.integer "oa_works_count" + t.bigint "year", null: false + t.bigint "works_count" + t.bigint "cited_by_count" + t.bigint "oa_works_count" t.datetime "created_at", null: false t.datetime "updated_at", null: false t.index ["author_id"], name: "index_authors_counts_by_years_on_author_id" @@ -41,8 +41,10 @@ t.bigint "author_id", null: false t.string "openalex" t.string "orcid" + t.string "scopus" + t.string "twitter" t.string "wikipedia" - t.integer "mag" + t.bigint "mag" t.datetime "created_at", null: false t.datetime "updated_at", null: false t.index ["author_id"], name: "index_authors_ids_on_author_id" @@ -51,10 +53,10 @@ create_table "concepts", force: :cascade do |t| t.string "wikidata" t.string "display_name" - t.integer "level" + t.bigint "level" t.string "description" - t.integer "works_count" - t.integer "cited_by_count" + t.bigint "works_count" + t.bigint "cited_by_count" t.string "image_url" t.string "image_thumbnail_url" t.string "works_api_url" @@ -69,10 +71,10 @@ create_table "concepts_counts_by_years", force: :cascade do |t| t.bigint "concept_id", null: false - t.integer "year", null: false - t.integer "works_count" - t.integer "cited_by_count" - t.integer "oa_works_count" + t.bigint "year", null: false + t.bigint "works_count" + t.bigint "cited_by_count" + t.bigint "oa_works_count" t.index ["concept_id"], name: "index_concepts_counts_by_years_on_concept_id" end @@ -83,7 +85,7 @@ t.string "wikipedia" t.jsonb "umls_aui" t.jsonb "umls_cui" - t.integer "mag" + t.bigint "mag" t.index ["concept_id"], name: "index_concepts_ids_on_concept_id" end @@ -94,31 +96,33 @@ end create_table "institutions", force: :cascade do |t| + t.string "openalex_id" t.string "ror" t.string "display_name" t.string "country_code" - t.string "type" + t.string "institution_type" t.string "homepage_url" t.string "image_url" t.string "image_thumbnail_url" t.jsonb "display_name_acronyms" t.jsonb "display_name_alternatives" - t.integer "works_count" - t.integer "cited_by_count" + t.bigint "works_count" + t.bigint "cited_by_count" t.string "works_api_url" end create_table "institutions_associated_institutions", force: :cascade do |t| - t.string "institution_id" - t.string "associated_institution_id" + t.integer "institution_id" + t.integer "associated_institution_id" t.string "relationship" end create_table "institutions_counts_by_years", force: :cascade do |t| t.bigint "institution_id", null: false - t.integer "year" - t.integer "works_count" - t.integer "oa_works_count" + t.bigint "year" + t.bigint "works_count" + t.bigint "cited_by_count" + t.bigint "oa_works_count" t.index ["institution_id"], name: "index_institutions_counts_by_years_on_institution_id" end @@ -141,7 +145,7 @@ t.string "grid" t.string "wikipedia" t.string "wikidata" - t.integer "mag" + t.bigint "mag" t.index ["institution_id"], name: "index_institutions_ids_on_institution_id" end @@ -149,19 +153,21 @@ t.string "display_name" t.jsonb "alternate_titles" t.jsonb "country_codes" - t.integer "hierarchy_level" + t.bigint "hierarchy_level" t.string "parent_publisher" - t.integer "works_count" - t.integer "cited_by_count" + t.bigint "works_count" + t.bigint "cited_by_count" t.string "sources_api_url" + t.string "openalex_id" + t.index ["openalex_id"], name: "index_publishers_on_openalex_id" end create_table "publishers_counts_by_years", force: :cascade do |t| t.bigint "publisher_id", null: false - t.integer "year" - t.integer "works_count" - t.integer "cited_by_count" - t.integer "oa_works_count" + t.bigint "year" + t.bigint "works_count" + t.bigint "cited_by_count" + t.bigint "oa_works_count" t.index ["publisher_id"], name: "index_publishers_counts_by_years_on_publisher_id" end @@ -178,8 +184,8 @@ t.jsonb "issn" t.string "display_name" t.string "publisher" - t.integer "works_count" - t.integer "cited_by_count" + t.bigint "works_count" + t.bigint "cited_by_count" t.boolean "is_oa" t.boolean "is_in_doaj" t.string "homepage_url" @@ -188,10 +194,10 @@ create_table "sources_counts_by_years", force: :cascade do |t| t.bigint "source_id", null: false - t.integer "year" - t.integer "works_count" - t.integer "cited_by_count" - t.integer "oa_works_count" + t.bigint "year" + t.bigint "works_count" + t.bigint "cited_by_count" + t.bigint "oa_works_count" t.index ["source_id"], name: "index_sources_counts_by_years_on_source_id" end @@ -200,7 +206,7 @@ t.string "openalex" t.string "issn_l" t.jsonb "issn" - t.integer "mag" + t.bigint "mag" t.string "wikidata" t.string "fatcat" t.index ["source_id"], name: "index_sources_ids_on_source_id" @@ -215,53 +221,21 @@ t.string "domain_id" t.string "domain_display_name" t.string "description" - t.string "keywords" + t.string "keywords", default: [], array: true t.string "works_api_url" t.string "wikipedia_id" - t.integer "works_count" - t.integer "cited_by_count" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - end - - create_table "venues", force: :cascade do |t| - t.string "issn_l" - t.string "issn" - t.string "display_name" - t.string "publisher" - t.integer "works_count" - t.integer "cited_by_count" - t.boolean "is_oa" - t.boolean "is_in_doaj" - t.string "homepage_url" - t.string "works_api_url" - end - - create_table "venues_counts_by_years", force: :cascade do |t| - t.bigint "venue_id", null: false - t.integer "year" - t.integer "works_count" - t.integer "cited_by_count" - t.index ["venue_id"], name: "index_venues_counts_by_years_on_venue_id" - end - - create_table "venues_ids", force: :cascade do |t| - t.bigint "venue_id", null: false - t.string "openalex" - t.string "issn_l" - t.string "issn" - t.integer "mag" - t.index ["venue_id"], name: "index_venues_ids_on_venue_id" + t.bigint "works_count" + t.bigint "cited_by_count" end create_table "works", force: :cascade do |t| t.string "doi" t.string "title" t.string "display_name" - t.integer "publication_year" + t.bigint "publication_year" t.string "publication_date" t.string "type" - t.integer "cited_by_count" + t.bigint "cited_by_count" t.boolean "is_retracted" t.boolean "is_paratext" t.string "cited_by_api_url" @@ -317,7 +291,7 @@ t.bigint "work_id", null: false t.string "openalex" t.string "doi" - t.integer "mag" + t.bigint "mag" t.string "pmid" t.string "pmcid" t.index ["work_id"], name: "index_works_ids_on_work_id" @@ -395,8 +369,6 @@ add_foreign_key "publishers_ids", "publishers" add_foreign_key "sources_counts_by_years", "sources" add_foreign_key "sources_ids", "sources" - add_foreign_key "venues_counts_by_years", "venues" - add_foreign_key "venues_ids", "venues" add_foreign_key "works_authorships", "authors" add_foreign_key "works_authorships", "institutions" add_foreign_key "works_authorships", "works" From 73dd5243bfcfff90eaa7461aefff1d52bc7748c5 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 16 Oct 2024 18:35:59 +0000 Subject: [PATCH 17/44] Start of reworking tests --- ..._author_node_and_edge_from_a_work_node.yml | 307 +- ..._an_author_s_works_to_an_investigation.yml | 6881 +++++++++-------- ..._an_author_s_works_to_an_investigation.yml | 6436 +++++++-------- ...a_work_s_citations_to_an_investigation.yml | 3305 ++++---- ..._work_s_references_to_an_investigation.yml | 2891 +++---- .../_resolve/can_create_an_author_node.yml | 858 +- .../_resolve/can_create_a_new_edge.yml | 3307 ++++---- .../_resolve/can_create_a_new_work_node.yml | 307 +- ..._update_the_coordinates_of_a_work_node.yml | 301 +- ...n_return_an_OpenalexWork_object_by_DOI.yml | 301 +- .../returns_an_OpenAlex_author_object.yml | 549 +- ..._an_array_of_OpenAlex_citation_objects.yml | 2902 +++---- ...an_array_of_OpenAlex_reference_objects.yml | 2590 +++---- .../returns_an_array_of_an_authors_works.yml | 6332 +++++++-------- ...returns_an_authors_works_by_openalexid.yml | 6332 +++++++-------- ..._on_citations_of_a_work_by_OpenAlex_ID.yml | 2902 +++---- ...on_references_of_a_work_by_OpenAlex_ID.yml | 2590 +++---- ...turns_author_information_by_openalexID.yml | 549 +- .../returns_details_about_a_work_by_DOI.yml | 301 +- .../mutations/create_author_node_spec.rb | 26 +- .../mutations/create_work_node_spec.rb | 10 +- 21 files changed, 25008 insertions(+), 24969 deletions(-) diff --git a/rails/spec/fixtures/vcr_cassettes/Mutations_AddAuthorNodeFromWorkNode/_resolve/can_create_a_new_author_node_and_edge_from_a_work_node.yml b/rails/spec/fixtures/vcr_cassettes/Mutations_AddAuthorNodeFromWorkNode/_resolve/can_create_a_new_author_node_and_edge_from_a_work_node.yml index 61ee0c6..aeeb7b4 100644 --- a/rails/spec/fixtures/vcr_cassettes/Mutations_AddAuthorNodeFromWorkNode/_resolve/can_create_a_new_author_node_and_edge_from_a_work_node.yml +++ b/rails/spec/fixtures/vcr_cassettes/Mutations_AddAuthorNodeFromWorkNode/_resolve/can_create_a_new_author_node_and_edge_from_a_work_node.yml @@ -1,157 +1,158 @@ --- http_interactions: -- request: - method: get - uri: https://api.openalex.org/works/https://doi.org/10.1145/3174781.3174785 - body: - encoding: US-ASCII - string: '' - headers: - User-Agent: - - Faraday v2.10.1 - Accept-Encoding: - - gzip;q=1.0,deflate;q=0.6,identity;q=0.3 - Accept: - - "*/*" - response: - status: - code: 200 - message: OK - headers: - Report-To: - - 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University"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1145/3174781.3174785","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=3174785&type=pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":24,"referenced_works":["https://openalex.org/W1581377344","https://openalex.org/W173029385","https://openalex.org/W1979990841","https://openalex.org/W2006091051","https://openalex.org/W2023300248","https://openalex.org/W2065926773","https://openalex.org/W2107096520","https://openalex.org/W2120629476","https://openalex.org/W2136583283","https://openalex.org/W2152619061","https://openalex.org/W2157984409","https://openalex.org/W2164886519","https://openalex.org/W2165855014","https://openalex.org/W2170923331","https://openalex.org/W2396601788","https://openalex.org/W2465021265","https://openalex.org/W2554919770","https://openalex.org/W2612252595","https://openalex.org/W2624900765","https://openalex.org/W2726866600","https://openalex.org/W2727300901","https://openalex.org/W2728220450","https://openalex.org/W2729462384","https://openalex.org/W2730891473"],"related_works":["https://openalex.org/W630040118","https://openalex.org/W4385933939","https://openalex.org/W2775582007","https://openalex.org/W2549211027","https://openalex.org/W2169893063","https://openalex.org/W2097099770","https://openalex.org/W2070902631","https://openalex.org/W2011425538","https://openalex.org/W1580492598","https://openalex.org/W1489503135"],"ngrams_url":"https://api.openalex.org/works/W2785752813/ngrams","abstract_inverted_index":{"Context.":[0],"Code":[1],"quality":[2,15,36,60],"is":[3,17,61],"a":[4,19,63],"key":[5,20],"issue":[6],"in":[7],"software":[8,16],"development.":[9],"The":[10],"ability":[11],"to":[12,33,50],"develop":[13],"high":[14],"therefore":[18,62],"learning":[21],"goal":[22],"of":[23,37,58],"computing":[24],"programs.":[25],"However,":[26],"there":[27,46],"are":[28,42,47],"no":[29],"universally":[30],"accepted":[31],"measures":[32],"assess":[34],"the":[35,56],"code":[38,51,59],"and":[39,54],"current":[40],"standards":[41],"considered":[43],"weak.":[44],"Furthermore,":[45],"many":[48,67],"facets":[49],"quality.":[52],"Defining":[53],"explaining":[55],"concept":[57],"challenge":[64],"faced":[65],"by":[66],"educators.":[68]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2785752813","counts_by_year":[{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2024-08-02T18:39:55.552678","created_date":"2018-02-23"} - ' - recorded_at: Mon, 05 Aug 2024 17:54:03 GMT + ' + recorded_at: Mon, 05 Aug 2024 17:54:03 GMT recorded_with: VCR 6.2.0 diff --git a/rails/spec/graphql/mutations/create_author_node_spec.rb b/rails/spec/graphql/mutations/create_author_node_spec.rb index 66402b4..a10116b 100644 --- a/rails/spec/graphql/mutations/create_author_node_spec.rb +++ b/rails/spec/graphql/mutations/create_author_node_spec.rb @@ -1,6 +1,6 @@ # frozen_string_literal: true -require "rails_helper" +require 'rails_helper' RSpec.describe Mutations::CreateAuthorNode, type: :request do def create_work_node_mutation @@ -37,8 +37,8 @@ def create_author_node_mutation GQL end - describe ".resolve" do - it "can create an author node", :vcr do + describe '.resolve' do + it 'can create an author node', :vcr do user_1 = FactoryBot.create(:user) investigation_1 = FactoryBot.create(:investigation, user_id: user_1.id) @@ -47,7 +47,7 @@ def create_author_node_mutation create_work_node_mutation, variables: { investigationId: investigation_1.id.to_s, - doi: "10.1145/3174781.3174785" + doi: '10.1145/3174781.3174785' }, context: { current_user: user_1 @@ -58,10 +58,10 @@ def create_author_node_mutation BookWormApiSchema.execute( create_author_node_mutation, variables: { - authorOpenalexId: "A5023888391", + authorOpenalexId: 'A5023888391', workOpenalexId: - work_node_response["data"]["createWorkNode"]["work"][ - "openalexId" + work_node_response['data']['createWorkNode']['work'][ + 'openalexId' ], investigationId: investigation_1.id.to_s }, @@ -71,14 +71,14 @@ def create_author_node_mutation ).to_h expect(response).to be_a(Hash) - expect(response.keys).to eq(["data"]) - expect(response["data"].keys).to eq(["createAuthorNode"]) - expect(response["data"]["createAuthorNode"].keys).to eq( + expect(response.keys).to eq(['data']) + expect(response['data'].keys).to eq(['createAuthorNode']) + expect(response['data']['createAuthorNode'].keys).to eq( %w[xCoordinate yCoordinate visible author] ) - expect(response["data"]["createAuthorNode"]["author"]).to be_a(Hash) - expect(response["data"]["createAuthorNode"]["author"]["name"]).to eq( - "Jason Priem" + expect(response['data']['createAuthorNode']['author']).to be_a(Hash) + expect(response['data']['createAuthorNode']['author']['name']).to eq( + 'Jason Priem' ) end end diff --git a/rails/spec/graphql/mutations/create_work_node_spec.rb b/rails/spec/graphql/mutations/create_work_node_spec.rb index 4e056db..25d57de 100644 --- a/rails/spec/graphql/mutations/create_work_node_spec.rb +++ b/rails/spec/graphql/mutations/create_work_node_spec.rb @@ -51,12 +51,16 @@ def create_work_node_mutation %w[id xCoordinate yCoordinate visible work] ) expect(response['data']['createWorkNode']['work']).to be_a(Hash) - expect(response['data']['createWorkNode']['work'].keys).to eq(['title', 'abstract']) + expect(response['data']['createWorkNode']['work'].keys).to eq( + %w[title abstract] + ) expect(response['data']['createWorkNode']['work']['title']).to eq( "\"I know it when I see it\" Perceptions of Code Quality" ) - expect(response['data']['createWorkNode']['work']['abstract']).to start_with( - "Context. Code quality is a key issue in software development." + expect( + response['data']['createWorkNode']['work']['abstract'] + ).to start_with( + 'Context. Code quality is a key issue in software development.' ) end end From 91fe7d9f0df41a8d753e5a62cee44016e17cd71e Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 16 Oct 2024 18:36:40 +0000 Subject: [PATCH 18/44] update gemfile --- rails/Gemfile | 2 -- 1 file changed, 2 deletions(-) diff --git a/rails/Gemfile b/rails/Gemfile index a052f2b..b080ec0 100644 --- a/rails/Gemfile +++ b/rails/Gemfile @@ -75,5 +75,3 @@ group :development do # Speed up commands on slow machines / big apps [https://github.com/rails/spring] # gem "spring" end - - From 96a37c4170238eb5b26a53e27e59be6f9a92b179 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 16 Oct 2024 18:37:21 +0000 Subject: [PATCH 19/44] Add addition gql types --- rails/app/graphql/types/author_type.rb | 26 ++++++++ .../types/authors_counts_by_year_type.rb | 17 +++++ rails/app/graphql/types/authors_ids_type.rb | 20 ++++++ rails/app/graphql/types/publisher_type.rb | 26 ++++++++ .../types/publishers_counts_by_year_type.rb | 17 +++++ .../app/graphql/types/publishers_ids_type.rb | 20 ++++++ rails/app/graphql/types/query_type.rb | 18 ++++++ rails/app/graphql/types/topic_type.rb | 26 ++++++++ rails/app/graphql/types/work_type.rb | 64 +++++++++++++++++++ 9 files changed, 234 insertions(+) create mode 100644 rails/app/graphql/types/author_type.rb create mode 100644 rails/app/graphql/types/authors_counts_by_year_type.rb create mode 100644 rails/app/graphql/types/authors_ids_type.rb create mode 100644 rails/app/graphql/types/publisher_type.rb create mode 100644 rails/app/graphql/types/publishers_counts_by_year_type.rb create mode 100644 rails/app/graphql/types/publishers_ids_type.rb create mode 100644 rails/app/graphql/types/topic_type.rb create mode 100644 rails/app/graphql/types/work_type.rb diff --git a/rails/app/graphql/types/author_type.rb b/rails/app/graphql/types/author_type.rb new file mode 100644 index 0000000..a285442 --- /dev/null +++ b/rails/app/graphql/types/author_type.rb @@ -0,0 +1,26 @@ +# frozen_string_literal: true + +module Types + class AuthorType < Types::BaseObject + field :id, ID, null: false + field :openalex_id, String + field :orcid, String + field :display_name, String + field :display_name_alternatives, String + field :works_count, Integer + field :cited_by_count, Integer + field :last_known_institution, String + field :works_api_url, String + + field :authors_ids, Types::AuthorsIdsType + field :authors_counts_by_year, [Types::AuthorsCountsByYearType] + + def authors_ids + object.authors_ids + end + + def authors_counts_by_year + object.authors_counts_by_year + end + end +end diff --git a/rails/app/graphql/types/authors_counts_by_year_type.rb b/rails/app/graphql/types/authors_counts_by_year_type.rb new file mode 100644 index 0000000..273698f --- /dev/null +++ b/rails/app/graphql/types/authors_counts_by_year_type.rb @@ -0,0 +1,17 @@ +# frozen_string_literal: true + +module Types + class AuthorsCountsByYearType < Types::BaseObject + field :id, ID, null: false + field :year, Integer + field :works_count, Integer + field :cited_by_count, Integer + field :oa_works_count, Integer + + field :author, Types::AuthorType + + def author + object.author + end + end +end diff --git a/rails/app/graphql/types/authors_ids_type.rb b/rails/app/graphql/types/authors_ids_type.rb new file mode 100644 index 0000000..15f38a0 --- /dev/null +++ b/rails/app/graphql/types/authors_ids_type.rb @@ -0,0 +1,20 @@ +# frozen_string_literal: true + +module Types + class AuthorsIdsType < Types::BaseObject + field :id, ID, null: false + field :author_id, Integer + field :openalex, String + field :orcid, String + field :scopus, String + field :twitter, String + field :wikipedia, String + field :mag, Integer + + field :author, Types::AuthorType + + def author + object.author + end + end +end diff --git a/rails/app/graphql/types/publisher_type.rb b/rails/app/graphql/types/publisher_type.rb new file mode 100644 index 0000000..44c2914 --- /dev/null +++ b/rails/app/graphql/types/publisher_type.rb @@ -0,0 +1,26 @@ +# frozen_string_literal: true + +module Types + class PublisherType < Types::BaseObject + field :id, ID, null: false + field :display_name, String + field :alternate_titles, String + field :country_codes, String + field :hierarchy_level, Integer + field :parent_publisher, String + field :works_count, Integer + field :cited_by_count, Integer + field :sources_api_url, String + + field :publishers_ids, Types::PublishersIdsType + field :publishers_counts_by_year, Types::PublishersCountsByYearType + + def publishers_ids + object.publishers_ids + end + + def publishers_counts_by_year + object.publishers_counts_by_year + end + end +end diff --git a/rails/app/graphql/types/publishers_counts_by_year_type.rb b/rails/app/graphql/types/publishers_counts_by_year_type.rb new file mode 100644 index 0000000..9737dc5 --- /dev/null +++ b/rails/app/graphql/types/publishers_counts_by_year_type.rb @@ -0,0 +1,17 @@ +# frozen_string_literal: true + +module Types + class PublishersCountsByYearType < Types::BaseObject + field :id, ID, null: false + field :year, Integer + field :works_count, Integer + field :cited_by_count, Integer + field :oa_works_count, Integer + + field :publisher, Types::PublisherType + + def publisher + object.publisher + end + end +end diff --git a/rails/app/graphql/types/publishers_ids_type.rb b/rails/app/graphql/types/publishers_ids_type.rb new file mode 100644 index 0000000..e1d41f1 --- /dev/null +++ b/rails/app/graphql/types/publishers_ids_type.rb @@ -0,0 +1,20 @@ +# frozen_string_literal: true + +module Types + class PublishersIdsType < Types::BaseObject + field :id, ID, null: false + field :institution_id, Integer + field :openalex, String + field :ror, String + field :grid, String + field :wikipedia, String + field :wikidata, String + field :mag, Integer + + field :publisher, Types::PublisherType + + def publisher + object.publisher + end + end +end diff --git a/rails/app/graphql/types/query_type.rb b/rails/app/graphql/types/query_type.rb index f0b0fbf..f26ba72 100644 --- a/rails/app/graphql/types/query_type.rb +++ b/rails/app/graphql/types/query_type.rb @@ -44,5 +44,23 @@ def institutions def institution(id:) Institution.find(id) end + + field :authors, + [Types::AuthorType], + null: true, + description: 'Fetch all authors' + def authors + Author.all + end + + field :author, + Types::AuthorType, + null: true, + description: 'Fetch author by ID' do + argument :id, ID, required: true + end + def author(id:) + Author.find(id) + end end end diff --git a/rails/app/graphql/types/topic_type.rb b/rails/app/graphql/types/topic_type.rb new file mode 100644 index 0000000..d453f51 --- /dev/null +++ b/rails/app/graphql/types/topic_type.rb @@ -0,0 +1,26 @@ +# frozen_string_literal: true + +module Types + class TopicType < Types::BaseObject + field :id, ID, null: false + field :display_name, String + field :subfield_id, String + field :subfield_display_name, String + field :field_id, String, + field :field_display_name, String + field :domain_id, String + field :domain_display_name, String + field :description, String + field :keywords, String + field :works_api_url, String + field :wikipedia_id, String + field :works_count, Integer + field :cited_by_count, Integer + + field :works, [Types::WorkType] + + def works + object.works + end + end +end diff --git a/rails/app/graphql/types/work_type.rb b/rails/app/graphql/types/work_type.rb new file mode 100644 index 0000000..a281b5d --- /dev/null +++ b/rails/app/graphql/types/work_type.rb @@ -0,0 +1,64 @@ +# frozen_string_literal: true + +module Types + class WorkType < Types::BaseObject + field :id, ID, null: false + field :doi, String + field :title, String + field :display_name, String + field :publication_year, Integer + field :work_type, String + field :cited_by_count, Integer + field :is_retracted, Boolean + field :is_paratext, Boolean + field :cited_by_api_url, String + field :abstract_inverted_index, String + field :language, String + + field :topics, [Type::TopicType] + field :authors, [Type::AuthorType] + field :institutions, [Type::InstitutionType] + field :works_biblio, [Type::WorksBiblioType] + field :works_ids, Type::WorksIdsType + field :works_open_access, Type::WorksOpenAccessType + field :works_mesh, Type::WorksMeshType + field :related_works, [Type::WorksType] + field :referenced_works, [Type::WorksType] + + def topics + object.topics + end + + def authors + object.authors + end + + def institutions + object.institutions + end + + def works_biblio + object.works_biblio + end + + def works_ids + object.works_ids + end + + def works_open_access + object.works_open_access + end + + def works_mesh + object.works_mesh + end + + def related_works + object.related_works + end + + def referenced_works + object.referenced_work + end + end +end From bb571cc924654da5841c72ba5fb848a56f99f064 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 16 Oct 2024 18:38:00 +0000 Subject: [PATCH 20/44] temp remove user context for development --- rails/app/controllers/graphql_controller.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rails/app/controllers/graphql_controller.rb b/rails/app/controllers/graphql_controller.rb index 2d0856f..7b5a8a2 100644 --- a/rails/app/controllers/graphql_controller.rb +++ b/rails/app/controllers/graphql_controller.rb @@ -12,7 +12,7 @@ def execute operation_name = params[:operationName] context = { # Query context goes here, for example: - current_user: current_user + # current_user: current_user } result = From ad2f2f77f07bd29de1f59a608c21d1a30656d30a Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 16 Oct 2024 18:38:38 +0000 Subject: [PATCH 21/44] temp db yml and routes updates --- rails/config/database.yml | 6 +++--- rails/config/routes.rb | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/rails/config/database.yml b/rails/config/database.yml index 7c825af..f25e8af 100644 --- a/rails/config/database.yml +++ b/rails/config/database.yml @@ -1,7 +1,9 @@ default: &default adapter: postgresql encoding: unicode - password: <%= ENV["POSTGRES_PASSWORD"] %> + username: bookworm + # password: <%= ENV["POSTGRES_PASSWORD"] %> + password: password pool: 5 development: @@ -9,7 +11,6 @@ development: <<: *default database: bookworm_development - test: host: localhost <<: *default @@ -19,5 +20,4 @@ test: production: <<: *default host: db - username: postgres database: bookworm_production diff --git a/rails/config/routes.rb b/rails/config/routes.rb index 1e16b6d..098807e 100644 --- a/rails/config/routes.rb +++ b/rails/config/routes.rb @@ -2,7 +2,7 @@ Rails.application.routes.draw do # using GQL for handling sessions - devise_for :users, skip: :sessions + # devise_for :users, skip: :sessions post '/graphql', to: 'graphql#execute' # Define your application routes per the DSL in https://guides.rubyonrails.org/routing.html From 83b4d8ca40cda7e24a5f94222cacd3c291a8a860 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 17 Oct 2024 01:08:23 +0000 Subject: [PATCH 22/44] Add topics import --- ...241003155628_add_open_alex_id_to_topics.rb | 6 +++ rails/db/schema.rb | 4 +- rails/lib/tasks/load_topics.rake | 38 +++++++++++++++++++ 3 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 rails/db/migrate/20241003155628_add_open_alex_id_to_topics.rb create mode 100644 rails/lib/tasks/load_topics.rake diff --git a/rails/db/migrate/20241003155628_add_open_alex_id_to_topics.rb b/rails/db/migrate/20241003155628_add_open_alex_id_to_topics.rb new file mode 100644 index 0000000..79fcb79 --- /dev/null +++ b/rails/db/migrate/20241003155628_add_open_alex_id_to_topics.rb @@ -0,0 +1,6 @@ +class AddOpenAlexIdToTopics < ActiveRecord::Migration[7.1] + def change + add_column :topics, :openalex_id, :string + add_index :topics, :openalex_id + end +end diff --git a/rails/db/schema.rb b/rails/db/schema.rb index 9df9ec9..4b282b5 100644 --- a/rails/db/schema.rb +++ b/rails/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema[7.1].define(version: 2024_10_03_155627) do +ActiveRecord::Schema[7.1].define(version: 2024_10_03_155628) do # These are extensions that must be enabled in order to support this database enable_extension "plpgsql" @@ -226,6 +226,8 @@ t.string "wikipedia_id" t.bigint "works_count" t.bigint "cited_by_count" + t.string "openalex_id" + t.index ["openalex_id"], name: "index_topics_on_openalex_id" end create_table "works", force: :cascade do |t| diff --git a/rails/lib/tasks/load_topics.rake b/rails/lib/tasks/load_topics.rake new file mode 100644 index 0000000..8799c62 --- /dev/null +++ b/rails/lib/tasks/load_topics.rake @@ -0,0 +1,38 @@ +require 'rake' +require 'zlib' +require 'csv' +require 'json' + +namespace :data_import do + desc 'Load Topics from gzipped csv to db' + task load_topics: :environment do + file_path = '/opt/bookworm/csv-files/topics.csv.gz' + topics = [] + + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip) + csv + .drop(1) + .each_with_index do |row, index| + topics << { + openalex_id: row[0].split('/').last, + display_name: row[1], + subfield_id: row[2].split('/').last, + subfield_display_name: row[3], + field_id: row[4].split('/').last, + field_display_name: row[5], + domain_id: row[6].split('/').last, + domain_display_name: row[7], + description: row[8], + keywords: row[9].split('; '), + works_api_url: row[10], + wikipedia_id: row[11], + works_count: row[12], + cited_by_count: row[13] + } + end + end + + Topic.insert_all(topics) + end +end From 36d1c0c96bec197023b98a5e25c1af98fc53f78b Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 30 Oct 2024 18:30:33 +0000 Subject: [PATCH 23/44] Migrations and models for work-author-institution relationships --- rails/app/models/author.rb | 4 +++- rails/app/models/institution.rb | 4 ++++ rails/app/models/work.rb | 4 +++- rails/app/models/works_authorship.rb | 8 +++++--- .../20241003155629_add_open_alex_id_to_works.rb | 6 ++++++ .../20241003155630_rename_type_on_works.rb | 5 +++++ ...1025010442_index_insitutions_on_openalex_id.rb | 5 +++++ ..._allow_null_institution_in_works_authorship.rb | 5 +++++ ...90712_allow_null_author_in_works_authorship.rb | 5 +++++ ...9190734_allow_null_work_in_works_authorship.rb | 5 +++++ ...3310_rename_id_columns_on_works_authorships.rb | 7 +++++++ ...1448_drop_and_remake_works_authorship_table.rb | 15 +++++++++++++++ ...1030154931_add_indexes_to_works_authorships.rb | 7 +++++++ 13 files changed, 75 insertions(+), 5 deletions(-) create mode 100644 rails/db/migrate/20241003155629_add_open_alex_id_to_works.rb create mode 100644 rails/db/migrate/20241003155630_rename_type_on_works.rb create mode 100644 rails/db/migrate/20241025010442_index_insitutions_on_openalex_id.rb create mode 100644 rails/db/migrate/20241028183837_allow_null_institution_in_works_authorship.rb create mode 100644 rails/db/migrate/20241029190712_allow_null_author_in_works_authorship.rb create mode 100644 rails/db/migrate/20241029190734_allow_null_work_in_works_authorship.rb create mode 100644 rails/db/migrate/20241029203310_rename_id_columns_on_works_authorships.rb create mode 100644 rails/db/migrate/20241029231448_drop_and_remake_works_authorship_table.rb create mode 100644 rails/db/migrate/20241030154931_add_indexes_to_works_authorships.rb diff --git a/rails/app/models/author.rb b/rails/app/models/author.rb index c8f1ae9..894d19d 100644 --- a/rails/app/models/author.rb +++ b/rails/app/models/author.rb @@ -3,6 +3,8 @@ class Author < ApplicationRecord has_one :authors_ids has_many :authors_counts_by_year - has_many :works_authorships + has_many :works_authorships, + primary_key: :openalex_id, + foreign_key: :author_openalex_id has_many :institutions, through: :works_authorships end diff --git a/rails/app/models/institution.rb b/rails/app/models/institution.rb index 2cc42d1..bbbc2e5 100644 --- a/rails/app/models/institution.rb +++ b/rails/app/models/institution.rb @@ -12,4 +12,8 @@ class Institution < ApplicationRecord has_many :associated_institutions, through: :institutions_associated_institutions, source: :institution + + has_many :works_authorships, + primary_key: :openalex_id, + foreign_key: :institution_openalex_id end diff --git a/rails/app/models/work.rb b/rails/app/models/work.rb index ef44cf5..644abc0 100644 --- a/rails/app/models/work.rb +++ b/rails/app/models/work.rb @@ -1,7 +1,9 @@ # frozen_string_literal: true class Work < ApplicationRecord - has_many :works_authorships + has_many :works_authorships, + primary_key: :openalex_id, + foreign_key: :work_openalex_id has_many :authors, through: :works_authorships has_many :institutions, through: :works_authorships diff --git a/rails/app/models/works_authorship.rb b/rails/app/models/works_authorship.rb index 565644e..b0352d1 100644 --- a/rails/app/models/works_authorship.rb +++ b/rails/app/models/works_authorship.rb @@ -1,5 +1,7 @@ class WorksAuthorship < ApplicationRecord - belongs_to :author - belongs_to :work - belongs_to :institution + belongs_to :author, primary_key: :author_openalex_id + + belongs_to :work, primary_key: :work_openalex_id + + belongs_to :institution, primary_key: :institution_openalex_id end diff --git a/rails/db/migrate/20241003155629_add_open_alex_id_to_works.rb b/rails/db/migrate/20241003155629_add_open_alex_id_to_works.rb new file mode 100644 index 0000000..3096841 --- /dev/null +++ b/rails/db/migrate/20241003155629_add_open_alex_id_to_works.rb @@ -0,0 +1,6 @@ +class AddOpenAlexIdToWorks < ActiveRecord::Migration[7.1] + def change + add_column :works, :openalex_id, :string + add_index :works, :openalex_id + end +end diff --git a/rails/db/migrate/20241003155630_rename_type_on_works.rb b/rails/db/migrate/20241003155630_rename_type_on_works.rb new file mode 100644 index 0000000..9985da2 --- /dev/null +++ b/rails/db/migrate/20241003155630_rename_type_on_works.rb @@ -0,0 +1,5 @@ +class RenameTypeOnWorks < ActiveRecord::Migration[7.1] + def change + rename_column :works, :type, :work_type + end +end diff --git a/rails/db/migrate/20241025010442_index_insitutions_on_openalex_id.rb b/rails/db/migrate/20241025010442_index_insitutions_on_openalex_id.rb new file mode 100644 index 0000000..5a33be3 --- /dev/null +++ b/rails/db/migrate/20241025010442_index_insitutions_on_openalex_id.rb @@ -0,0 +1,5 @@ +class IndexInsitutionsOnOpenalexId < ActiveRecord::Migration[7.1] + def change + add_index :institutions, :openalex_id + end +end diff --git a/rails/db/migrate/20241028183837_allow_null_institution_in_works_authorship.rb b/rails/db/migrate/20241028183837_allow_null_institution_in_works_authorship.rb new file mode 100644 index 0000000..1371ab0 --- /dev/null +++ b/rails/db/migrate/20241028183837_allow_null_institution_in_works_authorship.rb @@ -0,0 +1,5 @@ +class AllowNullInstitutionInWorksAuthorship < ActiveRecord::Migration[7.1] + def change + change_column_null(:works_authorships, :institution_id, true) + end +end diff --git a/rails/db/migrate/20241029190712_allow_null_author_in_works_authorship.rb b/rails/db/migrate/20241029190712_allow_null_author_in_works_authorship.rb new file mode 100644 index 0000000..2dbdc37 --- /dev/null +++ b/rails/db/migrate/20241029190712_allow_null_author_in_works_authorship.rb @@ -0,0 +1,5 @@ +class AllowNullAuthorInWorksAuthorship < ActiveRecord::Migration[7.1] + def change + change_column_null(:works_authorships, :author_id, true) + end +end diff --git a/rails/db/migrate/20241029190734_allow_null_work_in_works_authorship.rb b/rails/db/migrate/20241029190734_allow_null_work_in_works_authorship.rb new file mode 100644 index 0000000..2621f94 --- /dev/null +++ b/rails/db/migrate/20241029190734_allow_null_work_in_works_authorship.rb @@ -0,0 +1,5 @@ +class AllowNullWorkInWorksAuthorship < ActiveRecord::Migration[7.1] + def change + change_column_null(:works_authorships, :work_id, true) + end +end diff --git a/rails/db/migrate/20241029203310_rename_id_columns_on_works_authorships.rb b/rails/db/migrate/20241029203310_rename_id_columns_on_works_authorships.rb new file mode 100644 index 0000000..4e4204a --- /dev/null +++ b/rails/db/migrate/20241029203310_rename_id_columns_on_works_authorships.rb @@ -0,0 +1,7 @@ +class RenameIdColumnsOnWorksAuthorships < ActiveRecord::Migration[7.1] + def change + rename_column :works_authorships, :work_id, :work_openalex_id + rename_column :works_authorships, :author_id, :author_openalex_id + rename_column :works_authorships, :institution_id, :institution_openalex_id + end +end diff --git a/rails/db/migrate/20241029231448_drop_and_remake_works_authorship_table.rb b/rails/db/migrate/20241029231448_drop_and_remake_works_authorship_table.rb new file mode 100644 index 0000000..9e7a5d2 --- /dev/null +++ b/rails/db/migrate/20241029231448_drop_and_remake_works_authorship_table.rb @@ -0,0 +1,15 @@ +class DropAndRemakeWorksAuthorshipTable < ActiveRecord::Migration[7.1] + def change + drop_table :works_authorships + + create_table :works_authorships do |t| + t.string :author_position + t.string :work_openalex_id + t.string :author_openalex_id + t.string :institution_openalex_id + t.string :raw_affiliation_string + + t.timestamps + end + end +end diff --git a/rails/db/migrate/20241030154931_add_indexes_to_works_authorships.rb b/rails/db/migrate/20241030154931_add_indexes_to_works_authorships.rb new file mode 100644 index 0000000..871bf50 --- /dev/null +++ b/rails/db/migrate/20241030154931_add_indexes_to_works_authorships.rb @@ -0,0 +1,7 @@ +class AddIndexesToWorksAuthorships < ActiveRecord::Migration[7.1] + def change + add_index :works_authorships, :author_openalex_id + add_index :works_authorships, :work_openalex_id + add_index :works_authorships, :institution_openalex_id + end +end From 13e2f2c304161e887df14ca6b0642263705cace1 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Mon, 11 Nov 2024 20:32:55 +0000 Subject: [PATCH 24/44] Reworking migrations --- ...rs.rb => 20240628174720_create_authors.rb} | 3 +++ .../migrate/20240628174721_create_topics.rb | 21 --------------- ...28174723_create_authors_counts_by_years.rb | 13 --------- .../migrate/20240628174726_create_concepts.rb | 15 ----------- ...0240628174727_create_concepts_ancestors.rb | 11 -------- ...8174728_create_concepts_counts_by_years.rb | 11 -------- .../20240628174729_create_concepts_ids.rb | 13 --------- ...174730_create_concepts_related_concepts.rb | 11 -------- ...te_institutions_associated_institutions.rb | 9 ------- ...733_create_institutions_counts_by_years.rb | 11 -------- ...74737_create_publishers_counts_by_years.rb | 11 -------- ...28174740_create_sources_counts_by_years.rb | 11 -------- ...28174743_create_works_primary_locations.rb | 15 ----------- .../20240628174744_create_works_locations.rb | 15 ----------- ...28174745_create_works_best_oa_locations.rb | 15 ----------- ...20240628174746_create_works_authorships.rb | 13 --------- .../20240628174747_create_works_biblios.rb | 13 --------- .../20240628174748_create_works_topics.rb | 9 ------- .../20240628174749_create_works_concepts.rb | 10 ------- .../20240628174750_create_works_ids.rb | 12 --------- .../20240628174751_create_works_meshes.rb | 12 --------- ...240628174752_create_works_open_accesses.rb | 11 -------- ...628174753_create_works_referenced_works.rb | 10 ------- ...240628174754_create_works_related_works.rb | 10 ------- ...or_institutions_associated_institutions.rb | 21 --------------- ...41003155622_add_open_alex_id_to_authors.rb | 5 ---- ...623_change_openalex_id_type_for_authors.rb | 5 ---- ...624_add_openalex_id_indexing_to_authors.rb | 5 ---- ...03155625_add_open_alex_id_to_publishers.rb | 5 ---- ..._change_openalex_id_type_for_publishers.rb | 5 ---- ..._add_openalex_id_indexing_to_publishers.rb | 5 ---- ...241003155628_add_open_alex_id_to_topics.rb | 6 ----- ...0241003155629_add_open_alex_id_to_works.rb | 6 ----- .../20241003155630_rename_type_on_works.rb | 5 ---- ...010442_index_insitutions_on_openalex_id.rb | 5 ---- ...ow_null_institution_in_works_authorship.rb | 5 ---- ...2_allow_null_author_in_works_authorship.rb | 5 ---- ...734_allow_null_work_in_works_authorship.rb | 5 ---- ..._rename_id_columns_on_works_authorships.rb | 7 ----- ..._drop_and_remake_works_authorship_table.rb | 15 ----------- ...154931_add_indexes_to_works_authorships.rb | 7 ----- ...08160553_create_authors_counts_by_years.rb | 15 +++++++++++ ...b => 20241109014753_create_authors_ids.rb} | 7 ++--- ... => 20241109170738_create_institutions.rb} | 10 ++++--- ...te_institutions_associated_institutions.rb | 15 +++++++++++ ...4303_create_institutions_counts_by_year.rb | 15 +++++++++++ ...20241111174953_create_institutions_geo.rb} | 10 ++++--- ...20241111175452_create_institutions_ids.rb} | 9 ++++--- ...rb => 20241111180929_create_publishers.rb} | 11 +++++--- ...81804_create_publishers_counts_by_years.rb | 15 +++++++++++ ...> 20241111182314_create_publishers_ids.rb} | 7 +++-- ...es.rb => 20241111182742_create_sources.rb} | 9 +++++-- ...11194229_create_sources_counts_by_years.rb | 15 +++++++++++ ...b => 20241111200050_create_sources_ids.rb} | 13 +++++---- .../migrate/20241111200923_create_topics.rb | 27 +++++++++++++++++++ ...orks.rb => 20241111202907_create_works.rb} | 14 ++++++---- 56 files changed, 166 insertions(+), 428 deletions(-) rename rails/db/migrate/{20240628174722_create_authors.rb => 20240628174720_create_authors.rb} (80%) delete mode 100644 rails/db/migrate/20240628174721_create_topics.rb delete mode 100644 rails/db/migrate/20240628174723_create_authors_counts_by_years.rb delete mode 100644 rails/db/migrate/20240628174726_create_concepts.rb delete mode 100644 rails/db/migrate/20240628174727_create_concepts_ancestors.rb delete mode 100644 rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb delete mode 100644 rails/db/migrate/20240628174729_create_concepts_ids.rb delete mode 100644 rails/db/migrate/20240628174730_create_concepts_related_concepts.rb delete mode 100644 rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb delete mode 100644 rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb delete mode 100644 rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb delete mode 100644 rails/db/migrate/20240628174740_create_sources_counts_by_years.rb delete mode 100644 rails/db/migrate/20240628174743_create_works_primary_locations.rb delete mode 100644 rails/db/migrate/20240628174744_create_works_locations.rb delete mode 100644 rails/db/migrate/20240628174745_create_works_best_oa_locations.rb delete mode 100644 rails/db/migrate/20240628174746_create_works_authorships.rb delete mode 100644 rails/db/migrate/20240628174747_create_works_biblios.rb delete mode 100644 rails/db/migrate/20240628174748_create_works_topics.rb delete mode 100644 rails/db/migrate/20240628174749_create_works_concepts.rb delete mode 100644 rails/db/migrate/20240628174750_create_works_ids.rb delete mode 100644 rails/db/migrate/20240628174751_create_works_meshes.rb delete mode 100644 rails/db/migrate/20240628174752_create_works_open_accesses.rb delete mode 100644 rails/db/migrate/20240628174753_create_works_referenced_works.rb delete mode 100644 rails/db/migrate/20240628174754_create_works_related_works.rb delete mode 100644 rails/db/migrate/20241003012114_change_id_types_for_institutions_associated_institutions.rb delete mode 100644 rails/db/migrate/20241003155622_add_open_alex_id_to_authors.rb delete mode 100644 rails/db/migrate/20241003155623_change_openalex_id_type_for_authors.rb delete mode 100644 rails/db/migrate/20241003155624_add_openalex_id_indexing_to_authors.rb delete mode 100644 rails/db/migrate/20241003155625_add_open_alex_id_to_publishers.rb delete mode 100644 rails/db/migrate/20241003155626_change_openalex_id_type_for_publishers.rb delete mode 100644 rails/db/migrate/20241003155627_add_openalex_id_indexing_to_publishers.rb delete mode 100644 rails/db/migrate/20241003155628_add_open_alex_id_to_topics.rb delete mode 100644 rails/db/migrate/20241003155629_add_open_alex_id_to_works.rb delete mode 100644 rails/db/migrate/20241003155630_rename_type_on_works.rb delete mode 100644 rails/db/migrate/20241025010442_index_insitutions_on_openalex_id.rb delete mode 100644 rails/db/migrate/20241028183837_allow_null_institution_in_works_authorship.rb delete mode 100644 rails/db/migrate/20241029190712_allow_null_author_in_works_authorship.rb delete mode 100644 rails/db/migrate/20241029190734_allow_null_work_in_works_authorship.rb delete mode 100644 rails/db/migrate/20241029203310_rename_id_columns_on_works_authorships.rb delete mode 100644 rails/db/migrate/20241029231448_drop_and_remake_works_authorship_table.rb delete mode 100644 rails/db/migrate/20241030154931_add_indexes_to_works_authorships.rb create mode 100644 rails/db/migrate/20241108160553_create_authors_counts_by_years.rb rename rails/db/migrate/{20240628174724_create_authors_ids.rb => 20241109014753_create_authors_ids.rb} (69%) rename rails/db/migrate/{20240628174731_create_institutions.rb => 20241109170738_create_institutions.rb} (71%) create mode 100644 rails/db/migrate/20241111173702_create_institutions_associated_institutions.rb create mode 100644 rails/db/migrate/20241111174303_create_institutions_counts_by_year.rb rename rails/db/migrate/{20240628174734_create_institutions_geos.rb => 20241111174953_create_institutions_geo.rb} (50%) rename rails/db/migrate/{20240628174735_create_institutions_ids.rb => 20241111175452_create_institutions_ids.rb} (61%) rename rails/db/migrate/{20240628174736_create_publishers.rb => 20241111180929_create_publishers.rb} (57%) create mode 100644 rails/db/migrate/20241111181804_create_publishers_counts_by_years.rb rename rails/db/migrate/{20240628174738_create_publishers_ids.rb => 20241111182314_create_publishers_ids.rb} (60%) rename rails/db/migrate/{20240628174739_create_sources.rb => 20241111182742_create_sources.rb} (66%) create mode 100644 rails/db/migrate/20241111194229_create_sources_counts_by_years.rb rename rails/db/migrate/{20240628174741_create_sources_ids.rb => 20241111200050_create_sources_ids.rb} (50%) create mode 100644 rails/db/migrate/20241111200923_create_topics.rb rename rails/db/migrate/{20240628174742_create_works.rb => 20241111202907_create_works.rb} (63%) diff --git a/rails/db/migrate/20240628174722_create_authors.rb b/rails/db/migrate/20240628174720_create_authors.rb similarity index 80% rename from rails/db/migrate/20240628174722_create_authors.rb rename to rails/db/migrate/20240628174720_create_authors.rb index 8daa8b3..4abd1d0 100644 --- a/rails/db/migrate/20240628174722_create_authors.rb +++ b/rails/db/migrate/20240628174720_create_authors.rb @@ -1,6 +1,7 @@ class CreateAuthors < ActiveRecord::Migration[7.1] def change create_table :authors do |t| + t.string :author_openalex_id t.string :orcid t.string :display_name t.jsonb :display_name_alternatives @@ -9,5 +10,7 @@ def change t.string :last_known_institution t.string :works_api_url end + + add_index :authors, :author_openalex_id end end diff --git a/rails/db/migrate/20240628174721_create_topics.rb b/rails/db/migrate/20240628174721_create_topics.rb deleted file mode 100644 index a4a863a..0000000 --- a/rails/db/migrate/20240628174721_create_topics.rb +++ /dev/null @@ -1,21 +0,0 @@ -class CreateTopics < ActiveRecord::Migration[7.1] - def change - create_table :topics do |t| - t.string :display_name - t.string :subfield_id - t.string :subfield_display_name - t.string :field_id - t.string :field_display_name - t.string :domain_id - t.string :domain_display_name - t.string :description - t.string :keywords, array: true, default: [] - t.string :works_api_url - t.string :wikipedia_id - t.bigint :works_count - t.bigint :cited_by_count - - # siblings??? not documented but probably relationships of topics? - end - end -end diff --git a/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb b/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb deleted file mode 100644 index a2f8dbc..0000000 --- a/rails/db/migrate/20240628174723_create_authors_counts_by_years.rb +++ /dev/null @@ -1,13 +0,0 @@ -class CreateAuthorsCountsByYears < ActiveRecord::Migration[7.1] - def change - create_table :authors_counts_by_years do |t| - t.references :author, null: false, foreign_key: true - t.bigint :year, null: false - t.bigint :works_count - t.bigint :cited_by_count - t.bigint :oa_works_count - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240628174726_create_concepts.rb b/rails/db/migrate/20240628174726_create_concepts.rb deleted file mode 100644 index e1de0b6..0000000 --- a/rails/db/migrate/20240628174726_create_concepts.rb +++ /dev/null @@ -1,15 +0,0 @@ -class CreateConcepts < ActiveRecord::Migration[7.1] - def change - create_table :concepts do |t| - t.string :wikidata - t.string :display_name - t.bigint :level - t.string :description - t.bigint :works_count - t.bigint :cited_by_count - t.string :image_url - t.string :image_thumbnail_url - t.string :works_api_url - end - end -end diff --git a/rails/db/migrate/20240628174727_create_concepts_ancestors.rb b/rails/db/migrate/20240628174727_create_concepts_ancestors.rb deleted file mode 100644 index 6c3d709..0000000 --- a/rails/db/migrate/20240628174727_create_concepts_ancestors.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreateConceptsAncestors < ActiveRecord::Migration[7.1] - def change - create_table :concepts_ancestors do |t| - t.string :concept_id, null: false - t.string :ancestor_id, null: false - # this needs to be that self-referential many-to-many situation - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb b/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb deleted file mode 100644 index fc18132..0000000 --- a/rails/db/migrate/20240628174728_create_concepts_counts_by_years.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreateConceptsCountsByYears < ActiveRecord::Migration[7.1] - def change - create_table :concepts_counts_by_years do |t| - t.references :concept, null: false, foreign_key: true - t.bigint :year, null: false - t.bigint :works_count - t.bigint :cited_by_count - t.bigint :oa_works_count - end - end -end diff --git a/rails/db/migrate/20240628174729_create_concepts_ids.rb b/rails/db/migrate/20240628174729_create_concepts_ids.rb deleted file mode 100644 index 3b350a5..0000000 --- a/rails/db/migrate/20240628174729_create_concepts_ids.rb +++ /dev/null @@ -1,13 +0,0 @@ -class CreateConceptsIds < ActiveRecord::Migration[7.1] - def change - create_table :concepts_ids do |t| - t.references :concept, null: false, foreign_key: true - t.string :openalex - t.string :wikidata - t.string :wikipedia - t.jsonb :umls_aui - t.jsonb :umls_cui - t.bigint :mag - end - end -end diff --git a/rails/db/migrate/20240628174730_create_concepts_related_concepts.rb b/rails/db/migrate/20240628174730_create_concepts_related_concepts.rb deleted file mode 100644 index ac4bc88..0000000 --- a/rails/db/migrate/20240628174730_create_concepts_related_concepts.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreateConceptsRelatedConcepts < ActiveRecord::Migration[7.1] - def change - create_table :concepts_related_concepts do |t| - t.string :concept_id - t.string :related_concept_id - t.float :score - - # another self-referential many-to-many - end - end -end diff --git a/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb b/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb deleted file mode 100644 index 6d08390..0000000 --- a/rails/db/migrate/20240628174732_create_institutions_associated_institutions.rb +++ /dev/null @@ -1,9 +0,0 @@ -class CreateInstitutionsAssociatedInstitutions < ActiveRecord::Migration[7.1] - def change - create_table :institutions_associated_institutions do |t| - t.string :institution_id - t.string :associated_institution_id - t.string :relationship - end - end -end diff --git a/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb b/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb deleted file mode 100644 index cff24e0..0000000 --- a/rails/db/migrate/20240628174733_create_institutions_counts_by_years.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreateInstitutionsCountsByYears < ActiveRecord::Migration[7.1] - def change - create_table :institutions_counts_by_years do |t| - t.references :institution, null: false, foreign_key: true - t.bigint :year - t.bigint :works_count - t.bigint :cited_by_count - t.bigint :oa_works_count - end - end -end diff --git a/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb b/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb deleted file mode 100644 index d98aaed..0000000 --- a/rails/db/migrate/20240628174737_create_publishers_counts_by_years.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreatePublishersCountsByYears < ActiveRecord::Migration[7.1] - def change - create_table :publishers_counts_by_years do |t| - t.references :publisher, null: false, foreign_key: true - t.bigint :year - t.bigint :works_count - t.bigint :cited_by_count - t.bigint :oa_works_count - end - end -end diff --git a/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb b/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb deleted file mode 100644 index 707852d..0000000 --- a/rails/db/migrate/20240628174740_create_sources_counts_by_years.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreateSourcesCountsByYears < ActiveRecord::Migration[7.1] - def change - create_table :sources_counts_by_years do |t| - t.references :source, null: false, foreign_key: true - t.bigint :year - t.bigint :works_count - t.bigint :cited_by_count - t.bigint :oa_works_count - end - end -end diff --git a/rails/db/migrate/20240628174743_create_works_primary_locations.rb b/rails/db/migrate/20240628174743_create_works_primary_locations.rb deleted file mode 100644 index 01ed5d7..0000000 --- a/rails/db/migrate/20240628174743_create_works_primary_locations.rb +++ /dev/null @@ -1,15 +0,0 @@ -# frozen_string_literal: true - -class CreateWorksPrimaryLocations < ActiveRecord::Migration[7.1] - def change - create_table :works_primary_locations do |t| - t.references :work, null: false, foreign_key: true - t.references :source, null: false, foreign_key: true - t.string :landing_page_url - t.string :pdf_url - t.boolean :is_oa - t.string :version - t.string :license - end - end -end diff --git a/rails/db/migrate/20240628174744_create_works_locations.rb b/rails/db/migrate/20240628174744_create_works_locations.rb deleted file mode 100644 index b6ae9b4..0000000 --- a/rails/db/migrate/20240628174744_create_works_locations.rb +++ /dev/null @@ -1,15 +0,0 @@ -# frozen_string_literal: true - -class CreateWorksLocations < ActiveRecord::Migration[7.1] - def change - create_table :works_locations do |t| - t.references :work, null: false, foreign_key: true - t.references :source, null: false, foreign_key: true - t.string :landing_page_url - t.string :pdf_url - t.boolean :is_oa - t.string :version - t.string :license - end - end -end diff --git a/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb b/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb deleted file mode 100644 index 5e0f15e..0000000 --- a/rails/db/migrate/20240628174745_create_works_best_oa_locations.rb +++ /dev/null @@ -1,15 +0,0 @@ -# frozen_string_literal: true - -class CreateWorksBestOaLocations < ActiveRecord::Migration[7.1] - def change - create_table :works_best_oa_locations do |t| - t.references :work, null: false, foreign_key: true - t.references :source, null: false, foreign_key: true - t.string :landing_page_url - t.string :pdf_url - t.boolean :is_oa - t.string :version - t.string :license - end - end -end diff --git a/rails/db/migrate/20240628174746_create_works_authorships.rb b/rails/db/migrate/20240628174746_create_works_authorships.rb deleted file mode 100644 index d9466c1..0000000 --- a/rails/db/migrate/20240628174746_create_works_authorships.rb +++ /dev/null @@ -1,13 +0,0 @@ -class CreateWorksAuthorships < ActiveRecord::Migration[7.1] - def change - create_table :works_authorships do |t| - t.references :work, null: false, foreign_key: true - t.references :author, null: false, foreign_key: true - t.references :institution, null: false, foreign_key: true - t.string :author_position - t.string :raw_affiliation_string - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240628174747_create_works_biblios.rb b/rails/db/migrate/20240628174747_create_works_biblios.rb deleted file mode 100644 index fc2602a..0000000 --- a/rails/db/migrate/20240628174747_create_works_biblios.rb +++ /dev/null @@ -1,13 +0,0 @@ -class CreateWorksBiblios < ActiveRecord::Migration[7.1] - def change - create_table :works_biblios do |t| - t.references :work, null: false, foreign_key: true - t.string :volume - t.string :issue - t.string :first_page - t.string :last_page - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20240628174748_create_works_topics.rb b/rails/db/migrate/20240628174748_create_works_topics.rb deleted file mode 100644 index a389611..0000000 --- a/rails/db/migrate/20240628174748_create_works_topics.rb +++ /dev/null @@ -1,9 +0,0 @@ -class CreateWorksTopics < ActiveRecord::Migration[7.1] - def change - create_table :works_topics do |t| - t.references :work, null: false, foreign_key: true - t.references :topic, null: false, foreign_key: true - t.float :score - end - end -end diff --git a/rails/db/migrate/20240628174749_create_works_concepts.rb b/rails/db/migrate/20240628174749_create_works_concepts.rb deleted file mode 100644 index f1f0879..0000000 --- a/rails/db/migrate/20240628174749_create_works_concepts.rb +++ /dev/null @@ -1,10 +0,0 @@ -class CreateWorksConcepts < ActiveRecord::Migration[7.1] - def change - create_table :works_concepts do |t| - t.references :work, null: false, foreign_key: true - t.references :concept, null: false, foreign_key: true - - t.float :score - end - end -end diff --git a/rails/db/migrate/20240628174750_create_works_ids.rb b/rails/db/migrate/20240628174750_create_works_ids.rb deleted file mode 100644 index 2f2c91a..0000000 --- a/rails/db/migrate/20240628174750_create_works_ids.rb +++ /dev/null @@ -1,12 +0,0 @@ -class CreateWorksIds < ActiveRecord::Migration[7.1] - def change - create_table :works_ids do |t| - t.references :work, null: false, foreign_key: true - t.string :openalex - t.string :doi - t.bigint :mag - t.string :pmid - t.string :pmcid - end - end -end diff --git a/rails/db/migrate/20240628174751_create_works_meshes.rb b/rails/db/migrate/20240628174751_create_works_meshes.rb deleted file mode 100644 index 5d227b4..0000000 --- a/rails/db/migrate/20240628174751_create_works_meshes.rb +++ /dev/null @@ -1,12 +0,0 @@ -class CreateWorksMeshes < ActiveRecord::Migration[7.1] - def change - create_table :works_meshes do |t| - t.references :work, null: false, foreign_key: true - t.string :descriptor_ui - t.string :descriptor_name - t.string :qualifier_ui - t.string :qualifier_name - t.boolean :is_major_topic - end - end -end diff --git a/rails/db/migrate/20240628174752_create_works_open_accesses.rb b/rails/db/migrate/20240628174752_create_works_open_accesses.rb deleted file mode 100644 index 78ed98d..0000000 --- a/rails/db/migrate/20240628174752_create_works_open_accesses.rb +++ /dev/null @@ -1,11 +0,0 @@ -class CreateWorksOpenAccesses < ActiveRecord::Migration[7.1] - def change - create_table :works_open_accesses do |t| - t.references :work, null: false, foreign_key: true - t.boolean :is_oa - t.string :oa_status - t.string :oa_url - t.boolean :any_repository_has_fulltext - end - end -end diff --git a/rails/db/migrate/20240628174753_create_works_referenced_works.rb b/rails/db/migrate/20240628174753_create_works_referenced_works.rb deleted file mode 100644 index 7d5c4b4..0000000 --- a/rails/db/migrate/20240628174753_create_works_referenced_works.rb +++ /dev/null @@ -1,10 +0,0 @@ -class CreateWorksReferencedWorks < ActiveRecord::Migration[7.1] - def change - create_table :works_referenced_works do |t| - t.string :work_id - t.string :referenced_work_id - - # self-referential many-to-many - end - end -end diff --git a/rails/db/migrate/20240628174754_create_works_related_works.rb b/rails/db/migrate/20240628174754_create_works_related_works.rb deleted file mode 100644 index 18bf6b8..0000000 --- a/rails/db/migrate/20240628174754_create_works_related_works.rb +++ /dev/null @@ -1,10 +0,0 @@ -class CreateWorksRelatedWorks < ActiveRecord::Migration[7.1] - def change - create_table :works_related_works do |t| - t.string :work_id - t.string :related_work_id - - # self referential many-to-many - end - end -end diff --git a/rails/db/migrate/20241003012114_change_id_types_for_institutions_associated_institutions.rb b/rails/db/migrate/20241003012114_change_id_types_for_institutions_associated_institutions.rb deleted file mode 100644 index cc9e9fb..0000000 --- a/rails/db/migrate/20241003012114_change_id_types_for_institutions_associated_institutions.rb +++ /dev/null @@ -1,21 +0,0 @@ -class ChangeIdTypesForInstitutionsAssociatedInstitutions < ActiveRecord::Migration[ - 7.1 -] - def up - connection.execute( - ' - alter table institutions_associated_institutions - alter column institution_id - type integer using cast(institution_id as integer) - ' - ) - - connection.execute( - ' - alter table institutions_associated_institutions - alter column associated_institution_id - type integer using cast(associated_institution_id as integer) - ' - ) - end -end diff --git a/rails/db/migrate/20241003155622_add_open_alex_id_to_authors.rb b/rails/db/migrate/20241003155622_add_open_alex_id_to_authors.rb deleted file mode 100644 index 99b879e..0000000 --- a/rails/db/migrate/20241003155622_add_open_alex_id_to_authors.rb +++ /dev/null @@ -1,5 +0,0 @@ -class AddOpenAlexIdToAuthors < ActiveRecord::Migration[7.1] - def change - add_column :authors, :openalex_id, :integer - end -end diff --git a/rails/db/migrate/20241003155623_change_openalex_id_type_for_authors.rb b/rails/db/migrate/20241003155623_change_openalex_id_type_for_authors.rb deleted file mode 100644 index 6414343..0000000 --- a/rails/db/migrate/20241003155623_change_openalex_id_type_for_authors.rb +++ /dev/null @@ -1,5 +0,0 @@ -class ChangeOpenalexIdTypeForAuthors < ActiveRecord::Migration[7.1] - def change - change_column(:authors, :openalex_id, :string) - end -end diff --git a/rails/db/migrate/20241003155624_add_openalex_id_indexing_to_authors.rb b/rails/db/migrate/20241003155624_add_openalex_id_indexing_to_authors.rb deleted file mode 100644 index 1182f7f..0000000 --- a/rails/db/migrate/20241003155624_add_openalex_id_indexing_to_authors.rb +++ /dev/null @@ -1,5 +0,0 @@ -class AddOpenalexIdIndexingToAuthors < ActiveRecord::Migration[7.1] - def change - add_index :authors, :openalex_id - end -end diff --git a/rails/db/migrate/20241003155625_add_open_alex_id_to_publishers.rb b/rails/db/migrate/20241003155625_add_open_alex_id_to_publishers.rb deleted file mode 100644 index 4e66850..0000000 --- a/rails/db/migrate/20241003155625_add_open_alex_id_to_publishers.rb +++ /dev/null @@ -1,5 +0,0 @@ -class AddOpenAlexIdToPublishers < ActiveRecord::Migration[7.1] - def change - add_column :publishers, :openalex_id, :integer - end -end diff --git a/rails/db/migrate/20241003155626_change_openalex_id_type_for_publishers.rb b/rails/db/migrate/20241003155626_change_openalex_id_type_for_publishers.rb deleted file mode 100644 index dbdd22b..0000000 --- a/rails/db/migrate/20241003155626_change_openalex_id_type_for_publishers.rb +++ /dev/null @@ -1,5 +0,0 @@ -class ChangeOpenalexIdTypeForPublishers < ActiveRecord::Migration[7.1] - def change - change_column(:publishers, :openalex_id, :string) - end -end diff --git a/rails/db/migrate/20241003155627_add_openalex_id_indexing_to_publishers.rb b/rails/db/migrate/20241003155627_add_openalex_id_indexing_to_publishers.rb deleted file mode 100644 index 7ab0be0..0000000 --- a/rails/db/migrate/20241003155627_add_openalex_id_indexing_to_publishers.rb +++ /dev/null @@ -1,5 +0,0 @@ -class AddOpenalexIdIndexingToPublishers < ActiveRecord::Migration[7.1] - def change - add_index :publishers, :openalex_id - end -end diff --git a/rails/db/migrate/20241003155628_add_open_alex_id_to_topics.rb b/rails/db/migrate/20241003155628_add_open_alex_id_to_topics.rb deleted file mode 100644 index 79fcb79..0000000 --- a/rails/db/migrate/20241003155628_add_open_alex_id_to_topics.rb +++ /dev/null @@ -1,6 +0,0 @@ -class AddOpenAlexIdToTopics < ActiveRecord::Migration[7.1] - def change - add_column :topics, :openalex_id, :string - add_index :topics, :openalex_id - end -end diff --git a/rails/db/migrate/20241003155629_add_open_alex_id_to_works.rb b/rails/db/migrate/20241003155629_add_open_alex_id_to_works.rb deleted file mode 100644 index 3096841..0000000 --- a/rails/db/migrate/20241003155629_add_open_alex_id_to_works.rb +++ /dev/null @@ -1,6 +0,0 @@ -class AddOpenAlexIdToWorks < ActiveRecord::Migration[7.1] - def change - add_column :works, :openalex_id, :string - add_index :works, :openalex_id - end -end diff --git a/rails/db/migrate/20241003155630_rename_type_on_works.rb b/rails/db/migrate/20241003155630_rename_type_on_works.rb deleted file mode 100644 index 9985da2..0000000 --- a/rails/db/migrate/20241003155630_rename_type_on_works.rb +++ /dev/null @@ -1,5 +0,0 @@ -class RenameTypeOnWorks < ActiveRecord::Migration[7.1] - def change - rename_column :works, :type, :work_type - end -end diff --git a/rails/db/migrate/20241025010442_index_insitutions_on_openalex_id.rb b/rails/db/migrate/20241025010442_index_insitutions_on_openalex_id.rb deleted file mode 100644 index 5a33be3..0000000 --- a/rails/db/migrate/20241025010442_index_insitutions_on_openalex_id.rb +++ /dev/null @@ -1,5 +0,0 @@ -class IndexInsitutionsOnOpenalexId < ActiveRecord::Migration[7.1] - def change - add_index :institutions, :openalex_id - end -end diff --git a/rails/db/migrate/20241028183837_allow_null_institution_in_works_authorship.rb b/rails/db/migrate/20241028183837_allow_null_institution_in_works_authorship.rb deleted file mode 100644 index 1371ab0..0000000 --- a/rails/db/migrate/20241028183837_allow_null_institution_in_works_authorship.rb +++ /dev/null @@ -1,5 +0,0 @@ -class AllowNullInstitutionInWorksAuthorship < ActiveRecord::Migration[7.1] - def change - change_column_null(:works_authorships, :institution_id, true) - end -end diff --git a/rails/db/migrate/20241029190712_allow_null_author_in_works_authorship.rb b/rails/db/migrate/20241029190712_allow_null_author_in_works_authorship.rb deleted file mode 100644 index 2dbdc37..0000000 --- a/rails/db/migrate/20241029190712_allow_null_author_in_works_authorship.rb +++ /dev/null @@ -1,5 +0,0 @@ -class AllowNullAuthorInWorksAuthorship < ActiveRecord::Migration[7.1] - def change - change_column_null(:works_authorships, :author_id, true) - end -end diff --git a/rails/db/migrate/20241029190734_allow_null_work_in_works_authorship.rb b/rails/db/migrate/20241029190734_allow_null_work_in_works_authorship.rb deleted file mode 100644 index 2621f94..0000000 --- a/rails/db/migrate/20241029190734_allow_null_work_in_works_authorship.rb +++ /dev/null @@ -1,5 +0,0 @@ -class AllowNullWorkInWorksAuthorship < ActiveRecord::Migration[7.1] - def change - change_column_null(:works_authorships, :work_id, true) - end -end diff --git a/rails/db/migrate/20241029203310_rename_id_columns_on_works_authorships.rb b/rails/db/migrate/20241029203310_rename_id_columns_on_works_authorships.rb deleted file mode 100644 index 4e4204a..0000000 --- a/rails/db/migrate/20241029203310_rename_id_columns_on_works_authorships.rb +++ /dev/null @@ -1,7 +0,0 @@ -class RenameIdColumnsOnWorksAuthorships < ActiveRecord::Migration[7.1] - def change - rename_column :works_authorships, :work_id, :work_openalex_id - rename_column :works_authorships, :author_id, :author_openalex_id - rename_column :works_authorships, :institution_id, :institution_openalex_id - end -end diff --git a/rails/db/migrate/20241029231448_drop_and_remake_works_authorship_table.rb b/rails/db/migrate/20241029231448_drop_and_remake_works_authorship_table.rb deleted file mode 100644 index 9e7a5d2..0000000 --- a/rails/db/migrate/20241029231448_drop_and_remake_works_authorship_table.rb +++ /dev/null @@ -1,15 +0,0 @@ -class DropAndRemakeWorksAuthorshipTable < ActiveRecord::Migration[7.1] - def change - drop_table :works_authorships - - create_table :works_authorships do |t| - t.string :author_position - t.string :work_openalex_id - t.string :author_openalex_id - t.string :institution_openalex_id - t.string :raw_affiliation_string - - t.timestamps - end - end -end diff --git a/rails/db/migrate/20241030154931_add_indexes_to_works_authorships.rb b/rails/db/migrate/20241030154931_add_indexes_to_works_authorships.rb deleted file mode 100644 index 871bf50..0000000 --- a/rails/db/migrate/20241030154931_add_indexes_to_works_authorships.rb +++ /dev/null @@ -1,7 +0,0 @@ -class AddIndexesToWorksAuthorships < ActiveRecord::Migration[7.1] - def change - add_index :works_authorships, :author_openalex_id - add_index :works_authorships, :work_openalex_id - add_index :works_authorships, :institution_openalex_id - end -end diff --git a/rails/db/migrate/20241108160553_create_authors_counts_by_years.rb b/rails/db/migrate/20241108160553_create_authors_counts_by_years.rb new file mode 100644 index 0000000..de6f959 --- /dev/null +++ b/rails/db/migrate/20241108160553_create_authors_counts_by_years.rb @@ -0,0 +1,15 @@ +class CreateAuthorsCountsByYears < ActiveRecord::Migration[7.1] + def change + create_table :authors_counts_by_years do |t| + t.string :author_openalex_id + t.integer :year + t.integer :works_count + t.integer :cited_by_count + t.integer :oa_works_count + + t.timestamps + end + + add_index :authors_counts_by_years, :author_openalex_id + end +end diff --git a/rails/db/migrate/20240628174724_create_authors_ids.rb b/rails/db/migrate/20241109014753_create_authors_ids.rb similarity index 69% rename from rails/db/migrate/20240628174724_create_authors_ids.rb rename to rails/db/migrate/20241109014753_create_authors_ids.rb index 62c3bf3..9e9d983 100644 --- a/rails/db/migrate/20240628174724_create_authors_ids.rb +++ b/rails/db/migrate/20241109014753_create_authors_ids.rb @@ -1,15 +1,16 @@ class CreateAuthorsIds < ActiveRecord::Migration[7.1] def change create_table :authors_ids do |t| - t.references :author, null: false, foreign_key: true - t.string :openalex + t.string :author_openalex_id t.string :orcid t.string :scopus t.string :twitter t.string :wikipedia - t.bigint :mag + t.string :mag t.timestamps end + + add_index :authors_ids, :author_openalex_id end end diff --git a/rails/db/migrate/20240628174731_create_institutions.rb b/rails/db/migrate/20241109170738_create_institutions.rb similarity index 71% rename from rails/db/migrate/20240628174731_create_institutions.rb rename to rails/db/migrate/20241109170738_create_institutions.rb index 5de6342..02607a6 100644 --- a/rails/db/migrate/20240628174731_create_institutions.rb +++ b/rails/db/migrate/20241109170738_create_institutions.rb @@ -1,7 +1,7 @@ class CreateInstitutions < ActiveRecord::Migration[7.1] def change create_table :institutions do |t| - t.string :openalex_id + t.string :institution_openalex_id t.string :ror t.string :display_name t.string :country_code @@ -11,9 +11,13 @@ def change t.string :image_thumbnail_url t.jsonb :display_name_acronyms t.jsonb :display_name_alternatives - t.bigint :works_count - t.bigint :cited_by_count + t.integer :works_count + t.integer :cited_by_count t.string :works_api_url + + t.timestamps end + + add_index :institutions, :institution_openalex_id end end diff --git a/rails/db/migrate/20241111173702_create_institutions_associated_institutions.rb b/rails/db/migrate/20241111173702_create_institutions_associated_institutions.rb new file mode 100644 index 0000000..18c48cd --- /dev/null +++ b/rails/db/migrate/20241111173702_create_institutions_associated_institutions.rb @@ -0,0 +1,15 @@ +class CreateInstitutionsAssociatedInstitutions < ActiveRecord::Migration[7.1] + def change + create_table :institutions_associated_institutions do |t| + t.string :institution_openalex_id + t.string :associated_institution_openalex_id + t.string :relationship + + t.timestamps + end + + add_index :institutions_associated_institutions, :institution_openalex_id + add_index :institutions_associated_institutions, + :associated_institution_openalex_id + end +end diff --git a/rails/db/migrate/20241111174303_create_institutions_counts_by_year.rb b/rails/db/migrate/20241111174303_create_institutions_counts_by_year.rb new file mode 100644 index 0000000..a02843b --- /dev/null +++ b/rails/db/migrate/20241111174303_create_institutions_counts_by_year.rb @@ -0,0 +1,15 @@ +class CreateInstitutionsCountsByYear < ActiveRecord::Migration[7.1] + def change + create_table :institutions_counts_by_years do |t| + t.string :institution_openalex_id + t.integer :year + t.integer :works_count + t.integer :cited_by_count + t.integer :oa_works_count + + t.timestamps + end + + add_index :institutions_counts_by_years, :institution_openalex_id + end +end diff --git a/rails/db/migrate/20240628174734_create_institutions_geos.rb b/rails/db/migrate/20241111174953_create_institutions_geo.rb similarity index 50% rename from rails/db/migrate/20240628174734_create_institutions_geos.rb rename to rails/db/migrate/20241111174953_create_institutions_geo.rb index 46b742d..1d0f8af 100644 --- a/rails/db/migrate/20240628174734_create_institutions_geos.rb +++ b/rails/db/migrate/20241111174953_create_institutions_geo.rb @@ -1,14 +1,18 @@ -class CreateInstitutionsGeos < ActiveRecord::Migration[7.1] +class CreateInstitutionsGeo < ActiveRecord::Migration[7.1] def change create_table :institutions_geos do |t| - t.references :institution, null: false, foreign_key: true + t.string :institution_openalex_id t.string :city - t.string :geonames_city_id + t.integer :geonames_city_id t.string :region t.string :country_code t.string :country t.float :latitude t.float :longitude + + t.timestamps end + + add_index :institutions_geos, :institution_openalex_id end end diff --git a/rails/db/migrate/20240628174735_create_institutions_ids.rb b/rails/db/migrate/20241111175452_create_institutions_ids.rb similarity index 61% rename from rails/db/migrate/20240628174735_create_institutions_ids.rb rename to rails/db/migrate/20241111175452_create_institutions_ids.rb index 24f1b67..3efd2a1 100644 --- a/rails/db/migrate/20240628174735_create_institutions_ids.rb +++ b/rails/db/migrate/20241111175452_create_institutions_ids.rb @@ -1,13 +1,16 @@ class CreateInstitutionsIds < ActiveRecord::Migration[7.1] def change create_table :institutions_ids do |t| - t.references :institution, null: false, foreign_key: true - t.string :openalex + t.string :institution_openalex_id t.string :ror t.string :grid t.string :wikipedia t.string :wikidata - t.bigint :mag + t.string :mag + + t.timestamps end + + add_index :institutions_ids, :institution_openalex_id end end diff --git a/rails/db/migrate/20240628174736_create_publishers.rb b/rails/db/migrate/20241111180929_create_publishers.rb similarity index 57% rename from rails/db/migrate/20240628174736_create_publishers.rb rename to rails/db/migrate/20241111180929_create_publishers.rb index 59a8a18..72e47fb 100644 --- a/rails/db/migrate/20240628174736_create_publishers.rb +++ b/rails/db/migrate/20241111180929_create_publishers.rb @@ -1,14 +1,19 @@ class CreatePublishers < ActiveRecord::Migration[7.1] def change create_table :publishers do |t| + t.string :publisher_openalex_id t.string :display_name t.jsonb :alternate_titles t.jsonb :country_codes - t.bigint :hierarchy_level + t.integer :hierarchy_level t.string :parent_publisher - t.bigint :works_count - t.bigint :cited_by_count + t.integer :works_count + t.integer :cited_by_count t.string :sources_api_url + + t.timestamps end + + add_index :publishers, :publisher_openalex_id end end diff --git a/rails/db/migrate/20241111181804_create_publishers_counts_by_years.rb b/rails/db/migrate/20241111181804_create_publishers_counts_by_years.rb new file mode 100644 index 0000000..23ddef4 --- /dev/null +++ b/rails/db/migrate/20241111181804_create_publishers_counts_by_years.rb @@ -0,0 +1,15 @@ +class CreatePublishersCountsByYears < ActiveRecord::Migration[7.1] + def change + create_table :publishers_counts_by_years do |t| + t.string :publisher_openalex_id + t.integer :year + t.integer :works_count + t.integer :cited_by_count + t.integer :oa_works_count + + t.timestamps + end + + add_index :publishers_counts_by_years, :publisher_openalex_id + end +end diff --git a/rails/db/migrate/20240628174738_create_publishers_ids.rb b/rails/db/migrate/20241111182314_create_publishers_ids.rb similarity index 60% rename from rails/db/migrate/20240628174738_create_publishers_ids.rb rename to rails/db/migrate/20241111182314_create_publishers_ids.rb index be8ec72..c1f9871 100644 --- a/rails/db/migrate/20240628174738_create_publishers_ids.rb +++ b/rails/db/migrate/20241111182314_create_publishers_ids.rb @@ -1,10 +1,13 @@ class CreatePublishersIds < ActiveRecord::Migration[7.1] def change create_table :publishers_ids do |t| - t.references :publisher, null: false, foreign_key: true - t.string :openalex + t.string :publisher_openalex_id t.string :ror t.string :wikidata + + t.timestamps end + + add_index :publishers_ids, :publisher_openalex_id end end diff --git a/rails/db/migrate/20240628174739_create_sources.rb b/rails/db/migrate/20241111182742_create_sources.rb similarity index 66% rename from rails/db/migrate/20240628174739_create_sources.rb rename to rails/db/migrate/20241111182742_create_sources.rb index a338e4f..0028596 100644 --- a/rails/db/migrate/20240628174739_create_sources.rb +++ b/rails/db/migrate/20241111182742_create_sources.rb @@ -1,16 +1,21 @@ class CreateSources < ActiveRecord::Migration[7.1] def change create_table :sources do |t| + t.string :source_openalex_id t.string :issn_l t.jsonb :issn t.string :display_name t.string :publisher - t.bigint :works_count - t.bigint :cited_by_count + t.integer :works_count + t.integer :cited_by_count t.boolean :is_oa t.boolean :is_in_doaj t.string :homepage_url t.string :works_api_url + + t.timestamps end + + add_index :sources, :source_openalex_id end end diff --git a/rails/db/migrate/20241111194229_create_sources_counts_by_years.rb b/rails/db/migrate/20241111194229_create_sources_counts_by_years.rb new file mode 100644 index 0000000..5dce03b --- /dev/null +++ b/rails/db/migrate/20241111194229_create_sources_counts_by_years.rb @@ -0,0 +1,15 @@ +class CreateSourcesCountsByYears < ActiveRecord::Migration[7.1] + def change + create_table :sources_counts_by_years do |t| + t.string :source_openalex_id + t.integer :year + t.integer :works_count + t.integer :cited_by_count + t.integer :oa_works_count + + t.timestamps + end + + add_index :sources_counts_by_years, :source_openalex_id + end +end diff --git a/rails/db/migrate/20240628174741_create_sources_ids.rb b/rails/db/migrate/20241111200050_create_sources_ids.rb similarity index 50% rename from rails/db/migrate/20240628174741_create_sources_ids.rb rename to rails/db/migrate/20241111200050_create_sources_ids.rb index aadcc7f..875e5ab 100644 --- a/rails/db/migrate/20240628174741_create_sources_ids.rb +++ b/rails/db/migrate/20241111200050_create_sources_ids.rb @@ -1,13 +1,16 @@ class CreateSourcesIds < ActiveRecord::Migration[7.1] def change create_table :sources_ids do |t| - t.references :source, null: false, foreign_key: true - t.string :openalex - t.string :issn_l - t.jsonb :issn - t.bigint :mag + t.string :source_openalex_id + t.jsonb :issn_l + t.string :issn + t.string :mag t.string :wikidata t.string :fatcat + + t.timestamps end + + add_index :sources_ids, :source_openalex_id end end diff --git a/rails/db/migrate/20241111200923_create_topics.rb b/rails/db/migrate/20241111200923_create_topics.rb new file mode 100644 index 0000000..807754a --- /dev/null +++ b/rails/db/migrate/20241111200923_create_topics.rb @@ -0,0 +1,27 @@ +class CreateTopics < ActiveRecord::Migration[7.1] + def change + create_table :topics do |t| + t.string :topic_openalex_id + t.string :display_name + t.integer :openalex_subfield_id + t.string :openalex_subfield_display_name + t.integer :openalex_field_id + t.string :openalex_field_display_name + t.integer :openalex_domain_id + t.string :openalex_domain_display_name + t.string :description + t.string :keywords, array: true, default: [] + t.string :works_api_url + t.string :wikipedia_id + t.integer :works_count + t.integer :cited_by_count + + t.timestamps + end + + add_index :topics, :topic_openalex_id + add_index :topics, :openalex_subfield_id + add_index :topics, :openalex_field_id + add_index :topics, :openalex_domain_id + end +end diff --git a/rails/db/migrate/20240628174742_create_works.rb b/rails/db/migrate/20241111202907_create_works.rb similarity index 63% rename from rails/db/migrate/20240628174742_create_works.rb rename to rails/db/migrate/20241111202907_create_works.rb index 9e16d28..61706f6 100644 --- a/rails/db/migrate/20240628174742_create_works.rb +++ b/rails/db/migrate/20241111202907_create_works.rb @@ -1,20 +1,24 @@ -# frozen_string_literal: true - class CreateWorks < ActiveRecord::Migration[7.1] def change create_table :works do |t| + t.string :work_openalex_id t.string :doi t.string :title t.string :display_name - t.bigint :publication_year + t.integer :publication_year t.string :publication_date - t.string :type - t.bigint :cited_by_count + t.string :work_type + t.integer :cited_by_count t.boolean :is_retracted t.boolean :is_paratext t.string :cited_by_api_url t.jsonb :abstract_inverted_index t.string :language + + t.timestamps end + + add_index :works, :work_openalex_id + add_index :works, :doi end end From b5d46140026e5dbbd54e71c4b58de5fbc3b00160 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Mon, 11 Nov 2024 20:33:18 +0000 Subject: [PATCH 25/44] Reworking loading rake tasks --- rails/lib/tasks/load_authors.rake | 18 ++++---- .../tasks/load_authors_counts_by_years.rake | 17 +++----- rails/lib/tasks/load_authors_ids.rake | 37 +++++++--------- rails/lib/tasks/load_institutions.rake | 14 ++++-- ..._institutions_associated_institutions.rake | 36 ++++++---------- .../load_institutions_counts_by_year.rake | 18 ++++---- rails/lib/tasks/load_institutions_geo.rake | 18 ++++---- rails/lib/tasks/load_institutions_ids.rake | 17 +++++--- rails/lib/tasks/load_publishers.rake | 30 +++++++------ .../tasks/load_publishers_counts_by_year.rake | 13 +++--- rails/lib/tasks/load_publishers_ids.rake | 13 +++--- rails/lib/tasks/load_sources.rake | 40 +++++++++++++++++ .../tasks/load_sources_counts_by_years.rake | 36 ++++++++++++++++ rails/lib/tasks/load_sources_ids.rake | 36 ++++++++++++++++ rails/lib/tasks/load_topics.rake | 31 +++++++------ rails/lib/tasks/load_works.rake | 43 +++++++++++++++++++ rails/lib/tasks/load_works_authorships.rake | 39 +++++++++++++++++ .../tasks/load_works_best_oa_locations.rake | 37 ++++++++++++++++ rails/lib/tasks/load_works_biblios.rake | 35 +++++++++++++++ rails/lib/tasks/load_works_locations.rake | 37 ++++++++++++++++ rails/lib/tasks/load_works_open_accesses.rake | 35 +++++++++++++++ .../tasks/load_works_referenced_works.rake | 29 +++++++++++++ rails/lib/tasks/load_works_related_works.rake | 29 +++++++++++++ rails/lib/tasks/load_works_topics.rake | 33 ++++++++++++++ 24 files changed, 554 insertions(+), 137 deletions(-) create mode 100644 rails/lib/tasks/load_sources.rake create mode 100644 rails/lib/tasks/load_sources_counts_by_years.rake create mode 100644 rails/lib/tasks/load_sources_ids.rake create mode 100644 rails/lib/tasks/load_works.rake create mode 100644 rails/lib/tasks/load_works_authorships.rake create mode 100644 rails/lib/tasks/load_works_best_oa_locations.rake create mode 100644 rails/lib/tasks/load_works_biblios.rake create mode 100644 rails/lib/tasks/load_works_locations.rake create mode 100644 rails/lib/tasks/load_works_open_accesses.rake create mode 100644 rails/lib/tasks/load_works_referenced_works.rake create mode 100644 rails/lib/tasks/load_works_related_works.rake create mode 100644 rails/lib/tasks/load_works_topics.rake diff --git a/rails/lib/tasks/load_authors.rake b/rails/lib/tasks/load_authors.rake index 64f97eb..209f51a 100644 --- a/rails/lib/tasks/load_authors.rake +++ b/rails/lib/tasks/load_authors.rake @@ -5,17 +5,16 @@ require 'csv' namespace :data_import do desc 'Load Authors from gzipped csv to db' task load_authors: :environment do - file_paths = Dir['/opt/bookworm/csv-files/authors/author_split*'] + file_paths = Dir['/opt/bookworm/csv-files/authors.csv.gz'] file_paths.each do |file_path| authors = [] Zlib::GzipReader.open(file_path) do |gzip| csv = CSV.new(gzip) - csv - .drop(1) - .each_with_index do |row, index| # drop(1) handles the header row + csv.each_with_index do |row, index| + unless index == 0 authors << { - openalex_id: row[0].split('/').last, + author_openalex_id: row[0].split('/').last, orcid: row[1], display_name: row[2], display_name_alternatives: row[3], @@ -24,13 +23,14 @@ namespace :data_import do last_known_institution: row[6], works_api_url: row[7] } + end - if authors.count >= 100 - Author.insert_all(authors) + if authors.count >= 10_000 + Author.insert_all(authors) - authors = [] - end + authors = [] end + end end Author.insert_all(authors) end diff --git a/rails/lib/tasks/load_authors_counts_by_years.rake b/rails/lib/tasks/load_authors_counts_by_years.rake index 0cd86b6..9334c48 100644 --- a/rails/lib/tasks/load_authors_counts_by_years.rake +++ b/rails/lib/tasks/load_authors_counts_by_years.rake @@ -3,12 +3,9 @@ require 'zlib' require 'csv' namespace :data_import do - desc 'Load AuthorsCountsByYear from gzipped csv to db' - task load_authors_counts_by_year: :environment do - file_paths = - Dir[ - '/opt/bookworm/csv-files/authors_counts_by_year/authors_counts_by_year_split*' - ] + desc 'Load AuthorsCountsByYears from gzipped csv to db' + task load_authors_counts_by_years: :environment do + file_paths = Dir['/opt/bookworm/csv-files/authors_counts_by_year.csv.gz'] file_paths.each do |file_path| authors_counts_by_year = [] @@ -16,11 +13,9 @@ namespace :data_import do csv = CSV.new(gzip) csv.each_with_index do |row, index| # drop(1) handles the header row - author = Author.find_by(openalex_id: row[0].split('/').last) - - unless author.nil? + unless index == 0 authors_counts_by_year << { - author_id: author.id, + author_openalex_id: row[0].split('/').last, year: row[1], works_count: row[2], cited_by_count: row[3], @@ -28,7 +23,7 @@ namespace :data_import do } end - if authors_counts_by_year.count >= 1000 + if authors_counts_by_year.count >= 10_000 AuthorsCountsByYear.insert_all(authors_counts_by_year) authors_counts_by_year = [] diff --git a/rails/lib/tasks/load_authors_ids.rake b/rails/lib/tasks/load_authors_ids.rake index 9c788a4..3be0610 100644 --- a/rails/lib/tasks/load_authors_ids.rake +++ b/rails/lib/tasks/load_authors_ids.rake @@ -5,35 +5,30 @@ require 'csv' namespace :data_import do desc 'Load AuthorsIds from gzipped csv to db' task load_authors_ids: :environment do - file_paths = Dir['/opt/bookworm/csv-files/authors_ids/authors_ids_split*'] + file_paths = Dir['/opt/bookworm/csv-files/authors_ids.csv.gz'] file_paths.each do |file_path| authors_ids = [] Zlib::GzipReader.open(file_path) do |gzip| csv = CSV.new(gzip) - csv - .drop(1) - .each_with_index do |row, index| # drop(1) handles the header row - author = Author.find_by(openalex_id: row[1].split('/').last) - - unless author.nil? - authors_ids << { - author_id: author.id, - openalex: row[1].split('/').last, - orcid: row[2], - scopus: row[3], - twitter: row[4], - wikipedia: row[5], - mag: row[6] - } - end + csv.each_with_index do |row, index| # drop(1) handles the header row + unless index == 0 + authors_ids << { + author_openalex_id: row[1].split('/').last, + orcid: row[2], + scopus: row[3], + twitter: row[4], + wikipedia: row[5], + mag: row[6] + } + end - if authors_ids.count >= 100 - AuthorsIds.insert_all(authors_ids) + if authors_ids.count >= 10_000 + AuthorsIds.insert_all(authors_ids) - authors_ids = [] - end + authors_ids = [] end + end end AuthorsIds.insert_all(authors_ids) diff --git a/rails/lib/tasks/load_institutions.rake b/rails/lib/tasks/load_institutions.rake index c8f48c4..0703b36 100644 --- a/rails/lib/tasks/load_institutions.rake +++ b/rails/lib/tasks/load_institutions.rake @@ -11,11 +11,10 @@ namespace :data_import do '/opt/bookworm/csv-files/institutions.csv.gz' ) do |gzip| csv = CSV.new(gzip) - csv - .drop(1) - .each_with_index do |row, index| # drop(1) handles the header row + csv.each_with_index do |row, index| + unless index == 0 institutions << { - openalex_id: row[0].split('/').last, + institution_openalex_id: row[0].split('/').last, ror: row[1], display_name: row[2], country_code: row[3], @@ -30,6 +29,13 @@ namespace :data_import do works_api_url: row[12] } end + + if institutions.count >= 10_000 + Institution.insert_all(institutions) + + institutions = [] + end + end end Institution.insert_all(institutions) end diff --git a/rails/lib/tasks/load_institutions_associated_institutions.rake b/rails/lib/tasks/load_institutions_associated_institutions.rake index ee8e6ca..b6f3dbf 100644 --- a/rails/lib/tasks/load_institutions_associated_institutions.rake +++ b/rails/lib/tasks/load_institutions_associated_institutions.rake @@ -11,31 +11,23 @@ namespace :data_import do '/opt/bookworm/csv-files/institutions_associated_institutions.csv.gz' ) do |gzip| csv = CSV.new(gzip) + csv.each_with_index do |row, index| # drop(1) handles the header row + unless index == 0 + institutions_associated_institutions << { + institution_openalex_id: row[0].split('/').last, + associated_institution_openalex_id: row[1].split('/').last, + relationship: row[2] + } + end - csv - .drop(1) - .each_with_index do |row, index| # drop(1) handles the header row - institution = Institution.find_by(openalex_id: row[0].split('/').last) - - associated_institution = - Institution.find_by(openalex_id: row[1].split('/').last) - - unless institution.nil? || associated_institution.nil? - institutions_associated_institutions << { - institution_id: institution.id, - associated_institution_id: associated_institution.id, - relationship: row[2] - } - end - - if institutions_associated_institutions.count >= 100 - InstitutionsAssociatedInstitutions.insert_all( - institutions_associated_institutions - ) + if institutions_associated_institutions.count >= 100_000 + InstitutionsAssociatedInstitutions.insert_all( + institutions_associated_institutions + ) - institutions_associated_institutions = [] - end + institutions_associated_institutions = [] end + end end InstitutionsAssociatedInstitutions.insert_all( diff --git a/rails/lib/tasks/load_institutions_counts_by_year.rake b/rails/lib/tasks/load_institutions_counts_by_year.rake index 275b520..bd6c416 100644 --- a/rails/lib/tasks/load_institutions_counts_by_year.rake +++ b/rails/lib/tasks/load_institutions_counts_by_year.rake @@ -12,25 +12,23 @@ namespace :data_import do ) do |gzip| csv = CSV.new(gzip) - csv - .drop(1) - .each_with_index do |row, index| # drop(1) handles the header row - institution = Institution.find_by(openalex_id: row[0].split('/').last) - + csv.each_with_index do |row, index| + unless index == 0 institutions_counts_by_years << { - institution_id: institution.id, + institution_openalex_id: row[0].split('/').last, year: row[1], works_count: row[2], cited_by_count: row[3], oa_works_count: row[4] } + end - if institutions_counts_by_years.count >= 100 - InstitutionsCountsByYear.insert_all(institutions_counts_by_years) + if institutions_counts_by_years.count >= 10_000 + InstitutionsCountsByYear.insert_all(institutions_counts_by_years) - institutions_counts_by_years = [] - end + institutions_counts_by_years = [] end + end end InstitutionsCountsByYear.insert_all(institutions_counts_by_years) diff --git a/rails/lib/tasks/load_institutions_geo.rake b/rails/lib/tasks/load_institutions_geo.rake index 652bab0..fe3d092 100644 --- a/rails/lib/tasks/load_institutions_geo.rake +++ b/rails/lib/tasks/load_institutions_geo.rake @@ -11,13 +11,10 @@ namespace :data_import do '/opt/bookworm/csv-files/institutions_geo.csv.gz' ) do |gzip| csv = CSV.new(gzip) - csv - .drop(1) - .each_with_index do |row, index| # drop(1) handles the header row - institution = Institution.find_by(openalex_id: row[0].split('/').last) - + csv.each_with_index do |row, index| + unless index == 0 institutions_geos << { - institution_id: institution.id, + institution_openalex_id: row[0].split('/').last, city: row[1], geonames_city_id: row[2], region: row[3], @@ -26,13 +23,14 @@ namespace :data_import do latitude: row[6], longitude: row[7] } + end - if institutions_geos.count >= 100 - InstitutionsGeo.insert_all(institutions_geos) + if institutions_geos.count >= 10_000 + InstitutionsGeo.insert_all(institutions_geos) - institutions_geos = [] - end + institutions_geos = [] end + end end InstitutionsGeo.insert_all(institutions_geos) diff --git a/rails/lib/tasks/load_institutions_ids.rake b/rails/lib/tasks/load_institutions_ids.rake index 727e472..3148b0b 100644 --- a/rails/lib/tasks/load_institutions_ids.rake +++ b/rails/lib/tasks/load_institutions_ids.rake @@ -11,14 +11,10 @@ namespace :data_import do '/opt/bookworm/csv-files/institutions_ids.csv.gz' ) do |gzip| csv = CSV.new(gzip) - csv - .drop(1) - .each_with_index do |row, index| # drop(1) handles the header row - institution = Institution.find_by(openalex_id: row[0].split('/').last) - + csv.each_with_index do |row, index| + unless index == 0 institution_ids << { - institution_id: institution.id, - openalex: row[0].split('/').last, + institution_openalex_id: row[0].split('/').last, ror: row[2], grid: row[3], wikipedia: row[4], @@ -26,6 +22,13 @@ namespace :data_import do mag: row[6] } end + + if institution_ids.count >= 10_000 + InstitutionsIds.insert_all(institution_ids) + + institution_ids = [] + end + end end InstitutionsIds.insert_all(institution_ids) diff --git a/rails/lib/tasks/load_publishers.rake b/rails/lib/tasks/load_publishers.rake index 1c347f9..6c029a1 100644 --- a/rails/lib/tasks/load_publishers.rake +++ b/rails/lib/tasks/load_publishers.rake @@ -11,20 +11,22 @@ namespace :data_import do publishers = [] csv = CSV.new(gzip) - csv.drop(1).each_with_index do |row, index| - publishers << { - openalex_id: row[0].split('/').last, - display_name: row[1], - alternate_titles: row[2], - country_codes: row[3], - hierarchy_level: row[4], - parent_publisher: row[5], - works_count: row[6], - cited_by_count: row[7], - sources_api_url: row[8], - } + csv.each_with_index do |row, index| + unless index == 0 + publishers << { + publisher_openalex_id: row[0].split('/').last, + display_name: row[1], + alternate_titles: row[2], + country_codes: row[3], + hierarchy_level: row[4], + parent_publisher: row[5], + works_count: row[6], + cited_by_count: row[7], + sources_api_url: row[8] + } + end - if publishers.count >= 500 + if publishers.count >= 10_000 Publisher.insert_all(publishers) publishers = [] @@ -33,4 +35,4 @@ namespace :data_import do Publisher.insert_all(publishers) end end -end \ No newline at end of file +end diff --git a/rails/lib/tasks/load_publishers_counts_by_year.rake b/rails/lib/tasks/load_publishers_counts_by_year.rake index 610b945..efd41ff 100644 --- a/rails/lib/tasks/load_publishers_counts_by_year.rake +++ b/rails/lib/tasks/load_publishers_counts_by_year.rake @@ -7,16 +7,14 @@ namespace :data_import do task load_publishers_counts_by_year: :environment do file_path = '/opt/bookworm/csv-files/publishers_counts_by_year.csv.gz' - publishers_counts_by_years = [] Zlib::GzipReader.open(file_path) do |gzip| csv = CSV.new(gzip) + publishers_counts_by_years = [] csv.each_with_index do |row, index| - publisher = Publisher.find_by(openalex_id: row[0].split('/').last) - - unless publisher.nil? + unless index == 0 publishers_counts_by_years << { - publisher_id: publisher.id, + publisher_openalex_id: row[0].split('/').last, year: row[1], works_count: row[2], cited_by_count: row[3], @@ -30,8 +28,7 @@ namespace :data_import do publishers_counts_by_years = [] end end + PublishersCountsByYear.insert_all(publishers_counts_by_years) end - - PublishersCountsByYear.insert_all(publishers_counts_by_years) end -end \ No newline at end of file +end diff --git a/rails/lib/tasks/load_publishers_ids.rake b/rails/lib/tasks/load_publishers_ids.rake index d2bd20c..29a1417 100644 --- a/rails/lib/tasks/load_publishers_ids.rake +++ b/rails/lib/tasks/load_publishers_ids.rake @@ -6,29 +6,26 @@ namespace :data_import do desc 'Load PublishersIds from gzipped csv to db' task load_publishers_ids: :environment do file_path = '/opt/bookworm/csv-files/publishers_ids.csv.gz' - publishers_ids = [] Zlib::GzipReader.open(file_path) do |gzip| csv = CSV.new(gzip) + publishers_ids = [] csv.each_with_index do |row, index| - publisher = Publisher.find_by(openalex_id: row[0].split('/').last) - - unless publisher.nil? + unless index == 0 publishers_ids << { - publisher_id: publisher.id, - openalex: row[1].split('/').last, + publisher_openalex_id: row[0].split('/').last, ror: row[2], wikidata: row[3] } end - if publishers_ids.count >= 1000 + if publishers_ids.count >= 10_000 PublishersIds.insert_all(publishers_ids) publishers_ids = [] end end + PublishersIds.insert_all(publishers_ids) end - PublishersIds.insert_all(publishers_ids) end end diff --git a/rails/lib/tasks/load_sources.rake b/rails/lib/tasks/load_sources.rake new file mode 100644 index 0000000..108a6c0 --- /dev/null +++ b/rails/lib/tasks/load_sources.rake @@ -0,0 +1,40 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load Sources from gzipped csv' + task load_sources: :environment do + file_path = '/opt/bookworm/csv-files/sources.csv.gz' + + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip) + sources = [] + + csv.each_with_index do |row, index| + unless index == 0 + sources << { + source_openalex_id: row[0].split('/').last, + issn_l: row[1], + issn: row[2], + display_name: row[3], + publisher: row[4], + works_count: row[5], + cited_by_count: row[6], + is_oa: row[7], + is_in_doaj: row[8], + homepage_url: row[9], + works_api_url: row[10] + } + end + + if sources.count >= 10_000 + Source.insert_all(sources) + + sources = [] + end + end + Source.insert_all(sources) + end + end +end diff --git a/rails/lib/tasks/load_sources_counts_by_years.rake b/rails/lib/tasks/load_sources_counts_by_years.rake new file mode 100644 index 0000000..2f20cab --- /dev/null +++ b/rails/lib/tasks/load_sources_counts_by_years.rake @@ -0,0 +1,36 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load SourcesCountsByYears from gzipped csv to db' + task load_sources_counts_by_years: :environment do + file_paths = Dir['/opt/bookworm/csv-files/sources_counts_by_year.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip) + sources_counts_by_year = [] + + csv.each_with_index do |row, index| # drop(1) handles the header row + unless index == 0 + sources_counts_by_year << { + source_openalex_id: row[0].split('/').last, + year: row[1], + works_count: row[2], + cited_by_count: row[3], + oa_works_count: row[4] + } + end + + if sources_counts_by_year.count >= 10_000 + SourcesCountsByYear.insert_all(sources_counts_by_year) + + sources_counts_by_year = [] + end + end + SourcesCountsByYear.insert_all(sources_counts_by_year) + end + end + end +end diff --git a/rails/lib/tasks/load_sources_ids.rake b/rails/lib/tasks/load_sources_ids.rake new file mode 100644 index 0000000..cfe9114 --- /dev/null +++ b/rails/lib/tasks/load_sources_ids.rake @@ -0,0 +1,36 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load SourcesIds from gzipped csv to db' + task load_sources_ids: :environment do + file_paths = Dir['/opt/bookworm/csv-files/sources_ids.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + sources_ids = [] + csv = CSV.new(gzip) + csv.each_with_index do |row, index| + unless index == 0 + sources_ids << { + source_openalex_id: row[0].split('/').last, + issn_l: row[2], + issn: row[3], + mag: row[4], + wikidata: row[5], + fatcat: row[6] + } + end + + if sources_ids.count >= 10_000 + SourcesIds.insert_all(sources_ids) + + sources_ids = [] + end + end + SourcesIds.insert_all(sources_ids) + end + end + end +end diff --git a/rails/lib/tasks/load_topics.rake b/rails/lib/tasks/load_topics.rake index 8799c62..1550262 100644 --- a/rails/lib/tasks/load_topics.rake +++ b/rails/lib/tasks/load_topics.rake @@ -7,22 +7,21 @@ namespace :data_import do desc 'Load Topics from gzipped csv to db' task load_topics: :environment do file_path = '/opt/bookworm/csv-files/topics.csv.gz' - topics = [] Zlib::GzipReader.open(file_path) do |gzip| csv = CSV.new(gzip) - csv - .drop(1) - .each_with_index do |row, index| + topics = [] + csv.each_with_index do |row, index| + unless index == 0 topics << { - openalex_id: row[0].split('/').last, + topic_openalex_id: row[0].split('/').last, display_name: row[1], - subfield_id: row[2].split('/').last, - subfield_display_name: row[3], - field_id: row[4].split('/').last, - field_display_name: row[5], - domain_id: row[6].split('/').last, - domain_display_name: row[7], + openalex_subfield_id: row[2].split('/').last, + openalex_subfield_display_name: row[3], + openalex_field_id: row[4].split('/').last, + openalex_field_display_name: row[5], + openalex_domain_id: row[6].split('/').last, + openalex_domain_display_name: row[7], description: row[8], keywords: row[9].split('; '), works_api_url: row[10], @@ -31,8 +30,14 @@ namespace :data_import do cited_by_count: row[13] } end - end - Topic.insert_all(topics) + if topics.count >= 10_000 + Topic.insert_all(topics) + + topics = [] + end + end + Topic.insert_all(topics) + end end end diff --git a/rails/lib/tasks/load_works.rake b/rails/lib/tasks/load_works.rake new file mode 100644 index 0000000..004c346 --- /dev/null +++ b/rails/lib/tasks/load_works.rake @@ -0,0 +1,43 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load Works from gzipped csv to db' + task load_works: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip, encoding: 'utf-8') + works = [] + + csv.each_with_index do |row, index| + unless index == 0 + works << { + work_openalex_id: row[0].split('/').last, + doi: row[1], + title: row[2], + display_name: row[3], + publication_year: row[4], + publication_date: row[5], + work_type: row[6], + cited_by_count: row[7], + is_retracted: row[8], + is_paratext: row[9], + cited_by_api_url: row[10], + abstract_inverted_index: row[11], + language: row[12] + } + end + + if works.count >= 5000 + Work.insert_all(works) + works = [] + end + end + Work.insert_all(works) + end + end + end +end diff --git a/rails/lib/tasks/load_works_authorships.rake b/rails/lib/tasks/load_works_authorships.rake new file mode 100644 index 0000000..bcbf486 --- /dev/null +++ b/rails/lib/tasks/load_works_authorships.rake @@ -0,0 +1,39 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksAuthorships from gzipped csv to db' + task load_works_authorships: :environment do + file_paths = + Dir['/opt/bookworm/csv-files/works_authorships/works_authorships.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + works_authorships = [] + csv = CSV.new(gzip) + csv # .drop(1) + .each_with_index do |row, index| + work_openalex_id = row[0].present? ? row[0].split('/').last : nil + author_openalex_id = row[2].present? ? row[2].split('/').last : nil + institution_openalex_id = + row[3].present? ? row[3].split('/').last : nil + + works_authorships << { + work_openalex_id: work_openalex_id, + author_position: row[1], + author_openalex_id: author_openalex_id, + institution_openalex_id: institution_openalex_id, + raw_affiliation_string: row[4] + } + + if works_authorships.count >= 10_000 + WorksAuthorship.insert_all(works_authorships) + + works_authorships = [] + end + end + end + end + end +end diff --git a/rails/lib/tasks/load_works_best_oa_locations.rake b/rails/lib/tasks/load_works_best_oa_locations.rake new file mode 100644 index 0000000..7dbb2a9 --- /dev/null +++ b/rails/lib/tasks/load_works_best_oa_locations.rake @@ -0,0 +1,37 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksBestOALocations from gzipped csv to db' + task load_works_best_oa_locations: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works_best_oa_locations.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + works_best_oa_locations = [] + csv = CSV.new(gzip) + csv.each_with_index do |row, index| + unless index == 0 + works_best_oa_locations << { + work_openalex_id: row[0].split('/').last, + source_openalex_id: row[1].split('/').last, + landing_page_url: row[2], + pdf_url: row[3], + is_oa: row[4], + version: row[5], + license: row[6] + } + end + + if works_best_oa_locations.count >= 10_000 + WorksBestOaLocation.insert_all(works_best_oa_locations) + + works_best_oa_locations = [] + end + end + WorksBestOaLocation.insert_all(works_best_oa_locations) + end + end + end +end diff --git a/rails/lib/tasks/load_works_biblios.rake b/rails/lib/tasks/load_works_biblios.rake new file mode 100644 index 0000000..379bc4a --- /dev/null +++ b/rails/lib/tasks/load_works_biblios.rake @@ -0,0 +1,35 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksBiblios from gzipped csv to db' + task load_works_biblios: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works_biblio.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + works_biblios = [] + csv = CSV.new(gzip) + csv.each_with_index do |row, index| + unless index == 0 + works_biblios << { + work_openalex_id: row[0].split('/').last, + volume: row[1], + issue: row[2], + first_page: row[3], + last_page: row[4] + } + end + + if works_biblios.count >= 10_000 + WorksBiblio.insert_all(works_biblios) + + works_biblios = [] + end + end + WorksBiblio.insert_all(works_biblios) + end + end + end +end diff --git a/rails/lib/tasks/load_works_locations.rake b/rails/lib/tasks/load_works_locations.rake new file mode 100644 index 0000000..d5215c9 --- /dev/null +++ b/rails/lib/tasks/load_works_locations.rake @@ -0,0 +1,37 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksLocations from gzipped csv to db' + task load_works_locations: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works_locations.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + works_locations = [] + csv = CSV.new(gzip) + csv.each_with_index do |row, index| + unless index == 0 + works_locations << { + work_openalex_id: row[0].split('/').last, + source_openalex_id: row[1].split('/').last, + landing_page_url: row[2], + pdf_url: row[3], + is_oa: row[4], + version: row[5], + license: row[6] + } + end + + if works_locations.count >= 10_000 + WorksLocation.insert_all(works_locations) + + works_locations = [] + end + end + WorksLocation.insert_all(works_locations) + end + end + end +end diff --git a/rails/lib/tasks/load_works_open_accesses.rake b/rails/lib/tasks/load_works_open_accesses.rake new file mode 100644 index 0000000..4e22f50 --- /dev/null +++ b/rails/lib/tasks/load_works_open_accesses.rake @@ -0,0 +1,35 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksOpenAccess from gzipped csv to db' + task load_works_open_accesses: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works_open_access.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + works_open_accesses = [] + csv = CSV.new(gzip) + csv.each_with_index do |row, index| + unless index == 0 + works_open_accesses << { + work_openalex_id: row[0].split('/').last, + is_oa: row[1], + oa_status: row[2], + oa_url: row[3], + any_repository_has_fulltext: row[4] + } + end + + if works_open_accesses.count >= 10_000 + WorksOpenAccess.insert_all(works_open_accesses) + + works_open_accesses = [] + end + end + WorksOpenAccess.insert_all(works_open_accesses) + end + end + end +end diff --git a/rails/lib/tasks/load_works_referenced_works.rake b/rails/lib/tasks/load_works_referenced_works.rake new file mode 100644 index 0000000..dda5b95 --- /dev/null +++ b/rails/lib/tasks/load_works_referenced_works.rake @@ -0,0 +1,29 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksReferencedWorks from gzipped csv to db' + task load_works_referenced_works: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works_referenced_works.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + works_referenced_works = [] + csv = CSV.new(gzip) + csv.each_with_index do |row, index| + works_referenced_works << { + work_id: row[0].split('/').last, + referenced_work_id: row[1].split('/').last + } + + if works_referenced_works.count >= 10_000 + WorksReferencedWorks.insert_all(works_referenced_works) + + works_referenced_works = [] + end + end + end + end + end +end diff --git a/rails/lib/tasks/load_works_related_works.rake b/rails/lib/tasks/load_works_related_works.rake new file mode 100644 index 0000000..a16847a --- /dev/null +++ b/rails/lib/tasks/load_works_related_works.rake @@ -0,0 +1,29 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksRelatedWorks from gzipped csv to db' + task load_works_related_works: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works_related_works.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + works_related_works = [] + csv = CSV.new(gzip) + csv.each_with_index do |row, index| + works_related_works << { + work_id: row[0].split('/').last, + related_work_id: row[1].split('/').last + } + + if works_related_works.count >= 10_000 + WorksRelatedWorks.insert_all(works_related_works) + + works_related_works = [] + end + end + end + end + end +end diff --git a/rails/lib/tasks/load_works_topics.rake b/rails/lib/tasks/load_works_topics.rake new file mode 100644 index 0000000..3afd280 --- /dev/null +++ b/rails/lib/tasks/load_works_topics.rake @@ -0,0 +1,33 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksTopics from gzipped csv to db' + task load_works_topics: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works_topics.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + works_topics = [] + csv = CSV.new(gzip) + csv.each_with_index do |row, index| + unless index == 0 + works_topics << { + work_openalex_id: row[0].split('/').last, + topic_openalex_id: row[1].split('/').last, + score: row[2].to_f + } + end + + if works_topics.count >= 10_000 + WorksTopic.insert_all(works_topics) + + works_topics = [] + end + end + WorksTopic.insert_all(works_topics) + end + end + end +end From 23aa897e376873f779ca161394d5fa8f8dbaaf77 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 4 Dec 2024 18:11:44 +0000 Subject: [PATCH 26/44] Updated migrations for full data snapshot --- ...20241118172317_create_works_authorships.rb | 17 + ...21170930_create_works_best_oa_locations.rb | 18 + .../20241121184927_create_works_biblios.rb | 15 + .../20241122150715_create_works_ids.rb | 16 + .../20241123190513_create_works_locations.rb | 18 + ...241124185128_create_works_open_accesses.rb | 15 + ...25144747_create_works_primary_locations.rb | 18 + ...126012258_create_works_referenced_works.rb | 13 + ..._timestamps_from_works_referenced_works.rb | 6 + rails/db/schema.rb | 349 ++++++++---------- 10 files changed, 281 insertions(+), 204 deletions(-) create mode 100644 rails/db/migrate/20241118172317_create_works_authorships.rb create mode 100644 rails/db/migrate/20241121170930_create_works_best_oa_locations.rb create mode 100644 rails/db/migrate/20241121184927_create_works_biblios.rb create mode 100644 rails/db/migrate/20241122150715_create_works_ids.rb create mode 100644 rails/db/migrate/20241123190513_create_works_locations.rb create mode 100644 rails/db/migrate/20241124185128_create_works_open_accesses.rb create mode 100644 rails/db/migrate/20241125144747_create_works_primary_locations.rb create mode 100644 rails/db/migrate/20241126012258_create_works_referenced_works.rb create mode 100644 rails/db/migrate/20241202154712_remove_timestamps_from_works_referenced_works.rb diff --git a/rails/db/migrate/20241118172317_create_works_authorships.rb b/rails/db/migrate/20241118172317_create_works_authorships.rb new file mode 100644 index 0000000..bb769df --- /dev/null +++ b/rails/db/migrate/20241118172317_create_works_authorships.rb @@ -0,0 +1,17 @@ +class CreateWorksAuthorships < ActiveRecord::Migration[7.1] + def change + create_table :works_authorships do |t| + t.string :work_openalex_id + t.string :author_position + t.string :author_openalex_id + t.string :institution_openalex_id + t.string :raw_affiliation_string + + t.timestamps + end + + add_index :works_authorships, :work_openalex_id + add_index :works_authorships, :author_openalex_id + add_index :works_authorships, :institution_openalex_id + end +end diff --git a/rails/db/migrate/20241121170930_create_works_best_oa_locations.rb b/rails/db/migrate/20241121170930_create_works_best_oa_locations.rb new file mode 100644 index 0000000..93cedb2 --- /dev/null +++ b/rails/db/migrate/20241121170930_create_works_best_oa_locations.rb @@ -0,0 +1,18 @@ +class CreateWorksBestOaLocations < ActiveRecord::Migration[7.1] + def change + create_table :works_best_oa_locations do |t| + t.string :work_openalex_id + t.string :source_openalex_id + t.string :landing_page_url + t.string :pdf_url + t.boolean :is_oa + t.string :version + t.string :license + + t.timestamps + end + + add_index :works_best_oa_locations, :work_openalex_id + add_index :works_best_oa_locations, :source_openalex_id + end +end diff --git a/rails/db/migrate/20241121184927_create_works_biblios.rb b/rails/db/migrate/20241121184927_create_works_biblios.rb new file mode 100644 index 0000000..3f14f99 --- /dev/null +++ b/rails/db/migrate/20241121184927_create_works_biblios.rb @@ -0,0 +1,15 @@ +class CreateWorksBiblios < ActiveRecord::Migration[7.1] + def change + create_table :works_biblios do |t| + t.string :work_openalex_id + t.string :volume + t.string :issue + t.string :first_page + t.string :last_page + + t.timestamps + end + + add_index :works_biblios, :work_openalex_id + end +end diff --git a/rails/db/migrate/20241122150715_create_works_ids.rb b/rails/db/migrate/20241122150715_create_works_ids.rb new file mode 100644 index 0000000..1eab34b --- /dev/null +++ b/rails/db/migrate/20241122150715_create_works_ids.rb @@ -0,0 +1,16 @@ +class CreateWorksIds < ActiveRecord::Migration[7.1] + def change + create_table :works_ids do |t| + t.string :work_openalex_id + t.string :doi + t.string :mag + t.string :pmid + t.string :pmcid + + t.timestamps + end + + add_index :works_ids, :work_openalex_id + add_index :works_ids, :doi + end +end diff --git a/rails/db/migrate/20241123190513_create_works_locations.rb b/rails/db/migrate/20241123190513_create_works_locations.rb new file mode 100644 index 0000000..c1164be --- /dev/null +++ b/rails/db/migrate/20241123190513_create_works_locations.rb @@ -0,0 +1,18 @@ +class CreateWorksLocations < ActiveRecord::Migration[7.1] + def change + create_table :works_locations do |t| + t.string :work_openalex_id + t.string :source_openalex_id + t.string :landing_page_url + t.string :pdf_url + t.boolean :is_oa + t.string :version + t.string :license + + t.timestamps + end + + add_index :works_locations, :work_openalex_id + add_index :works_locations, :source_openalex_id + end +end diff --git a/rails/db/migrate/20241124185128_create_works_open_accesses.rb b/rails/db/migrate/20241124185128_create_works_open_accesses.rb new file mode 100644 index 0000000..f9b098a --- /dev/null +++ b/rails/db/migrate/20241124185128_create_works_open_accesses.rb @@ -0,0 +1,15 @@ +class CreateWorksOpenAccesses < ActiveRecord::Migration[7.1] + def change + create_table :works_open_accesses do |t| + t.string :work_openalex_id + t.boolean :is_oa + t.string :oa_status + t.string :oa_url + t.boolean :any_repository_has_fulltext + + t.timestamps + end + + add_index :works_open_accesses, :work_openalex_id + end +end diff --git a/rails/db/migrate/20241125144747_create_works_primary_locations.rb b/rails/db/migrate/20241125144747_create_works_primary_locations.rb new file mode 100644 index 0000000..b2526da --- /dev/null +++ b/rails/db/migrate/20241125144747_create_works_primary_locations.rb @@ -0,0 +1,18 @@ +class CreateWorksPrimaryLocations < ActiveRecord::Migration[7.1] + def change + create_table :works_primary_locations do |t| + t.string :work_openalex_id + t.string :source_openalex_id + t.string :landing_page_url + t.string :pdf_url + t.boolean :is_oa + t.string :version + t.string :license + + t.timestamps + end + + add_index :works_primary_locations, :work_openalex_id + add_index :works_primary_locations, :source_openalex_id + end +end diff --git a/rails/db/migrate/20241126012258_create_works_referenced_works.rb b/rails/db/migrate/20241126012258_create_works_referenced_works.rb new file mode 100644 index 0000000..c7a3731 --- /dev/null +++ b/rails/db/migrate/20241126012258_create_works_referenced_works.rb @@ -0,0 +1,13 @@ +class CreateWorksReferencedWorks < ActiveRecord::Migration[7.1] + def change + create_table :works_referenced_works do |t| + t.string :work_openalex_id + t.string :referenced_work_openalex_id + + t.timestamps + end + + add_index :works_referenced_works, :work_openalex_id + add_index :works_referenced_works, :referenced_work_openalex_id + end +end diff --git a/rails/db/migrate/20241202154712_remove_timestamps_from_works_referenced_works.rb b/rails/db/migrate/20241202154712_remove_timestamps_from_works_referenced_works.rb new file mode 100644 index 0000000..16f5963 --- /dev/null +++ b/rails/db/migrate/20241202154712_remove_timestamps_from_works_referenced_works.rb @@ -0,0 +1,6 @@ +class RemoveTimestampsFromWorksReferencedWorks < ActiveRecord::Migration[7.1] + def change + remove_column :works_referenced_works, :created_at, :string + remove_column :works_referenced_works, :updated_at, :string + end +end diff --git a/rails/db/schema.rb b/rails/db/schema.rb index 4b282b5..34efa03 100644 --- a/rails/db/schema.rb +++ b/rails/db/schema.rb @@ -10,11 +10,12 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema[7.1].define(version: 2024_10_03_155628) do +ActiveRecord::Schema[7.1].define(version: 2024_12_02_154712) do # These are extensions that must be enabled in order to support this database enable_extension "plpgsql" create_table "authors", force: :cascade do |t| + t.string "author_openalex_id" t.string "orcid" t.string "display_name" t.jsonb "display_name_alternatives" @@ -22,81 +23,34 @@ t.bigint "cited_by_count" t.string "last_known_institution" t.string "works_api_url" - t.string "openalex_id" - t.index ["openalex_id"], name: "index_authors_on_openalex_id" + t.index ["author_openalex_id"], name: "index_authors_on_author_openalex_id" end create_table "authors_counts_by_years", force: :cascade do |t| - t.bigint "author_id", null: false - t.bigint "year", null: false - t.bigint "works_count" - t.bigint "cited_by_count" - t.bigint "oa_works_count" + t.string "author_openalex_id" + t.integer "year" + t.integer "works_count" + t.integer "cited_by_count" + t.integer "oa_works_count" t.datetime "created_at", null: false t.datetime "updated_at", null: false - t.index ["author_id"], name: "index_authors_counts_by_years_on_author_id" + t.index ["author_openalex_id"], name: "index_authors_counts_by_years_on_author_openalex_id" end create_table "authors_ids", force: :cascade do |t| - t.bigint "author_id", null: false - t.string "openalex" + t.string "author_openalex_id" t.string "orcid" t.string "scopus" t.string "twitter" t.string "wikipedia" - t.bigint "mag" - t.datetime "created_at", null: false - t.datetime "updated_at", null: false - t.index ["author_id"], name: "index_authors_ids_on_author_id" - end - - create_table "concepts", force: :cascade do |t| - t.string "wikidata" - t.string "display_name" - t.bigint "level" - t.string "description" - t.bigint "works_count" - t.bigint "cited_by_count" - t.string "image_url" - t.string "image_thumbnail_url" - t.string "works_api_url" - end - - create_table "concepts_ancestors", force: :cascade do |t| - t.string "concept_id", null: false - t.string "ancestor_id", null: false + t.string "mag" t.datetime "created_at", null: false t.datetime "updated_at", null: false - end - - create_table "concepts_counts_by_years", force: :cascade do |t| - t.bigint "concept_id", null: false - t.bigint "year", null: false - t.bigint "works_count" - t.bigint "cited_by_count" - t.bigint "oa_works_count" - t.index ["concept_id"], name: "index_concepts_counts_by_years_on_concept_id" - end - - create_table "concepts_ids", force: :cascade do |t| - t.bigint "concept_id", null: false - t.string "openalex" - t.string "wikidata" - t.string "wikipedia" - t.jsonb "umls_aui" - t.jsonb "umls_cui" - t.bigint "mag" - t.index ["concept_id"], name: "index_concepts_ids_on_concept_id" - end - - create_table "concepts_related_concepts", force: :cascade do |t| - t.string "concept_id" - t.string "related_concept_id" - t.float "score" + t.index ["author_openalex_id"], name: "index_authors_ids_on_author_openalex_id" end create_table "institutions", force: :cascade do |t| - t.string "openalex_id" + t.string "institution_openalex_id" t.string "ror" t.string "display_name" t.string "country_code" @@ -106,286 +60,273 @@ t.string "image_thumbnail_url" t.jsonb "display_name_acronyms" t.jsonb "display_name_alternatives" - t.bigint "works_count" - t.bigint "cited_by_count" + t.integer "works_count" + t.integer "cited_by_count" t.string "works_api_url" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["institution_openalex_id"], name: "index_institutions_on_institution_openalex_id" end create_table "institutions_associated_institutions", force: :cascade do |t| - t.integer "institution_id" - t.integer "associated_institution_id" + t.string "institution_openalex_id" + t.string "associated_institution_openalex_id" t.string "relationship" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["associated_institution_openalex_id"], name: "idx_on_associated_institution_openalex_id_0b6f4e76cc" + t.index ["institution_openalex_id"], name: "idx_on_institution_openalex_id_2cfe9cc51b" end create_table "institutions_counts_by_years", force: :cascade do |t| - t.bigint "institution_id", null: false - t.bigint "year" - t.bigint "works_count" - t.bigint "cited_by_count" - t.bigint "oa_works_count" - t.index ["institution_id"], name: "index_institutions_counts_by_years_on_institution_id" + t.string "institution_openalex_id" + t.integer "year" + t.integer "works_count" + t.integer "cited_by_count" + t.integer "oa_works_count" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["institution_openalex_id"], name: "index_institutions_counts_by_years_on_institution_openalex_id" end create_table "institutions_geos", force: :cascade do |t| - t.bigint "institution_id", null: false + t.string "institution_openalex_id" t.string "city" - t.string "geonames_city_id" + t.integer "geonames_city_id" t.string "region" t.string "country_code" t.string "country" t.float "latitude" t.float "longitude" - t.index ["institution_id"], name: "index_institutions_geos_on_institution_id" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["institution_openalex_id"], name: "index_institutions_geos_on_institution_openalex_id" end create_table "institutions_ids", force: :cascade do |t| - t.bigint "institution_id", null: false - t.string "openalex" + t.string "institution_openalex_id" t.string "ror" t.string "grid" t.string "wikipedia" t.string "wikidata" - t.bigint "mag" - t.index ["institution_id"], name: "index_institutions_ids_on_institution_id" + t.string "mag" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["institution_openalex_id"], name: "index_institutions_ids_on_institution_openalex_id" end create_table "publishers", force: :cascade do |t| + t.string "publisher_openalex_id" t.string "display_name" t.jsonb "alternate_titles" t.jsonb "country_codes" - t.bigint "hierarchy_level" + t.integer "hierarchy_level" t.string "parent_publisher" - t.bigint "works_count" - t.bigint "cited_by_count" + t.integer "works_count" + t.integer "cited_by_count" t.string "sources_api_url" - t.string "openalex_id" - t.index ["openalex_id"], name: "index_publishers_on_openalex_id" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["publisher_openalex_id"], name: "index_publishers_on_publisher_openalex_id" end create_table "publishers_counts_by_years", force: :cascade do |t| - t.bigint "publisher_id", null: false - t.bigint "year" - t.bigint "works_count" - t.bigint "cited_by_count" - t.bigint "oa_works_count" - t.index ["publisher_id"], name: "index_publishers_counts_by_years_on_publisher_id" + t.string "publisher_openalex_id" + t.integer "year" + t.integer "works_count" + t.integer "cited_by_count" + t.integer "oa_works_count" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["publisher_openalex_id"], name: "index_publishers_counts_by_years_on_publisher_openalex_id" end create_table "publishers_ids", force: :cascade do |t| - t.bigint "publisher_id", null: false - t.string "openalex" + t.string "publisher_openalex_id" t.string "ror" t.string "wikidata" - t.index ["publisher_id"], name: "index_publishers_ids_on_publisher_id" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["publisher_openalex_id"], name: "index_publishers_ids_on_publisher_openalex_id" end create_table "sources", force: :cascade do |t| + t.string "source_openalex_id" t.string "issn_l" t.jsonb "issn" t.string "display_name" t.string "publisher" - t.bigint "works_count" - t.bigint "cited_by_count" + t.integer "works_count" + t.integer "cited_by_count" t.boolean "is_oa" t.boolean "is_in_doaj" t.string "homepage_url" t.string "works_api_url" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["source_openalex_id"], name: "index_sources_on_source_openalex_id" end create_table "sources_counts_by_years", force: :cascade do |t| - t.bigint "source_id", null: false - t.bigint "year" - t.bigint "works_count" - t.bigint "cited_by_count" - t.bigint "oa_works_count" - t.index ["source_id"], name: "index_sources_counts_by_years_on_source_id" + t.string "source_openalex_id" + t.integer "year" + t.integer "works_count" + t.integer "cited_by_count" + t.integer "oa_works_count" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["source_openalex_id"], name: "index_sources_counts_by_years_on_source_openalex_id" end create_table "sources_ids", force: :cascade do |t| - t.bigint "source_id", null: false - t.string "openalex" - t.string "issn_l" - t.jsonb "issn" - t.bigint "mag" + t.string "source_openalex_id" + t.jsonb "issn_l" + t.string "issn" + t.string "mag" t.string "wikidata" t.string "fatcat" - t.index ["source_id"], name: "index_sources_ids_on_source_id" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["source_openalex_id"], name: "index_sources_ids_on_source_openalex_id" end create_table "topics", force: :cascade do |t| + t.string "topic_openalex_id" t.string "display_name" - t.string "subfield_id" - t.string "subfield_display_name" - t.string "field_id" - t.string "field_display_name" - t.string "domain_id" - t.string "domain_display_name" + t.integer "openalex_subfield_id" + t.string "openalex_subfield_display_name" + t.integer "openalex_field_id" + t.string "openalex_field_display_name" + t.integer "openalex_domain_id" + t.string "openalex_domain_display_name" t.string "description" t.string "keywords", default: [], array: true t.string "works_api_url" t.string "wikipedia_id" - t.bigint "works_count" - t.bigint "cited_by_count" - t.string "openalex_id" - t.index ["openalex_id"], name: "index_topics_on_openalex_id" + t.integer "works_count" + t.integer "cited_by_count" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["openalex_domain_id"], name: "index_topics_on_openalex_domain_id" + t.index ["openalex_field_id"], name: "index_topics_on_openalex_field_id" + t.index ["openalex_subfield_id"], name: "index_topics_on_openalex_subfield_id" + t.index ["topic_openalex_id"], name: "index_topics_on_topic_openalex_id" end create_table "works", force: :cascade do |t| + t.string "work_openalex_id" t.string "doi" t.string "title" t.string "display_name" - t.bigint "publication_year" + t.integer "publication_year" t.string "publication_date" - t.string "type" - t.bigint "cited_by_count" + t.string "work_type" + t.integer "cited_by_count" t.boolean "is_retracted" t.boolean "is_paratext" t.string "cited_by_api_url" t.jsonb "abstract_inverted_index" t.string "language" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["doi"], name: "index_works_on_doi" + t.index ["work_openalex_id"], name: "index_works_on_work_openalex_id" end create_table "works_authorships", force: :cascade do |t| - t.bigint "work_id", null: false - t.bigint "author_id", null: false - t.bigint "institution_id", null: false + t.string "work_openalex_id" t.string "author_position" + t.string "author_openalex_id" + t.string "institution_openalex_id" t.string "raw_affiliation_string" t.datetime "created_at", null: false t.datetime "updated_at", null: false - t.index ["author_id"], name: "index_works_authorships_on_author_id" - t.index ["institution_id"], name: "index_works_authorships_on_institution_id" - t.index ["work_id"], name: "index_works_authorships_on_work_id" + t.index ["author_openalex_id"], name: "index_works_authorships_on_author_openalex_id" + t.index ["institution_openalex_id"], name: "index_works_authorships_on_institution_openalex_id" + t.index ["work_openalex_id"], name: "index_works_authorships_on_work_openalex_id" end create_table "works_best_oa_locations", force: :cascade do |t| - t.bigint "work_id", null: false - t.bigint "source_id", null: false + t.string "work_openalex_id" + t.string "source_openalex_id" t.string "landing_page_url" t.string "pdf_url" t.boolean "is_oa" t.string "version" t.string "license" - t.index ["source_id"], name: "index_works_best_oa_locations_on_source_id" - t.index ["work_id"], name: "index_works_best_oa_locations_on_work_id" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["source_openalex_id"], name: "index_works_best_oa_locations_on_source_openalex_id" + t.index ["work_openalex_id"], name: "index_works_best_oa_locations_on_work_openalex_id" end create_table "works_biblios", force: :cascade do |t| - t.bigint "work_id", null: false + t.string "work_openalex_id" t.string "volume" t.string "issue" t.string "first_page" t.string "last_page" t.datetime "created_at", null: false t.datetime "updated_at", null: false - t.index ["work_id"], name: "index_works_biblios_on_work_id" - end - - create_table "works_concepts", force: :cascade do |t| - t.bigint "work_id", null: false - t.bigint "concept_id", null: false - t.float "score" - t.index ["concept_id"], name: "index_works_concepts_on_concept_id" - t.index ["work_id"], name: "index_works_concepts_on_work_id" + t.index ["work_openalex_id"], name: "index_works_biblios_on_work_openalex_id" end create_table "works_ids", force: :cascade do |t| - t.bigint "work_id", null: false - t.string "openalex" + t.string "work_openalex_id" t.string "doi" - t.bigint "mag" + t.string "mag" t.string "pmid" t.string "pmcid" - t.index ["work_id"], name: "index_works_ids_on_work_id" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["doi"], name: "index_works_ids_on_doi" + t.index ["work_openalex_id"], name: "index_works_ids_on_work_openalex_id" end create_table "works_locations", force: :cascade do |t| - t.bigint "work_id", null: false - t.bigint "source_id", null: false + t.string "work_openalex_id" + t.string "source_openalex_id" t.string "landing_page_url" t.string "pdf_url" t.boolean "is_oa" t.string "version" t.string "license" - t.index ["source_id"], name: "index_works_locations_on_source_id" - t.index ["work_id"], name: "index_works_locations_on_work_id" - end - - create_table "works_meshes", force: :cascade do |t| - t.bigint "work_id", null: false - t.string "descriptor_ui" - t.string "descriptor_name" - t.string "qualifier_ui" - t.string "qualifier_name" - t.boolean "is_major_topic" - t.index ["work_id"], name: "index_works_meshes_on_work_id" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["source_openalex_id"], name: "index_works_locations_on_source_openalex_id" + t.index ["work_openalex_id"], name: "index_works_locations_on_work_openalex_id" end create_table "works_open_accesses", force: :cascade do |t| - t.bigint "work_id", null: false + t.string "work_openalex_id" t.boolean "is_oa" t.string "oa_status" t.string "oa_url" t.boolean "any_repository_has_fulltext" - t.index ["work_id"], name: "index_works_open_accesses_on_work_id" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["work_openalex_id"], name: "index_works_open_accesses_on_work_openalex_id" end create_table "works_primary_locations", force: :cascade do |t| - t.bigint "work_id", null: false - t.bigint "source_id", null: false + t.string "work_openalex_id" + t.string "source_openalex_id" t.string "landing_page_url" t.string "pdf_url" t.boolean "is_oa" t.string "version" t.string "license" - t.index ["source_id"], name: "index_works_primary_locations_on_source_id" - t.index ["work_id"], name: "index_works_primary_locations_on_work_id" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["source_openalex_id"], name: "index_works_primary_locations_on_source_openalex_id" + t.index ["work_openalex_id"], name: "index_works_primary_locations_on_work_openalex_id" end create_table "works_referenced_works", force: :cascade do |t| - t.string "work_id" - t.string "referenced_work_id" - end - - create_table "works_related_works", force: :cascade do |t| - t.string "work_id" - t.string "related_work_id" - end - - create_table "works_topics", force: :cascade do |t| - t.bigint "work_id", null: false - t.bigint "topic_id", null: false - t.float "score" - t.index ["topic_id"], name: "index_works_topics_on_topic_id" - t.index ["work_id"], name: "index_works_topics_on_work_id" + t.string "work_openalex_id" + t.string "referenced_work_openalex_id" + t.index ["referenced_work_openalex_id"], name: "index_works_referenced_works_on_referenced_work_openalex_id" + t.index ["work_openalex_id"], name: "index_works_referenced_works_on_work_openalex_id" end - add_foreign_key "authors_counts_by_years", "authors" - add_foreign_key "authors_ids", "authors" - add_foreign_key "concepts_counts_by_years", "concepts" - add_foreign_key "concepts_ids", "concepts" - add_foreign_key "institutions_counts_by_years", "institutions" - add_foreign_key "institutions_geos", "institutions" - add_foreign_key "institutions_ids", "institutions" - add_foreign_key "publishers_counts_by_years", "publishers" - add_foreign_key "publishers_ids", "publishers" - add_foreign_key "sources_counts_by_years", "sources" - add_foreign_key "sources_ids", "sources" - add_foreign_key "works_authorships", "authors" - add_foreign_key "works_authorships", "institutions" - add_foreign_key "works_authorships", "works" - add_foreign_key "works_best_oa_locations", "sources" - add_foreign_key "works_best_oa_locations", "works" - add_foreign_key "works_biblios", "works" - add_foreign_key "works_concepts", "concepts" - add_foreign_key "works_concepts", "works" - add_foreign_key "works_ids", "works" - add_foreign_key "works_locations", "sources" - add_foreign_key "works_locations", "works" - add_foreign_key "works_meshes", "works" - add_foreign_key "works_open_accesses", "works" - add_foreign_key "works_primary_locations", "sources" - add_foreign_key "works_primary_locations", "works" - add_foreign_key "works_topics", "topics" - add_foreign_key "works_topics", "works" end From d07f8ba6eb07fb3f7df1406d17bfe443f4103e8f Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 4 Dec 2024 18:12:23 +0000 Subject: [PATCH 27/44] Update data_import rake tasks --- rails/lib/tasks/load_works.rake | 55 +++++++++---------- rails/lib/tasks/load_works_authorships.rake | 29 +++++----- rails/lib/tasks/load_works_ids.rake | 36 ++++++++++++ rails/lib/tasks/load_works_locations.rake | 2 +- .../tasks/load_works_primary_locations.rake | 37 +++++++++++++ .../tasks/load_works_referenced_works.rake | 13 +++-- 6 files changed, 121 insertions(+), 51 deletions(-) create mode 100644 rails/lib/tasks/load_works_ids.rake create mode 100644 rails/lib/tasks/load_works_primary_locations.rake diff --git a/rails/lib/tasks/load_works.rake b/rails/lib/tasks/load_works.rake index 004c346..545f807 100644 --- a/rails/lib/tasks/load_works.rake +++ b/rails/lib/tasks/load_works.rake @@ -5,39 +5,36 @@ require 'csv' namespace :data_import do desc 'Load Works from gzipped csv to db' task load_works: :environment do - file_paths = Dir['/opt/bookworm/csv-files/works.csv.gz'] + scrub_converter = lambda { |field, _| field.try(:scrub) } - file_paths.each do |file_path| - Zlib::GzipReader.open(file_path) do |gzip| - csv = CSV.new(gzip, encoding: 'utf-8') - works = [] - - csv.each_with_index do |row, index| - unless index == 0 - works << { - work_openalex_id: row[0].split('/').last, - doi: row[1], - title: row[2], - display_name: row[3], - publication_year: row[4], - publication_date: row[5], - work_type: row[6], - cited_by_count: row[7], - is_retracted: row[8], - is_paratext: row[9], - cited_by_api_url: row[10], - abstract_inverted_index: row[11], - language: row[12] - } - end + works = [] + CSV.foreach( + ('/opt/bookworm/csv-files/works.csv'), + headers: true, + col_sep: ',', + converters: [scrub_converter] + ) do |row| + works << { + work_openalex_id: row[0].split('/').last, + doi: row[1], + title: row[2], + display_name: row[3], + publication_year: row[4], + publication_date: row[5], + work_type: row[6], + cited_by_count: row[7], + is_retracted: row[8], + is_paratext: row[9], + cited_by_api_url: row[10], + abstract_inverted_index: row[11], + language: row[12] + } - if works.count >= 5000 - Work.insert_all(works) - works = [] - end - end + if works.count >= 5000 Work.insert_all(works) + works = [] end end + Work.insert_all(works) end end diff --git a/rails/lib/tasks/load_works_authorships.rake b/rails/lib/tasks/load_works_authorships.rake index bcbf486..1677aa7 100644 --- a/rails/lib/tasks/load_works_authorships.rake +++ b/rails/lib/tasks/load_works_authorships.rake @@ -5,27 +5,23 @@ require 'csv' namespace :data_import do desc 'Load WorksAuthorships from gzipped csv to db' task load_works_authorships: :environment do - file_paths = - Dir['/opt/bookworm/csv-files/works_authorships/works_authorships.csv.gz'] + file_paths = Dir['/opt/bookworm/csv-files/works_authorships.csv.gz'] file_paths.each do |file_path| Zlib::GzipReader.open(file_path) do |gzip| works_authorships = [] csv = CSV.new(gzip) - csv # .drop(1) - .each_with_index do |row, index| - work_openalex_id = row[0].present? ? row[0].split('/').last : nil - author_openalex_id = row[2].present? ? row[2].split('/').last : nil - institution_openalex_id = - row[3].present? ? row[3].split('/').last : nil - - works_authorships << { - work_openalex_id: work_openalex_id, - author_position: row[1], - author_openalex_id: author_openalex_id, - institution_openalex_id: institution_openalex_id, - raw_affiliation_string: row[4] - } + csv.each_with_index do |row, index| + unless index == 0 + works_authorships << { + work_openalex_id: row[0].split('/').last, + author_position: row[1], + author_openalex_id: row[2].split('/').last, + institution_openalex_id: + row[3].present? ? row[3].split('/').last : nil, + raw_affiliation_string: row[4] + } + end if works_authorships.count >= 10_000 WorksAuthorship.insert_all(works_authorships) @@ -33,6 +29,7 @@ namespace :data_import do works_authorships = [] end end + WorksAuthorship.insert_all(works_authorships) end end end diff --git a/rails/lib/tasks/load_works_ids.rake b/rails/lib/tasks/load_works_ids.rake new file mode 100644 index 0000000..86d76da --- /dev/null +++ b/rails/lib/tasks/load_works_ids.rake @@ -0,0 +1,36 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksIds from gzipped csv to db' + task load_works_ids: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works_ids.csv.gz'] + + file_paths.each do |file_path| + works_ids = [] + Zlib::GzipReader.open(file_path) do |gzip| + csv = CSV.new(gzip) + csv.each_with_index do |row, index| # drop(1) handles the header row + unless index == 0 + works_ids << { + work_openalex_id: row[0].split('/').last, + doi: row[2], + mag: row[3], + pmid: row[4], + pmcid: row[5] + } + end + + if works_ids.count >= 10_000 + WorksIds.insert_all(works_ids) + + works_ids = [] + end + end + end + + WorksIds.insert_all(works_ids) + end + end +end diff --git a/rails/lib/tasks/load_works_locations.rake b/rails/lib/tasks/load_works_locations.rake index d5215c9..5955eae 100644 --- a/rails/lib/tasks/load_works_locations.rake +++ b/rails/lib/tasks/load_works_locations.rake @@ -24,7 +24,7 @@ namespace :data_import do } end - if works_locations.count >= 10_000 + if works_locations.count >= 100_000 WorksLocation.insert_all(works_locations) works_locations = [] diff --git a/rails/lib/tasks/load_works_primary_locations.rake b/rails/lib/tasks/load_works_primary_locations.rake new file mode 100644 index 0000000..a40741e --- /dev/null +++ b/rails/lib/tasks/load_works_primary_locations.rake @@ -0,0 +1,37 @@ +require 'rake' +require 'zlib' +require 'csv' + +namespace :data_import do + desc 'Load WorksPrimaryLocations from gzipped csv to db' + task load_works_primary_locations: :environment do + file_paths = Dir['/opt/bookworm/csv-files/works_primary_locations.csv.gz'] + + file_paths.each do |file_path| + Zlib::GzipReader.open(file_path) do |gzip| + works_primary_locations = [] + csv = CSV.new(gzip) + csv.each_with_index do |row, index| + unless index == 0 + works_primary_locations << { + work_openalex_id: row[0].split('/').last, + source_openalex_id: row[1].split('/').last, + landing_page_url: row[2], + pdf_url: row[3], + is_oa: row[4], + version: row[5], + license: row[6] + } + end + + if works_primary_locations.count >= 100_000 + WorksPrimaryLocation.insert_all(works_primary_locations) + + works_primary_locations = [] + end + end + WorksPrimaryLocation.insert_all(works_primary_locations) + end + end + end +end diff --git a/rails/lib/tasks/load_works_referenced_works.rake b/rails/lib/tasks/load_works_referenced_works.rake index dda5b95..3dace16 100644 --- a/rails/lib/tasks/load_works_referenced_works.rake +++ b/rails/lib/tasks/load_works_referenced_works.rake @@ -12,17 +12,20 @@ namespace :data_import do works_referenced_works = [] csv = CSV.new(gzip) csv.each_with_index do |row, index| - works_referenced_works << { - work_id: row[0].split('/').last, - referenced_work_id: row[1].split('/').last - } + if index >= 1_407_400_000 + works_referenced_works << { + work_openalex_id: row[0].split('/').last, + referenced_work_openalex_id: row[1].split('/').last + } + end - if works_referenced_works.count >= 10_000 + if works_referenced_works.count >= 100_000 WorksReferencedWorks.insert_all(works_referenced_works) works_referenced_works = [] end end + WorksReferencedWorks.insert_all(works_referenced_works) end end end From 669edc9febf60e3f5bf0b74135472694b240d9ea Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 4 Dec 2024 18:13:04 +0000 Subject: [PATCH 28/44] Update models for full snapshot --- rails/app/models/author.rb | 2 +- rails/app/models/institution.rb | 6 +++-- .../institutions_associated_institutions.rb | 7 ++---- rails/app/models/source.rb | 4 ++++ rails/app/models/sources_counts_by_year.rb | 5 ++++ rails/app/models/sources_ids.rb | 5 ++++ rails/app/models/work.rb | 15 ++++++------ rails/app/models/works_authorship.rb | 14 +++++++---- rails/app/models/works_best_oa_location.rb | 5 ++++ rails/app/models/works_location.rb | 5 ++++ rails/app/models/works_primary_location.rb | 5 ++++ rails/app/poros/openalex_author.rb | 24 +++++++++---------- rails/app/poros/openalex_work.rb | 18 +++++++------- 13 files changed, 74 insertions(+), 41 deletions(-) create mode 100644 rails/app/models/source.rb create mode 100644 rails/app/models/sources_counts_by_year.rb create mode 100644 rails/app/models/sources_ids.rb create mode 100644 rails/app/models/works_best_oa_location.rb create mode 100644 rails/app/models/works_location.rb create mode 100644 rails/app/models/works_primary_location.rb diff --git a/rails/app/models/author.rb b/rails/app/models/author.rb index 894d19d..b9af400 100644 --- a/rails/app/models/author.rb +++ b/rails/app/models/author.rb @@ -4,7 +4,7 @@ class Author < ApplicationRecord has_one :authors_ids has_many :authors_counts_by_year has_many :works_authorships, - primary_key: :openalex_id, + primary_key: :author_openalex_id, foreign_key: :author_openalex_id has_many :institutions, through: :works_authorships end diff --git a/rails/app/models/institution.rb b/rails/app/models/institution.rb index bbbc2e5..20bf1f5 100644 --- a/rails/app/models/institution.rb +++ b/rails/app/models/institution.rb @@ -6,7 +6,7 @@ class Institution < ApplicationRecord has_one :institutions_ids has_many :institutions_associated_institutions, - foreign_key: :associated_institution_id, + foreign_key: :associated_institution_openalex_id, class_name: 'InstitutionsAssociatedInstitutions' has_many :associated_institutions, @@ -14,6 +14,8 @@ class Institution < ApplicationRecord source: :institution has_many :works_authorships, - primary_key: :openalex_id, + primary_key: :institution_openalex_id, foreign_key: :institution_openalex_id + + has_many :authors, through: :works_authorships end diff --git a/rails/app/models/institutions_associated_institutions.rb b/rails/app/models/institutions_associated_institutions.rb index 3bcd2d2..b26867b 100644 --- a/rails/app/models/institutions_associated_institutions.rb +++ b/rails/app/models/institutions_associated_institutions.rb @@ -1,13 +1,10 @@ # frozen_string_literal: true class InstitutionsAssociatedInstitutions < ApplicationRecord - validates :institution_id, presence: true - validates :associated_institution_id, presence: true - belongs_to :institution, - foreign_key: 'institution_id', + foreign_key: 'institution_openalex_id', class_name: 'Institution' belongs_to :associated_institution, - foreign_key: 'associated_institution_id', + foreign_key: 'associated_institution_openalex_id', class_name: 'Institution' end diff --git a/rails/app/models/source.rb b/rails/app/models/source.rb new file mode 100644 index 0000000..7af98cd --- /dev/null +++ b/rails/app/models/source.rb @@ -0,0 +1,4 @@ +# frozen_string_literal: true + +class Source < ApplicationRecord +end diff --git a/rails/app/models/sources_counts_by_year.rb b/rails/app/models/sources_counts_by_year.rb new file mode 100644 index 0000000..cc645d0 --- /dev/null +++ b/rails/app/models/sources_counts_by_year.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class SourcesCountsByYear < ApplicationRecord + belongs_to :source +end diff --git a/rails/app/models/sources_ids.rb b/rails/app/models/sources_ids.rb new file mode 100644 index 0000000..37faef7 --- /dev/null +++ b/rails/app/models/sources_ids.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class SourcesIds < ApplicationRecord + belongs_to :source +end diff --git a/rails/app/models/work.rb b/rails/app/models/work.rb index 644abc0..a929cfa 100644 --- a/rails/app/models/work.rb +++ b/rails/app/models/work.rb @@ -2,8 +2,9 @@ class Work < ApplicationRecord has_many :works_authorships, - primary_key: :openalex_id, + primary_key: :work_openalex_id, foreign_key: :work_openalex_id + has_many :authors, through: :works_authorships has_many :institutions, through: :works_authorships @@ -20,15 +21,15 @@ class Work < ApplicationRecord has_many :topics, through: :works_topics # reference_connections "names" the Connection join table for accessing through the reference association - has_many :works_related_works, - foreign_key: :related_work_id, - class_name: 'WorksRelatedWorks' - # source: :reference matches with the belong_to :reference identification in the Connection model - has_many :related_works, through: :works_related_works, source: :related_work + # has_many :works_related_works, + # foreign_key: :related_work_openalex_id, + # class_name: 'WorksRelatedWorks' + # # source: :reference matches with the belong_to :reference identification in the Connection model + # has_many :related_works, through: :works_related_works, source: :related_work # citation_connections "names" the Connection join table for accessing through the citation association has_many :works_referenced_works, - foreign_key: :referenced_work_id, + foreign_key: :referenced_work_openalex_id, class_name: 'WorksReferencedWorks' # source: :citation matches with the belong_to :citation identification in the Connection model diff --git a/rails/app/models/works_authorship.rb b/rails/app/models/works_authorship.rb index b0352d1..783a99f 100644 --- a/rails/app/models/works_authorship.rb +++ b/rails/app/models/works_authorship.rb @@ -1,7 +1,11 @@ class WorksAuthorship < ApplicationRecord - belongs_to :author, primary_key: :author_openalex_id - - belongs_to :work, primary_key: :work_openalex_id - - belongs_to :institution, primary_key: :institution_openalex_id + belongs_to :author, + primary_key: :author_openalex_id, + foreign_key: :author_openalex_id + belongs_to :work, + primary_key: :work_openalex_id, + foreign_key: :work_openalex_id + belongs_to :institution, + primary_key: :institution_openalex_id, + foreign_key: :institution_openalex_id end diff --git a/rails/app/models/works_best_oa_location.rb b/rails/app/models/works_best_oa_location.rb new file mode 100644 index 0000000..0e50e45 --- /dev/null +++ b/rails/app/models/works_best_oa_location.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class WorksBestOaLocation < ApplicationRecord + belongs_to :work +end diff --git a/rails/app/models/works_location.rb b/rails/app/models/works_location.rb new file mode 100644 index 0000000..ea4bdc5 --- /dev/null +++ b/rails/app/models/works_location.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class WorksLocation < ApplicationRecord + belongs_to :work +end diff --git a/rails/app/models/works_primary_location.rb b/rails/app/models/works_primary_location.rb new file mode 100644 index 0000000..c822d3c --- /dev/null +++ b/rails/app/models/works_primary_location.rb @@ -0,0 +1,5 @@ +# frozen_string_literal: true + +class WorksPrimaryLocation < ApplicationRecord + belongs_to :work +end diff --git a/rails/app/poros/openalex_author.rb b/rails/app/poros/openalex_author.rb index 79fe071..54a4db2 100644 --- a/rails/app/poros/openalex_author.rb +++ b/rails/app/poros/openalex_author.rb @@ -12,20 +12,20 @@ class OpenalexAuthor def initialize(data) if data[:id] - @openalex_id = data[:id].split("https://openalex.org/").last + @openalex_id = data[:id].split('https://openalex.org/').last else - @openalex_id = "Not found" + @openalex_id = 'Not found' end if data[:orcid] - @orcid = data[:orcid].split("https://orcid.org/").last + @orcid = data[:orcid].split('https://orcid.org/').last else - @orcid = "Not found" + @orcid = 'Not found' end - @display_name = data[:display_name] || "Not found" - @works_count = data[:works_count] || "Not found" - @cited_by_count = data[:cited_by_count] || "Not found" + @display_name = data[:display_name] || 'Not found' + @works_count = data[:works_count] || 'Not found' + @cited_by_count = data[:cited_by_count] || 'Not found' @h_index = data[:summary_stats][:h_index] @i10_index = data[:summary_stats][:i10_index] @@ -39,19 +39,19 @@ def initialize(data) if institution[:display_name].present? institution[:display_name] else - "Not found" + 'Not found' end ), openalex_id: ( if institution[:id].present? - institution[:id].split("/").last + institution[:id].split('/').last else - "Not found" + 'Not found' end ), - type: institution[:type].present? ? institution[:type] : "Not found", - years: data[:years].present? ? data[:years] : "Not found" + type: institution[:type].present? ? institution[:type] : 'Not found', + years: data[:years].present? ? data[:years] : 'Not found' } end end diff --git a/rails/app/poros/openalex_work.rb b/rails/app/poros/openalex_work.rb index 02b01c4..f1dbc5e 100644 --- a/rails/app/poros/openalex_work.rb +++ b/rails/app/poros/openalex_work.rb @@ -22,12 +22,12 @@ class OpenalexWork :abstract def initialize(data) - @openalex_id = data[:ids][:openalex].split("/").last || "Not found" + @openalex_id = data[:ids][:openalex].split('/').last || 'Not found' if data[:doi] - @doi = data[:doi].split("/").last + @doi = data[:doi].split('/').last else - @doi = "Not found" + @doi = 'Not found' end if data[:abstract_inverted_index] @@ -39,7 +39,7 @@ def initialize(data) end end - @abstract = uninverted_arr.join(" ") + @abstract = uninverted_arr.join(' ') end @title = data[:title] || [] @@ -58,23 +58,23 @@ def initialize(data) if author_data[:author][:display_name].present? author_data[:author][:display_name] else - "Not found" + 'Not found' end ), orcid: ( if author_data[:author][:orcid].present? - author_data[:author][:orcid].split("/").last + author_data[:author][:orcid].split('/').last else - "Not found" + 'Not found' end ), openalex_id: ( if author_data[:author][:id].present? - author_data[:author][:id].split("/").last + author_data[:author][:id].split('/').last else - "Not found" + 'Not found' end ) } From 33b98f50061d6c5f201d216aa3a08ae44b552f61 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 5 Dec 2024 15:42:34 +0000 Subject: [PATCH 29/44] Fix many-to-many self referrential join for works/citations/references --- rails/app/models/work.rb | 45 +++++++++++++--------- rails/app/models/works_referenced_works.rb | 10 +++-- 2 files changed, 33 insertions(+), 22 deletions(-) diff --git a/rails/app/models/work.rb b/rails/app/models/work.rb index a929cfa..867625b 100644 --- a/rails/app/models/work.rb +++ b/rails/app/models/work.rb @@ -8,32 +8,41 @@ class Work < ApplicationRecord has_many :authors, through: :works_authorships has_many :institutions, through: :works_authorships - # these might need to be has_many - has_one :works_biblio - has_one :works_ids - has_one :works_open_access - has_one :works_mesh + has_one :works_biblio, + primary_key: :work_openalex_id, + foreign_key: :work_openalex_id - has_many :works_concepts - has_many :concepts, through: :works_concepts + has_one :works_ids, + primary_key: :work_openalex_id, + foreign_key: :work_openalex_id + + has_one :works_open_access, + primary_key: :work_openalex_id, + foreign_key: :work_openalex_id has_many :works_topics has_many :topics, through: :works_topics - # reference_connections "names" the Connection join table for accessing through the reference association - # has_many :works_related_works, - # foreign_key: :related_work_openalex_id, - # class_name: 'WorksRelatedWorks' - # # source: :reference matches with the belong_to :reference identification in the Connection model - # has_many :related_works, through: :works_related_works, source: :related_work + # Below here is magic join table nonsense that will break if you touch it + # Connects a 'work' to works that it references ('referenced_works') + # and to works the reference the original work ('referencing_works') + # through the WorksReferencedWorks table - # citation_connections "names" the Connection join table for accessing through the citation association - has_many :works_referenced_works, - foreign_key: :referenced_work_openalex_id, + has_many :referenced_works_connections, + primary_key: :work_openalex_id, + foreign_key: :work_openalex_id, class_name: 'WorksReferencedWorks' - # source: :citation matches with the belong_to :citation identification in the Connection model has_many :referenced_works, - through: :works_referenced_works, + through: :referenced_works_connections, source: :referenced_work + + has_many :referencing_works_connections, + primary_key: :work_openalex_id, + foreign_key: :referenced_work_openalex_id, + class_name: 'WorksReferencedWorks' + + has_many :referencing_works, + through: :referencing_works_connections, + source: :referencing_work end diff --git a/rails/app/models/works_referenced_works.rb b/rails/app/models/works_referenced_works.rb index 977d41a..ce8b93f 100644 --- a/rails/app/models/works_referenced_works.rb +++ b/rails/app/models/works_referenced_works.rb @@ -1,11 +1,13 @@ # frozen_string_literal: true class WorksReferencedWorks < ApplicationRecord - validates :work_id, presence: true - validates :referenced_work_id, presence: true + belongs_to :referencing_work, + primary_key: :work_openalex_id, + foreign_key: :work_openalex_id, + class_name: 'Work' - belongs_to :work, foreign_key: 'work_id', class_name: 'Work' belongs_to :referenced_work, - foreign_key: 'referenced_work_id', + primary_key: :work_openalex_id, + foreign_key: :referenced_work_openalex_id, class_name: 'Work' end From d02117068951401e61aea86a7303bc4b13d153dc Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 5 Dec 2024 16:39:34 +0000 Subject: [PATCH 30/44] update author model with author_openalex_id --- rails/app/models/author.rb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/rails/app/models/author.rb b/rails/app/models/author.rb index b9af400..dc90a79 100644 --- a/rails/app/models/author.rb +++ b/rails/app/models/author.rb @@ -1,10 +1,15 @@ # frozen_string_literal: true class Author < ApplicationRecord - has_one :authors_ids - has_many :authors_counts_by_year + has_one :authors_ids, + primary_key: :author_openalex_id, + foreign_key: :author_openalex_id + has_many :authors_counts_by_year, + primary_key: :author_openalex_id, + foreign_key: :author_openalex_id has_many :works_authorships, primary_key: :author_openalex_id, foreign_key: :author_openalex_id has_many :institutions, through: :works_authorships + has_many :works, through: :works_authorships end From 4dbbd5ac0d0a36beb7f5b68f0c918c15e31342c7 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 5 Dec 2024 18:07:50 +0000 Subject: [PATCH 31/44] Remove _api from schema name --- rails/app/controllers/graphql_controller.rb | 2 +- .../{book_worm_api_schema.rb => book_worm_schema.rb} | 2 +- rails/spec/graphql/mutations/add_author_works_spec.rb | 4 ++-- rails/spec/graphql/mutations/add_citations_spec.rb | 4 ++-- rails/spec/graphql/mutations/add_references_spec.rb | 6 +++--- rails/spec/graphql/mutations/create_author_node_spec.rb | 4 ++-- rails/spec/graphql/mutations/create_investigation_spec.rb | 2 +- rails/spec/graphql/mutations/create_note_node_spec.rb | 2 +- rails/spec/graphql/mutations/create_work_node_spec.rb | 2 +- rails/spec/graphql/mutations/delete_note_node_spec.rb | 4 ++-- rails/spec/graphql/mutations/register_user_spec.rb | 8 ++++---- rails/spec/graphql/mutations/sign_in_spec.rb | 6 +++--- rails/spec/graphql/mutations/update_work_node_spec.rb | 4 ++-- 13 files changed, 25 insertions(+), 25 deletions(-) rename rails/app/graphql/{book_worm_api_schema.rb => book_worm_schema.rb} (96%) diff --git a/rails/app/controllers/graphql_controller.rb b/rails/app/controllers/graphql_controller.rb index 7b5a8a2..e3bd35e 100644 --- a/rails/app/controllers/graphql_controller.rb +++ b/rails/app/controllers/graphql_controller.rb @@ -16,7 +16,7 @@ def execute } result = - BookWormApiSchema.execute(query, variables:, context:, operation_name:) + BookWormSchema.execute(query, variables:, context:, operation_name:) render json: result rescue StandardError => e diff --git a/rails/app/graphql/book_worm_api_schema.rb b/rails/app/graphql/book_worm_schema.rb similarity index 96% rename from rails/app/graphql/book_worm_api_schema.rb rename to rails/app/graphql/book_worm_schema.rb index 63f7751..3d461c0 100644 --- a/rails/app/graphql/book_worm_api_schema.rb +++ b/rails/app/graphql/book_worm_schema.rb @@ -1,6 +1,6 @@ # frozen_string_literal: true -class BookWormApiSchema < GraphQL::Schema +class BookWormSchema < GraphQL::Schema mutation(Types::MutationType) query(Types::QueryType) diff --git a/rails/spec/graphql/mutations/add_author_works_spec.rb b/rails/spec/graphql/mutations/add_author_works_spec.rb index 79f953c..a7d9ff7 100644 --- a/rails/spec/graphql/mutations/add_author_works_spec.rb +++ b/rails/spec/graphql/mutations/add_author_works_spec.rb @@ -47,7 +47,7 @@ def create_author_node_mutation # creating an author node author_node_response = - BookWormApiSchema.execute( + BookWormSchema.execute( create_author_node_mutation, variables: { openalexId: 'A5023888391', @@ -59,7 +59,7 @@ def create_author_node_mutation ).to_h response = - BookWormApiSchema.execute( + BookWormSchema.execute( add_author_works_mutation, variables: { openalexId: 'A5023888391', diff --git a/rails/spec/graphql/mutations/add_citations_spec.rb b/rails/spec/graphql/mutations/add_citations_spec.rb index 9b5672c..9085b7e 100644 --- a/rails/spec/graphql/mutations/add_citations_spec.rb +++ b/rails/spec/graphql/mutations/add_citations_spec.rb @@ -45,7 +45,7 @@ def create_work_node_mutation # create initial work node work_node_response = - BookWormApiSchema.execute( + BookWormSchema.execute( create_work_node_mutation, variables: { investigationId: investigation_1.id.to_s, @@ -60,7 +60,7 @@ def create_work_node_mutation work_node_response['data']['createWorkNode']['work']['openalexId'] response = - BookWormApiSchema.execute( + BookWormSchema.execute( add_citations_mutation, variables: { openalexId: work_node_openalex_id, diff --git a/rails/spec/graphql/mutations/add_references_spec.rb b/rails/spec/graphql/mutations/add_references_spec.rb index 2350ce6..fd8be59 100644 --- a/rails/spec/graphql/mutations/add_references_spec.rb +++ b/rails/spec/graphql/mutations/add_references_spec.rb @@ -81,7 +81,7 @@ def investigation_query # create initial work node work_node_response = - BookWormApiSchema.execute( + BookWormSchema.execute( create_work_node_mutation, variables: { investigationId: investigation_1.id.to_s, @@ -96,7 +96,7 @@ def investigation_query work_node_response['data']['createWorkNode']['work']['openalexId'] response = - BookWormApiSchema.execute( + BookWormSchema.execute( add_references_mutation, variables: { openalexId: work_node_openalex_id, @@ -108,7 +108,7 @@ def investigation_query ).to_h investigation_response = - BookWormApiSchema.execute( + BookWormSchema.execute( investigation_query, variables: { id: investigation_1.id diff --git a/rails/spec/graphql/mutations/create_author_node_spec.rb b/rails/spec/graphql/mutations/create_author_node_spec.rb index a10116b..2db696b 100644 --- a/rails/spec/graphql/mutations/create_author_node_spec.rb +++ b/rails/spec/graphql/mutations/create_author_node_spec.rb @@ -43,7 +43,7 @@ def create_author_node_mutation investigation_1 = FactoryBot.create(:investigation, user_id: user_1.id) work_node_response = - BookWormApiSchema.execute( + BookWormSchema.execute( create_work_node_mutation, variables: { investigationId: investigation_1.id.to_s, @@ -55,7 +55,7 @@ def create_author_node_mutation ).to_h response = - BookWormApiSchema.execute( + BookWormSchema.execute( create_author_node_mutation, variables: { authorOpenalexId: 'A5023888391', diff --git a/rails/spec/graphql/mutations/create_investigation_spec.rb b/rails/spec/graphql/mutations/create_investigation_spec.rb index 62b7a16..3d53275 100644 --- a/rails/spec/graphql/mutations/create_investigation_spec.rb +++ b/rails/spec/graphql/mutations/create_investigation_spec.rb @@ -19,7 +19,7 @@ def create_investigation_mutation user_1 = FactoryBot.create(:user) response = - BookWormApiSchema.execute( + BookWormSchema.execute( create_investigation_mutation, variables: { name: 'My new investigation' diff --git a/rails/spec/graphql/mutations/create_note_node_spec.rb b/rails/spec/graphql/mutations/create_note_node_spec.rb index 25b0f38..e05b3e5 100644 --- a/rails/spec/graphql/mutations/create_note_node_spec.rb +++ b/rails/spec/graphql/mutations/create_note_node_spec.rb @@ -23,7 +23,7 @@ def create_note_node_mutation it 'can create a new note node' do response = - BookWormApiSchema.execute( + BookWormSchema.execute( create_note_node_mutation, variables: { investigationId: @investigation_1.id.to_s, diff --git a/rails/spec/graphql/mutations/create_work_node_spec.rb b/rails/spec/graphql/mutations/create_work_node_spec.rb index 25d57de..c528a58 100644 --- a/rails/spec/graphql/mutations/create_work_node_spec.rb +++ b/rails/spec/graphql/mutations/create_work_node_spec.rb @@ -31,7 +31,7 @@ def create_work_node_mutation describe '.resolve' do it 'can create a new work node', :vcr do response = - BookWormApiSchema.execute( + BookWormSchema.execute( create_work_node_mutation, variables: { investigationId: @investigation_1.id.to_s, diff --git a/rails/spec/graphql/mutations/delete_note_node_spec.rb b/rails/spec/graphql/mutations/delete_note_node_spec.rb index 6d7b3a6..0892d02 100644 --- a/rails/spec/graphql/mutations/delete_note_node_spec.rb +++ b/rails/spec/graphql/mutations/delete_note_node_spec.rb @@ -33,7 +33,7 @@ def delete_note_node_mutation investigation_1 = FactoryBot.create(:investigation, user_id: user_1.id) note_node_response = - BookWormApiSchema.execute( + BookWormSchema.execute( create_note_node_mutation, variables: { investigationId: investigation_1.id.to_s, @@ -49,7 +49,7 @@ def delete_note_node_mutation expect(NoteNode.count).to eq(1) response = - BookWormApiSchema.execute( + BookWormSchema.execute( delete_note_node_mutation, variables: { investigationId: investigation_1.id.to_s, diff --git a/rails/spec/graphql/mutations/register_user_spec.rb b/rails/spec/graphql/mutations/register_user_spec.rb index ce738cc..ed23f69 100644 --- a/rails/spec/graphql/mutations/register_user_spec.rb +++ b/rails/spec/graphql/mutations/register_user_spec.rb @@ -17,7 +17,7 @@ def register_user_mutation describe '.resolve' do it 'can create a new user, given a valid email and password' do response = - BookWormApiSchema.execute( + BookWormSchema.execute( register_user_mutation, variables: { email: 'sandwichpkitty@email.com', @@ -38,7 +38,7 @@ def register_user_mutation User.create(email: 'sandwichpkitty@email.com', password: 'pjassword') response = - BookWormApiSchema.execute( + BookWormSchema.execute( register_user_mutation, variables: { email: 'sandwichpkitty@email.com', @@ -56,7 +56,7 @@ def register_user_mutation it 'does not register a new user if email is invalid' do response = - BookWormApiSchema.execute( + BookWormSchema.execute( register_user_mutation, variables: { email: 'sandwichpkitty', @@ -74,7 +74,7 @@ def register_user_mutation it 'does not register a new user if password is too short' do response = - BookWormApiSchema.execute( + BookWormSchema.execute( register_user_mutation, variables: { email: 'sandwichpkitty@email.com', diff --git a/rails/spec/graphql/mutations/sign_in_spec.rb b/rails/spec/graphql/mutations/sign_in_spec.rb index d28e4c8..fac6074 100644 --- a/rails/spec/graphql/mutations/sign_in_spec.rb +++ b/rails/spec/graphql/mutations/sign_in_spec.rb @@ -21,7 +21,7 @@ def sign_in_mutation describe '.resolve' do it 'signs in a user with correct email and password' do response = - BookWormApiSchema.execute( + BookWormSchema.execute( sign_in_mutation, variables: { email: @user_1.email, @@ -41,7 +41,7 @@ def sign_in_mutation it 'does not sign in a user that does not exist' do response = - BookWormApiSchema.execute( + BookWormSchema.execute( sign_in_mutation, variables: { email: 'imnotarealuser@email.com', @@ -60,7 +60,7 @@ def sign_in_mutation it 'does not sign in an existing user with an incorrect password' do response = - BookWormApiSchema.execute( + BookWormSchema.execute( sign_in_mutation, variables: { email: @user_1.email, diff --git a/rails/spec/graphql/mutations/update_work_node_spec.rb b/rails/spec/graphql/mutations/update_work_node_spec.rb index 9f8fbbe..87990cf 100644 --- a/rails/spec/graphql/mutations/update_work_node_spec.rb +++ b/rails/spec/graphql/mutations/update_work_node_spec.rb @@ -38,7 +38,7 @@ def update_work_node_mutation #create work node initial_work_node = - BookWormApiSchema.execute( + BookWormSchema.execute( create_work_node_mutation, variables: { investigationId: investigation_1.id.to_s, @@ -56,7 +56,7 @@ def update_work_node_mutation initial_work_node['data']['createWorkNode']['yCoordinate'] response = - BookWormApiSchema.execute( + BookWormSchema.execute( update_work_node_mutation, variables: { workNodeId: initial_work_node_id.to_s, From 915a2e9efd164cdfdff688d5fd77527bb23ca9dd Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Fri, 6 Dec 2024 01:00:55 +0000 Subject: [PATCH 32/44] Start of reworking gql types --- rails/app/graphql/types/author_type.rb | 2 +- rails/app/graphql/types/institution_type.rb | 2 +- rails/app/graphql/types/query_type.rb | 30 +++++---------------- 3 files changed, 9 insertions(+), 25 deletions(-) diff --git a/rails/app/graphql/types/author_type.rb b/rails/app/graphql/types/author_type.rb index a285442..956556c 100644 --- a/rails/app/graphql/types/author_type.rb +++ b/rails/app/graphql/types/author_type.rb @@ -3,7 +3,7 @@ module Types class AuthorType < Types::BaseObject field :id, ID, null: false - field :openalex_id, String + field :author_openalex_id, String field :orcid, String field :display_name, String field :display_name_alternatives, String diff --git a/rails/app/graphql/types/institution_type.rb b/rails/app/graphql/types/institution_type.rb index bc546ce..78ad271 100644 --- a/rails/app/graphql/types/institution_type.rb +++ b/rails/app/graphql/types/institution_type.rb @@ -3,7 +3,7 @@ module Types class InstitutionType < Types::BaseObject field :id, ID, null: false - field :openalex_id, String + field :institution_openalex_id, String field :ror, String field :display_name, String field :country_code, String diff --git a/rails/app/graphql/types/query_type.rb b/rails/app/graphql/types/query_type.rb index f26ba72..91799b3 100644 --- a/rails/app/graphql/types/query_type.rb +++ b/rails/app/graphql/types/query_type.rb @@ -27,40 +27,24 @@ def nodes(ids:) # Add root-level fields here. # They will be entry points for queries on your schema. - field :institutions, - [Types::InstitutionType], - null: true, - description: 'Fetch all institutions' - def institutions - Institution.all - end - field :institution, Types::InstitutionType, null: true, - description: 'Fetches an institution by ID' do - argument :id, ID, required: true + description: 'Fetches an institution by institution_openalex_id' do + argument :institution_openalex_id, String, required: true end - def institution(id:) - Institution.find(id) - end - - field :authors, - [Types::AuthorType], - null: true, - description: 'Fetch all authors' - def authors - Author.all + def institution(institution_openalex_id:) + Institution.find_by(institution_openalex_id: institution_openalex_id) end field :author, Types::AuthorType, null: true, description: 'Fetch author by ID' do - argument :id, ID, required: true + argument :author_openalex_id, String, required: true end - def author(id:) - Author.find(id) + def author(author_openalex_id:) + Author.find_by(author_openalex_id: author_openalex_id) end end end From 45f6a8b93e6f586e21a7240a5f076d86bb0f03d5 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Fri, 6 Dec 2024 01:26:41 +0000 Subject: [PATCH 33/44] update worktype --- rails/app/graphql/types/query_type.rb | 7 ++++ rails/app/graphql/types/work_type.rb | 52 +++------------------------ 2 files changed, 12 insertions(+), 47 deletions(-) diff --git a/rails/app/graphql/types/query_type.rb b/rails/app/graphql/types/query_type.rb index 91799b3..40766fa 100644 --- a/rails/app/graphql/types/query_type.rb +++ b/rails/app/graphql/types/query_type.rb @@ -46,5 +46,12 @@ def institution(institution_openalex_id:) def author(author_openalex_id:) Author.find_by(author_openalex_id: author_openalex_id) end + + field :work, Types::WorkType, null: true, description: 'Fetch work by ID' do + argument :work_openalex_id, String, required: true + end + def work(work_openalex_id:) + Work.find_by(work_openalex_id: work_openalex_id) + end end end diff --git a/rails/app/graphql/types/work_type.rb b/rails/app/graphql/types/work_type.rb index a281b5d..8f84cc9 100644 --- a/rails/app/graphql/types/work_type.rb +++ b/rails/app/graphql/types/work_type.rb @@ -3,62 +3,20 @@ module Types class WorkType < Types::BaseObject field :id, ID, null: false + field :work_openalex_id, String field :doi, String field :title, String field :display_name, String field :publication_year, Integer + field :publication_date, String field :work_type, String field :cited_by_count, Integer field :is_retracted, Boolean field :is_paratext, Boolean field :cited_by_api_url, String - field :abstract_inverted_index, String + field :abstract_inverted_index, GraphQL::Types::JSON field :language, String - - field :topics, [Type::TopicType] - field :authors, [Type::AuthorType] - field :institutions, [Type::InstitutionType] - field :works_biblio, [Type::WorksBiblioType] - field :works_ids, Type::WorksIdsType - field :works_open_access, Type::WorksOpenAccessType - field :works_mesh, Type::WorksMeshType - field :related_works, [Type::WorksType] - field :referenced_works, [Type::WorksType] - - def topics - object.topics - end - - def authors - object.authors - end - - def institutions - object.institutions - end - - def works_biblio - object.works_biblio - end - - def works_ids - object.works_ids - end - - def works_open_access - object.works_open_access - end - - def works_mesh - object.works_mesh - end - - def related_works - object.related_works - end - - def referenced_works - object.referenced_work - end + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end From 7eb78babc7a714e14b5d4382010b9663c26ebe9a Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Fri, 6 Dec 2024 02:39:54 +0000 Subject: [PATCH 34/44] new generated types, need to pare back --- rails/app/graphql/types/author_type.rb | 8 ++---- .../types/authors_counts_by_year_type.rb | 9 +++---- rails/app/graphql/types/authors_ids_type.rb | 13 +++------ rails/app/graphql/types/institution_type.rb | 27 +++++-------------- ...stitutions_associated_institutions_type.rb | 12 +++++++++ .../types/institutions_counts_by_year_type.rb | 9 +++---- .../graphql/types/institutions_geo_type.rb | 11 +++----- .../graphql/types/institutions_ids_type.rb | 13 +++------ rails/app/graphql/types/publisher_type.rb | 18 ++++--------- .../types/publishers_counts_by_year_type.rb | 9 +++---- .../app/graphql/types/publishers_ids_type.rb | 14 +++------- rails/app/graphql/types/publishers_type.rb | 6 +++++ rails/app/graphql/types/source_type.rb | 20 ++++++++++++++ .../types/sources_counts_by_year_type.rb | 14 ++++++++++ rails/app/graphql/types/sources_ids_type.rb | 15 +++++++++++ rails/app/graphql/types/topic_type.rb | 21 +++++++-------- rails/app/graphql/types/work_type.rb | 21 +++++++++++++++ .../graphql/types/works_authorship_type.rb | 14 ++++++++++ .../types/works_best_oa_location_type.rb | 16 +++++++++++ rails/app/graphql/types/works_biblio_type.rb | 14 ++++++++++ rails/app/graphql/types/works_ids_type.rb | 14 ++++++++++ .../app/graphql/types/works_location_type.rb | 16 +++++++++++ .../graphql/types/works_open_access_type.rb | 14 ++++++++++ .../types/works_primary_location_type.rb | 16 +++++++++++ 24 files changed, 239 insertions(+), 105 deletions(-) create mode 100644 rails/app/graphql/types/institutions_associated_institutions_type.rb create mode 100644 rails/app/graphql/types/publishers_type.rb create mode 100644 rails/app/graphql/types/source_type.rb create mode 100644 rails/app/graphql/types/sources_counts_by_year_type.rb create mode 100644 rails/app/graphql/types/sources_ids_type.rb create mode 100644 rails/app/graphql/types/works_authorship_type.rb create mode 100644 rails/app/graphql/types/works_best_oa_location_type.rb create mode 100644 rails/app/graphql/types/works_biblio_type.rb create mode 100644 rails/app/graphql/types/works_ids_type.rb create mode 100644 rails/app/graphql/types/works_location_type.rb create mode 100644 rails/app/graphql/types/works_open_access_type.rb create mode 100644 rails/app/graphql/types/works_primary_location_type.rb diff --git a/rails/app/graphql/types/author_type.rb b/rails/app/graphql/types/author_type.rb index 956556c..7dde100 100644 --- a/rails/app/graphql/types/author_type.rb +++ b/rails/app/graphql/types/author_type.rb @@ -6,21 +6,17 @@ class AuthorType < Types::BaseObject field :author_openalex_id, String field :orcid, String field :display_name, String - field :display_name_alternatives, String + field :display_name_alternatives, GraphQL::Types::JSON field :works_count, Integer field :cited_by_count, Integer field :last_known_institution, String field :works_api_url, String field :authors_ids, Types::AuthorsIdsType - field :authors_counts_by_year, [Types::AuthorsCountsByYearType] + field :works, [Types::WorkType] def authors_ids object.authors_ids end - - def authors_counts_by_year - object.authors_counts_by_year - end end end diff --git a/rails/app/graphql/types/authors_counts_by_year_type.rb b/rails/app/graphql/types/authors_counts_by_year_type.rb index 273698f..a81de89 100644 --- a/rails/app/graphql/types/authors_counts_by_year_type.rb +++ b/rails/app/graphql/types/authors_counts_by_year_type.rb @@ -3,15 +3,12 @@ module Types class AuthorsCountsByYearType < Types::BaseObject field :id, ID, null: false + field :author_openalex_id, String field :year, Integer field :works_count, Integer field :cited_by_count, Integer field :oa_works_count, Integer - - field :author, Types::AuthorType - - def author - object.author - end + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end diff --git a/rails/app/graphql/types/authors_ids_type.rb b/rails/app/graphql/types/authors_ids_type.rb index 15f38a0..3acef48 100644 --- a/rails/app/graphql/types/authors_ids_type.rb +++ b/rails/app/graphql/types/authors_ids_type.rb @@ -3,18 +3,13 @@ module Types class AuthorsIdsType < Types::BaseObject field :id, ID, null: false - field :author_id, Integer - field :openalex, String + field :author_openalex_id, String field :orcid, String field :scopus, String field :twitter, String field :wikipedia, String - field :mag, Integer - - field :author, Types::AuthorType - - def author - object.author - end + field :mag, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end diff --git a/rails/app/graphql/types/institution_type.rb b/rails/app/graphql/types/institution_type.rb index 78ad271..33fe4f9 100644 --- a/rails/app/graphql/types/institution_type.rb +++ b/rails/app/graphql/types/institution_type.rb @@ -11,31 +11,18 @@ class InstitutionType < Types::BaseObject field :homepage_url, String field :image_url, String field :image_thumbnail_url, String - field :display_name_acronyms, String - field :display_name_alternatives, String + field :display_name_acronyms, GraphQL::Types::JSON + field :display_name_alternatives, GraphQL::Types::JSON field :works_count, Integer field :cited_by_count, Integer field :works_api_url, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false - field :institutions_ids, Types::InstitutionsIdsType - field :institutions_geo, Types::InstitutionsGeoType - field :institutions_counts_by_year, [Types::InstitutionsCountsByYearType] - field :associated_institutions, [Types::InstitutionType] + field :authors, [Types::AuthorType] - def institutions_ids - object.institutions_ids - end - - def institutions_geo - object.institutions_geo - end - - def institutions_counts_by_year - object.institutions_counts_by_year - end - - def associated_institutions - object.associated_institutions + def authors + object.authors end end end diff --git a/rails/app/graphql/types/institutions_associated_institutions_type.rb b/rails/app/graphql/types/institutions_associated_institutions_type.rb new file mode 100644 index 0000000..2d5d95e --- /dev/null +++ b/rails/app/graphql/types/institutions_associated_institutions_type.rb @@ -0,0 +1,12 @@ +# frozen_string_literal: true + +module Types + class InstitutionsAssociatedInstitutionsType < Types::BaseObject + field :id, ID, null: false + field :institution_openalex_id, String + field :associated_institution_openalex_id, String + field :relationship, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/institutions_counts_by_year_type.rb b/rails/app/graphql/types/institutions_counts_by_year_type.rb index e6077c6..d321539 100644 --- a/rails/app/graphql/types/institutions_counts_by_year_type.rb +++ b/rails/app/graphql/types/institutions_counts_by_year_type.rb @@ -3,15 +3,12 @@ module Types class InstitutionsCountsByYearType < Types::BaseObject field :id, ID, null: false + field :institution_openalex_id, String field :year, Integer field :works_count, Integer field :cited_by_count, Integer field :oa_works_count, Integer - - field :institution, Types::InstitutionType - - def institution - object.institution - end + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end diff --git a/rails/app/graphql/types/institutions_geo_type.rb b/rails/app/graphql/types/institutions_geo_type.rb index 7aab8e6..55e1c1f 100644 --- a/rails/app/graphql/types/institutions_geo_type.rb +++ b/rails/app/graphql/types/institutions_geo_type.rb @@ -3,18 +3,15 @@ module Types class InstitutionsGeoType < Types::BaseObject field :id, ID, null: false - field :institution_id, Integer + field :institution_openalex_id, String field :city, String + field :geonames_city_id, Integer field :region, String field :country_code, String field :country, String field :latitude, Float field :longitude, Float - - field :institution, Types::InstitutionType - - def institution - object.institution - end + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end diff --git a/rails/app/graphql/types/institutions_ids_type.rb b/rails/app/graphql/types/institutions_ids_type.rb index 780179e..6028b06 100644 --- a/rails/app/graphql/types/institutions_ids_type.rb +++ b/rails/app/graphql/types/institutions_ids_type.rb @@ -3,18 +3,13 @@ module Types class InstitutionsIdsType < Types::BaseObject field :id, ID, null: false - field :institution_id, Integer - field :openalex, String + field :institution_openalex_id, String field :ror, String field :grid, String field :wikipedia, String field :wikidata, String - field :mag, Integer - - field :institution, Types::InstitutionType - - def institution - object.institution - end + field :mag, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end diff --git a/rails/app/graphql/types/publisher_type.rb b/rails/app/graphql/types/publisher_type.rb index 44c2914..36219f7 100644 --- a/rails/app/graphql/types/publisher_type.rb +++ b/rails/app/graphql/types/publisher_type.rb @@ -3,24 +3,16 @@ module Types class PublisherType < Types::BaseObject field :id, ID, null: false + field :publisher_openalex_id, String field :display_name, String - field :alternate_titles, String - field :country_codes, String + field :alternate_titles, GraphQL::Types::JSON + field :country_codes, GraphQL::Types::JSON field :hierarchy_level, Integer field :parent_publisher, String field :works_count, Integer field :cited_by_count, Integer field :sources_api_url, String - - field :publishers_ids, Types::PublishersIdsType - field :publishers_counts_by_year, Types::PublishersCountsByYearType - - def publishers_ids - object.publishers_ids - end - - def publishers_counts_by_year - object.publishers_counts_by_year - end + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end diff --git a/rails/app/graphql/types/publishers_counts_by_year_type.rb b/rails/app/graphql/types/publishers_counts_by_year_type.rb index 9737dc5..ece0584 100644 --- a/rails/app/graphql/types/publishers_counts_by_year_type.rb +++ b/rails/app/graphql/types/publishers_counts_by_year_type.rb @@ -3,15 +3,12 @@ module Types class PublishersCountsByYearType < Types::BaseObject field :id, ID, null: false + field :publisher_openalex_id, String field :year, Integer field :works_count, Integer field :cited_by_count, Integer field :oa_works_count, Integer - - field :publisher, Types::PublisherType - - def publisher - object.publisher - end + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end diff --git a/rails/app/graphql/types/publishers_ids_type.rb b/rails/app/graphql/types/publishers_ids_type.rb index e1d41f1..1f075c5 100644 --- a/rails/app/graphql/types/publishers_ids_type.rb +++ b/rails/app/graphql/types/publishers_ids_type.rb @@ -3,18 +3,10 @@ module Types class PublishersIdsType < Types::BaseObject field :id, ID, null: false - field :institution_id, Integer - field :openalex, String + field :publisher_openalex_id, String field :ror, String - field :grid, String - field :wikipedia, String field :wikidata, String - field :mag, Integer - - field :publisher, Types::PublisherType - - def publisher - object.publisher - end + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end diff --git a/rails/app/graphql/types/publishers_type.rb b/rails/app/graphql/types/publishers_type.rb new file mode 100644 index 0000000..029b709 --- /dev/null +++ b/rails/app/graphql/types/publishers_type.rb @@ -0,0 +1,6 @@ +# frozen_string_literal: true + +module Types + class PublishersType < Types::BaseObject + end +end diff --git a/rails/app/graphql/types/source_type.rb b/rails/app/graphql/types/source_type.rb new file mode 100644 index 0000000..b9f2888 --- /dev/null +++ b/rails/app/graphql/types/source_type.rb @@ -0,0 +1,20 @@ +# frozen_string_literal: true + +module Types + class SourceType < Types::BaseObject + field :id, ID, null: false + field :source_openalex_id, String + field :issn_l, String + field :issn, GraphQL::Types::JSON + field :display_name, String + field :publisher, String + field :works_count, Integer + field :cited_by_count, Integer + field :is_oa, Boolean + field :is_in_doaj, Boolean + field :homepage_url, String + field :works_api_url, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/sources_counts_by_year_type.rb b/rails/app/graphql/types/sources_counts_by_year_type.rb new file mode 100644 index 0000000..53efd0a --- /dev/null +++ b/rails/app/graphql/types/sources_counts_by_year_type.rb @@ -0,0 +1,14 @@ +# frozen_string_literal: true + +module Types + class SourcesCountsByYearType < Types::BaseObject + field :id, ID, null: false + field :source_openalex_id, String + field :year, Integer + field :works_count, Integer + field :cited_by_count, Integer + field :oa_works_count, Integer + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/sources_ids_type.rb b/rails/app/graphql/types/sources_ids_type.rb new file mode 100644 index 0000000..6b1f4af --- /dev/null +++ b/rails/app/graphql/types/sources_ids_type.rb @@ -0,0 +1,15 @@ +# frozen_string_literal: true + +module Types + class SourcesIdsType < Types::BaseObject + field :id, ID, null: false + field :source_openalex_id, String + field :issn_l, GraphQL::Types::JSON + field :issn, String + field :mag, String + field :wikidata, String + field :fatcat, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/topic_type.rb b/rails/app/graphql/types/topic_type.rb index d453f51..e9f7b07 100644 --- a/rails/app/graphql/types/topic_type.rb +++ b/rails/app/graphql/types/topic_type.rb @@ -3,24 +3,21 @@ module Types class TopicType < Types::BaseObject field :id, ID, null: false + field :topic_openalex_id, String field :display_name, String - field :subfield_id, String - field :subfield_display_name, String - field :field_id, String, - field :field_display_name, String - field :domain_id, String - field :domain_display_name, String + field :openalex_subfield_id, Integer + field :openalex_subfield_display_name, String + field :openalex_field_id, Integer + field :openalex_field_display_name, String + field :openalex_domain_id, Integer + field :openalex_domain_display_name, String field :description, String field :keywords, String field :works_api_url, String field :wikipedia_id, String field :works_count, Integer field :cited_by_count, Integer - - field :works, [Types::WorkType] - - def works - object.works - end + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false end end diff --git a/rails/app/graphql/types/work_type.rb b/rails/app/graphql/types/work_type.rb index 8f84cc9..47a39e9 100644 --- a/rails/app/graphql/types/work_type.rb +++ b/rails/app/graphql/types/work_type.rb @@ -18,5 +18,26 @@ class WorkType < Types::BaseObject field :language, String field :created_at, GraphQL::Types::ISO8601DateTime, null: false field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + + field :authors, [Types::AuthorType] + field :institutions, [Types::InstitutionType] + field :referenced_works, [Types::WorkType] + field :referencing_works, [Types::WorkType] + + def authors + object.authors + end + + def referenced_works + object.referenced_works + end + + def referencing_works + object.referencing_works + end + + def institutions + object.institutions + end end end diff --git a/rails/app/graphql/types/works_authorship_type.rb b/rails/app/graphql/types/works_authorship_type.rb new file mode 100644 index 0000000..f9054fb --- /dev/null +++ b/rails/app/graphql/types/works_authorship_type.rb @@ -0,0 +1,14 @@ +# frozen_string_literal: true + +module Types + class WorksAuthorshipType < Types::BaseObject + field :id, ID, null: false + field :work_openalex_id, String + field :author_position, String + field :author_openalex_id, String + field :institution_openalex_id, String + field :raw_affiliation_string, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/works_best_oa_location_type.rb b/rails/app/graphql/types/works_best_oa_location_type.rb new file mode 100644 index 0000000..2c06f86 --- /dev/null +++ b/rails/app/graphql/types/works_best_oa_location_type.rb @@ -0,0 +1,16 @@ +# frozen_string_literal: true + +module Types + class WorksBestOaLocationType < Types::BaseObject + field :id, ID, null: false + field :work_openalex_id, String + field :source_openalex_id, String + field :landing_page_url, String + field :pdf_url, String + field :is_oa, Boolean + field :version, String + field :license, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/works_biblio_type.rb b/rails/app/graphql/types/works_biblio_type.rb new file mode 100644 index 0000000..94e26fe --- /dev/null +++ b/rails/app/graphql/types/works_biblio_type.rb @@ -0,0 +1,14 @@ +# frozen_string_literal: true + +module Types + class WorksBiblioType < Types::BaseObject + field :id, ID, null: false + field :work_openalex_id, String + field :volume, String + field :issue, String + field :first_page, String + field :last_page, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/works_ids_type.rb b/rails/app/graphql/types/works_ids_type.rb new file mode 100644 index 0000000..23b327f --- /dev/null +++ b/rails/app/graphql/types/works_ids_type.rb @@ -0,0 +1,14 @@ +# frozen_string_literal: true + +module Types + class WorksIdsType < Types::BaseObject + field :id, ID, null: false + field :work_openalex_id, String + field :doi, String + field :mag, String + field :pmid, String + field :pmcid, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/works_location_type.rb b/rails/app/graphql/types/works_location_type.rb new file mode 100644 index 0000000..6ae3234 --- /dev/null +++ b/rails/app/graphql/types/works_location_type.rb @@ -0,0 +1,16 @@ +# frozen_string_literal: true + +module Types + class WorksLocationType < Types::BaseObject + field :id, ID, null: false + field :work_openalex_id, String + field :source_openalex_id, String + field :landing_page_url, String + field :pdf_url, String + field :is_oa, Boolean + field :version, String + field :license, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/works_open_access_type.rb b/rails/app/graphql/types/works_open_access_type.rb new file mode 100644 index 0000000..22ec290 --- /dev/null +++ b/rails/app/graphql/types/works_open_access_type.rb @@ -0,0 +1,14 @@ +# frozen_string_literal: true + +module Types + class WorksOpenAccessType < Types::BaseObject + field :id, ID, null: false + field :work_openalex_id, String + field :is_oa, Boolean + field :oa_status, String + field :oa_url, String + field :any_repository_has_fulltext, Boolean + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end diff --git a/rails/app/graphql/types/works_primary_location_type.rb b/rails/app/graphql/types/works_primary_location_type.rb new file mode 100644 index 0000000..213b3cc --- /dev/null +++ b/rails/app/graphql/types/works_primary_location_type.rb @@ -0,0 +1,16 @@ +# frozen_string_literal: true + +module Types + class WorksPrimaryLocationType < Types::BaseObject + field :id, ID, null: false + field :work_openalex_id, String + field :source_openalex_id, String + field :landing_page_url, String + field :pdf_url, String + field :is_oa, Boolean + field :version, String + field :license, String + field :created_at, GraphQL::Types::ISO8601DateTime, null: false + field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + end +end From c8eb30873020e4d3de03cbf0fc1ce647d255cb91 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 18 Dec 2024 17:08:45 +0000 Subject: [PATCH 35/44] addition author and institution indexing --- rails/db/migrate/20241218170109_index_authors_on_orcid.rb | 5 +++++ rails/db/migrate/20241218170259_index_institutions_on_ror.rb | 5 +++++ 2 files changed, 10 insertions(+) create mode 100644 rails/db/migrate/20241218170109_index_authors_on_orcid.rb create mode 100644 rails/db/migrate/20241218170259_index_institutions_on_ror.rb diff --git a/rails/db/migrate/20241218170109_index_authors_on_orcid.rb b/rails/db/migrate/20241218170109_index_authors_on_orcid.rb new file mode 100644 index 0000000..f86200c --- /dev/null +++ b/rails/db/migrate/20241218170109_index_authors_on_orcid.rb @@ -0,0 +1,5 @@ +class IndexAuthorsOnOrcid < ActiveRecord::Migration[7.1] + def change + add_index :authors, :orcid + end +end diff --git a/rails/db/migrate/20241218170259_index_institutions_on_ror.rb b/rails/db/migrate/20241218170259_index_institutions_on_ror.rb new file mode 100644 index 0000000..e451457 --- /dev/null +++ b/rails/db/migrate/20241218170259_index_institutions_on_ror.rb @@ -0,0 +1,5 @@ +class IndexInstitutionsOnRor < ActiveRecord::Migration[7.1] + def change + add_index :institutions, :ror + end +end From babe35653576499c95a97fcee010cc2d3ec19fe3 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 18 Dec 2024 17:09:23 +0000 Subject: [PATCH 36/44] updated schema --- rails/db/schema.rb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/rails/db/schema.rb b/rails/db/schema.rb index 34efa03..24821b7 100644 --- a/rails/db/schema.rb +++ b/rails/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema[7.1].define(version: 2024_12_02_154712) do +ActiveRecord::Schema[7.1].define(version: 2024_12_18_170259) do # These are extensions that must be enabled in order to support this database enable_extension "plpgsql" @@ -24,6 +24,7 @@ t.string "last_known_institution" t.string "works_api_url" t.index ["author_openalex_id"], name: "index_authors_on_author_openalex_id" + t.index ["orcid"], name: "index_authors_on_orcid" end create_table "authors_counts_by_years", force: :cascade do |t| @@ -66,6 +67,7 @@ t.datetime "created_at", null: false t.datetime "updated_at", null: false t.index ["institution_openalex_id"], name: "index_institutions_on_institution_openalex_id" + t.index ["ror"], name: "index_institutions_on_ror" end create_table "institutions_associated_institutions", force: :cascade do |t| From a15e5594976ac5a549ffa3a78ab403f06ec9aff8 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 19 Dec 2024 17:19:05 +0000 Subject: [PATCH 37/44] remove concepts models --- rails/app/models/concept.rb | 16 ---------------- rails/app/models/concepts_ancestors.rb | 6 ------ rails/app/models/concepts_counts_by_year.rb | 5 ----- rails/app/models/concepts_ids.rb | 5 ----- rails/app/models/concepts_related_concepts.rb | 8 -------- 5 files changed, 40 deletions(-) delete mode 100644 rails/app/models/concept.rb delete mode 100644 rails/app/models/concepts_ancestors.rb delete mode 100644 rails/app/models/concepts_counts_by_year.rb delete mode 100644 rails/app/models/concepts_ids.rb delete mode 100644 rails/app/models/concepts_related_concepts.rb diff --git a/rails/app/models/concept.rb b/rails/app/models/concept.rb deleted file mode 100644 index 7204d45..0000000 --- a/rails/app/models/concept.rb +++ /dev/null @@ -1,16 +0,0 @@ -# frozen_string_literal: true - -class Concept < ApplicationRecord - has_many :works_concepts - has_many :works, through: :works_concepts - has_one :concepts_counts_by_year - has_one :concepts_ids - - has_many :concepts_related_concepts, - foreign_key: :related_concept_id, - class_name: 'ConceptsRelatedConcepts' - - has_many :related_concepts, - through: :concepts_related_concepts, - source: :related_concept -end diff --git a/rails/app/models/concepts_ancestors.rb b/rails/app/models/concepts_ancestors.rb deleted file mode 100644 index e26ed9f..0000000 --- a/rails/app/models/concepts_ancestors.rb +++ /dev/null @@ -1,6 +0,0 @@ -# frozen_string_literal: true - -class ConceptsAncestors < ApplicationRecord - belongs_to :concept, foreign_key: 'concept_id', class_name: 'Concept' - belongs_to :ancestor, foreign_key: 'ancestor_id', class_name: 'Concept' -end diff --git a/rails/app/models/concepts_counts_by_year.rb b/rails/app/models/concepts_counts_by_year.rb deleted file mode 100644 index dff941f..0000000 --- a/rails/app/models/concepts_counts_by_year.rb +++ /dev/null @@ -1,5 +0,0 @@ -# frozen_string_literal: true - -class ConceptsCountsByYear < ApplicationRecord - belongs_to :concept -end diff --git a/rails/app/models/concepts_ids.rb b/rails/app/models/concepts_ids.rb deleted file mode 100644 index 13bf08c..0000000 --- a/rails/app/models/concepts_ids.rb +++ /dev/null @@ -1,5 +0,0 @@ -# frozen_string_literal: true - -class ConceptsIds < ApplicationRecord - belongs_to :concept -end diff --git a/rails/app/models/concepts_related_concepts.rb b/rails/app/models/concepts_related_concepts.rb deleted file mode 100644 index 563e972..0000000 --- a/rails/app/models/concepts_related_concepts.rb +++ /dev/null @@ -1,8 +0,0 @@ -# frozen_string_literal: true - -class ConceptsRelatedConcepts < ApplicationRecord - belongs_to :concept, foreign_key: 'concept_id', class_name: 'Concept' - belongs_to :related_concept, - foreign_key: 'related_concept_id', - class_name: 'Concept' -end From 8498d5c0c6f3c8de8470fa9ad7db64013a16b065 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 19 Dec 2024 17:28:06 +0000 Subject: [PATCH 38/44] Remove works_concept and works_mesh models --- rails/app/models/works_concept.rb | 6 ------ rails/app/models/works_mesh.rb | 5 ----- 2 files changed, 11 deletions(-) delete mode 100644 rails/app/models/works_concept.rb delete mode 100644 rails/app/models/works_mesh.rb diff --git a/rails/app/models/works_concept.rb b/rails/app/models/works_concept.rb deleted file mode 100644 index 69bdeea..0000000 --- a/rails/app/models/works_concept.rb +++ /dev/null @@ -1,6 +0,0 @@ -# frozen_string_literal: true - -class WorksConcept < ApplicationRecord - belongs_to :work - belongs_to :concept -end diff --git a/rails/app/models/works_mesh.rb b/rails/app/models/works_mesh.rb deleted file mode 100644 index b21276e..0000000 --- a/rails/app/models/works_mesh.rb +++ /dev/null @@ -1,5 +0,0 @@ -# frozen_string_literal: true - -class WorksMesh < ApplicationRecord - belongs_to :work -end From 245928013dab5a1b848e01ac452a75ce230968ff Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 19 Dec 2024 18:19:54 +0000 Subject: [PATCH 39/44] add topics --- rails/app/graphql/types/query_type.rb | 52 +++++++++++++++++++++----- rails/app/graphql/types/work_type.rb | 26 ++++++++++--- rails/app/models/topic.rb | 5 ++- rails/app/models/work.rb | 5 ++- rails/app/models/works_topic.rb | 9 ++++- rails/db/schema.rb | 12 +++++- rails/lib/tasks/load_works_topics.rake | 2 +- 7 files changed, 90 insertions(+), 21 deletions(-) diff --git a/rails/app/graphql/types/query_type.rb b/rails/app/graphql/types/query_type.rb index 40766fa..50768ec 100644 --- a/rails/app/graphql/types/query_type.rb +++ b/rails/app/graphql/types/query_type.rb @@ -24,10 +24,7 @@ def nodes(ids:) ids.map { |id| context.schema.object_from_id(id, context) } end - # Add root-level fields here. - # They will be entry points for queries on your schema. - - field :institution, + field :institution_by_openalex_id, Types::InstitutionType, null: true, description: 'Fetches an institution by institution_openalex_id' do @@ -37,21 +34,58 @@ def institution(institution_openalex_id:) Institution.find_by(institution_openalex_id: institution_openalex_id) end - field :author, + field :institution_by_ror, + Types::InstitutionType, + null: true, + description: 'Fetches an institution by ROR' do + argument :ror, String, required: true + end + def institution(institution_openalex_id:) + Institution.find_by(ror: ror) + end + + # author entry points + + field :author_by_openalex_id, Types::AuthorType, null: true, - description: 'Fetch author by ID' do + description: 'Fetch author by OpenAlex ID' do argument :author_openalex_id, String, required: true end - def author(author_openalex_id:) + def author_by_openalex_id(author_openalex_id:) Author.find_by(author_openalex_id: author_openalex_id) end - field :work, Types::WorkType, null: true, description: 'Fetch work by ID' do + field :author_by_orcid, + Types::AuthorType, + null: true, + description: 'Fetch author by OpenAlex ID' do + argument :orcid, String, required: true + end + def author_by_orcid(orcid:) + Author.find_by(orcid: orcid) + end + + # work entry points + + field :work_by_openalex_id, + Types::WorkType, + null: true, + description: 'Fetch work by OpenAlex ID' do argument :work_openalex_id, String, required: true end - def work(work_openalex_id:) + def work_by_openalex_id(work_openalex_id:) Work.find_by(work_openalex_id: work_openalex_id) end + + field :work_by_doi, + Types::WorkType, + null: true, + description: 'Fetch work by DOI' do + argument :doi, String, required: true + end + def work_by_doi(doi:) + Work.find_by(doi: doi) + end end end diff --git a/rails/app/graphql/types/work_type.rb b/rails/app/graphql/types/work_type.rb index 47a39e9..01898da 100644 --- a/rails/app/graphql/types/work_type.rb +++ b/rails/app/graphql/types/work_type.rb @@ -20,24 +20,38 @@ class WorkType < Types::BaseObject field :updated_at, GraphQL::Types::ISO8601DateTime, null: false field :authors, [Types::AuthorType] - field :institutions, [Types::InstitutionType] - field :referenced_works, [Types::WorkType] - field :referencing_works, [Types::WorkType] - def authors object.authors end + field :institutions, [Types::InstitutionType] + def institutions + object.institutions + end + + field :referenced_works, [Types::WorkType] def referenced_works object.referenced_works end + field :referencing_works, [Types::WorkType] def referencing_works object.referencing_works end - def institutions - object.institutions + field :works_open_access, Types::WorksOpenAccessType + def works_open_access + object.works_open_access + end + + field :works_biblio, Types::WorksBiblioType + def works_biblio + object.works_biblio + end + + field :topics, [Types::TopicType] + def topics + object.topics end end end diff --git a/rails/app/models/topic.rb b/rails/app/models/topic.rb index d967643..d018c2d 100644 --- a/rails/app/models/topic.rb +++ b/rails/app/models/topic.rb @@ -1,6 +1,9 @@ # frozen_string_literal: true class Topic < ApplicationRecord - has_many :works_topics + has_many :works_topics, + primary_key: :topic_openalex_id, + foreign_key: :topic_openalex_id + has_many :works, through: :works_topics end diff --git a/rails/app/models/work.rb b/rails/app/models/work.rb index 867625b..c9f0f1e 100644 --- a/rails/app/models/work.rb +++ b/rails/app/models/work.rb @@ -20,7 +20,10 @@ class Work < ApplicationRecord primary_key: :work_openalex_id, foreign_key: :work_openalex_id - has_many :works_topics + has_many :works_topics, + primary_key: :work_openalex_id, + foreign_key: :work_openalex_id + has_many :topics, through: :works_topics # Below here is magic join table nonsense that will break if you touch it diff --git a/rails/app/models/works_topic.rb b/rails/app/models/works_topic.rb index d6dd7b5..95640a7 100644 --- a/rails/app/models/works_topic.rb +++ b/rails/app/models/works_topic.rb @@ -1,6 +1,11 @@ # frozen_string_literal: true class WorksTopic < ApplicationRecord - belongs_to :work - belongs_to :topic + belongs_to :work, + primary_key: :work_openalex_id, + foreign_key: :work_openalex_id + + belongs_to :topic, + primary_key: :topic_openalex_id, + foreign_key: :topic_openalex_id end diff --git a/rails/db/schema.rb b/rails/db/schema.rb index 24821b7..36959ee 100644 --- a/rails/db/schema.rb +++ b/rails/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema[7.1].define(version: 2024_12_18_170259) do +ActiveRecord::Schema[7.1].define(version: 2024_12_18_202214) do # These are extensions that must be enabled in order to support this database enable_extension "plpgsql" @@ -331,4 +331,14 @@ t.index ["work_openalex_id"], name: "index_works_referenced_works_on_work_openalex_id" end + create_table "works_topics", force: :cascade do |t| + t.string "work_openalex_id" + t.string "topic_openalex_id" + t.float "score" + t.datetime "created_at", null: false + t.datetime "updated_at", null: false + t.index ["topic_openalex_id"], name: "index_works_topics_on_topic_openalex_id" + t.index ["work_openalex_id"], name: "index_works_topics_on_work_openalex_id" + end + end diff --git a/rails/lib/tasks/load_works_topics.rake b/rails/lib/tasks/load_works_topics.rake index 3afd280..e59f403 100644 --- a/rails/lib/tasks/load_works_topics.rake +++ b/rails/lib/tasks/load_works_topics.rake @@ -20,7 +20,7 @@ namespace :data_import do } end - if works_topics.count >= 10_000 + if works_topics.count >= 100_000 WorksTopic.insert_all(works_topics) works_topics = [] From 997f3ccf6d8ed2f6252f39cacef401ece65fb537 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 19 Dec 2024 18:23:46 +0000 Subject: [PATCH 40/44] work_topics migration --- .../migrate/20241218202214_create_works_topics.rb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 rails/db/migrate/20241218202214_create_works_topics.rb diff --git a/rails/db/migrate/20241218202214_create_works_topics.rb b/rails/db/migrate/20241218202214_create_works_topics.rb new file mode 100644 index 0000000..e278152 --- /dev/null +++ b/rails/db/migrate/20241218202214_create_works_topics.rb @@ -0,0 +1,14 @@ +class CreateWorksTopics < ActiveRecord::Migration[7.1] + def change + create_table :works_topics do |t| + t.string :work_openalex_id + t.string :topic_openalex_id + t.float :score + + t.timestamps + end + + add_index :works_topics, :work_openalex_id + add_index :works_topics, :topic_openalex_id + end +end From de3d2b34054c5816e9aafd6c7b9e88055caf9ebe Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 2 Jan 2025 16:02:29 +0000 Subject: [PATCH 41/44] Fix all text -> bool castings resulting in false --- rails/lib/tasks/load_sources.rake | 4 ++-- rails/lib/tasks/load_works.rake | 4 ++-- rails/lib/tasks/load_works_best_oa_locations.rake | 2 +- rails/lib/tasks/load_works_locations.rake | 2 +- rails/lib/tasks/load_works_open_accesses.rake | 7 ++++--- rails/lib/tasks/load_works_primary_locations.rake | 2 +- 6 files changed, 11 insertions(+), 10 deletions(-) diff --git a/rails/lib/tasks/load_sources.rake b/rails/lib/tasks/load_sources.rake index 108a6c0..c3dd5c1 100644 --- a/rails/lib/tasks/load_sources.rake +++ b/rails/lib/tasks/load_sources.rake @@ -21,8 +21,8 @@ namespace :data_import do publisher: row[4], works_count: row[5], cited_by_count: row[6], - is_oa: row[7], - is_in_doaj: row[8], + is_oa: ActiveModel::Type::Boolean.new.cast(row[7].downcase), + is_in_doaj: ActiveModel::Type::Boolean.new.cast(row[8].downcase), homepage_url: row[9], works_api_url: row[10] } diff --git a/rails/lib/tasks/load_works.rake b/rails/lib/tasks/load_works.rake index 545f807..49c0aa3 100644 --- a/rails/lib/tasks/load_works.rake +++ b/rails/lib/tasks/load_works.rake @@ -23,8 +23,8 @@ namespace :data_import do publication_date: row[5], work_type: row[6], cited_by_count: row[7], - is_retracted: row[8], - is_paratext: row[9], + is_retracted: ActiveModel::Type::Boolean.new.cast(row[8].downcase), + is_paratext: ActiveModel::Type::Boolean.new.cast(row[9].downcase), cited_by_api_url: row[10], abstract_inverted_index: row[11], language: row[12] diff --git a/rails/lib/tasks/load_works_best_oa_locations.rake b/rails/lib/tasks/load_works_best_oa_locations.rake index 7dbb2a9..059ef14 100644 --- a/rails/lib/tasks/load_works_best_oa_locations.rake +++ b/rails/lib/tasks/load_works_best_oa_locations.rake @@ -18,7 +18,7 @@ namespace :data_import do source_openalex_id: row[1].split('/').last, landing_page_url: row[2], pdf_url: row[3], - is_oa: row[4], + is_oa: ActiveModel::Type::Boolean.new.cast(row[4].downcase), version: row[5], license: row[6] } diff --git a/rails/lib/tasks/load_works_locations.rake b/rails/lib/tasks/load_works_locations.rake index 5955eae..d0c1a4e 100644 --- a/rails/lib/tasks/load_works_locations.rake +++ b/rails/lib/tasks/load_works_locations.rake @@ -18,7 +18,7 @@ namespace :data_import do source_openalex_id: row[1].split('/').last, landing_page_url: row[2], pdf_url: row[3], - is_oa: row[4], + is_oa: ActiveModel::Type::Boolean.new.cast(row[4].downcase), version: row[5], license: row[6] } diff --git a/rails/lib/tasks/load_works_open_accesses.rake b/rails/lib/tasks/load_works_open_accesses.rake index 4e22f50..ff7ca1a 100644 --- a/rails/lib/tasks/load_works_open_accesses.rake +++ b/rails/lib/tasks/load_works_open_accesses.rake @@ -15,14 +15,15 @@ namespace :data_import do unless index == 0 works_open_accesses << { work_openalex_id: row[0].split('/').last, - is_oa: row[1], + is_oa: ActiveModel::Type::Boolean.new.cast(row[1].downcase), oa_status: row[2], oa_url: row[3], - any_repository_has_fulltext: row[4] + any_repository_has_fulltext: + ActiveModel::Type::Boolean.new.cast(row[4].downcase) } end - if works_open_accesses.count >= 10_000 + if works_open_accesses.count >= 100_000 WorksOpenAccess.insert_all(works_open_accesses) works_open_accesses = [] diff --git a/rails/lib/tasks/load_works_primary_locations.rake b/rails/lib/tasks/load_works_primary_locations.rake index a40741e..2273336 100644 --- a/rails/lib/tasks/load_works_primary_locations.rake +++ b/rails/lib/tasks/load_works_primary_locations.rake @@ -18,7 +18,7 @@ namespace :data_import do source_openalex_id: row[1].split('/').last, landing_page_url: row[2], pdf_url: row[3], - is_oa: row[4], + is_oa: ActiveModel::Type::Boolean.new.cast(row[4].downcase), version: row[5], license: row[6] } From 148267572f7fd1141b55fe6e9a7f0d8f117720dc Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 2 Jan 2025 16:03:46 +0000 Subject: [PATCH 42/44] rename to bookworm --- rails/config/application.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rails/config/application.rb b/rails/config/application.rb index 4542d05..3908cf2 100644 --- a/rails/config/application.rb +++ b/rails/config/application.rb @@ -10,7 +10,7 @@ # you've limited to :test, :development, or :production. Bundler.require(*Rails.groups) -module BookWormApi +module BookWorm class Application < Rails::Application # Initialize configuration defaults for originally generated Rails version. config.load_defaults 7.1 From 4eeb0837828deda75485966b7637d1ea1b1e5676 Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Wed, 15 Jan 2025 23:25:27 -0500 Subject: [PATCH 43/44] Work on frontend simplification and connection with backend --- react/package-lock.json | 2164 ++++++++++++++++- react/package.json | 3 + react/src/components/InvestigationCard.tsx | 34 - react/src/components/SideBar.tsx | 107 - .../src/components/graph/AuthorshipGraph.tsx | 104 + react/src/components/graph/WorkGraph.tsx | 28 + .../components/graph/nodes/AuthorDetails.tsx | 32 +- .../src/components/graph/nodes/AuthorNode.tsx | 47 +- react/src/components/graph/nodes/NoteNode.tsx | 1 - .../components/graph/nodes/WorkDetails.tsx | 120 +- react/src/components/graph/nodes/WorkNode.tsx | 92 +- react/src/components/pages/AuthorPage.tsx | 33 + .../src/components/pages/CustomQueryPage.tsx | 11 + .../components/pages/InvestigationPage.tsx | 47 - .../components/pages/InvestigationsPage.tsx | 70 - react/src/components/pages/WorkPage.tsx | 35 + react/src/hooks/ADD_AUTHOR_WORKS.tsx | 16 - react/src/hooks/ADD_CITATIONS.tsx | 16 - react/src/hooks/ADD_REFERENCES.tsx | 16 - react/src/hooks/CREATE_AUTHOR_NODE.tsx | 24 - react/src/hooks/CREATE_INVESTIGATION.tsx | 10 - react/src/hooks/CREATE_WORK_NODE.tsx | 15 - react/src/hooks/UPDATE_WORK_NODE.tsx | 24 - react/src/hooks/useAuthorshipGraph.tsx | 42 + react/src/hooks/useInvestigation.tsx | 24 - react/src/hooks/useInvestigationGraph.tsx | 90 - react/src/hooks/useInvestigations.tsx | 20 - react/src/hooks/useWorkGraph.tsx | 25 + react/src/main.tsx | 18 +- react/src/root.tsx | 2 - 30 files changed, 2487 insertions(+), 783 deletions(-) delete mode 100644 react/src/components/InvestigationCard.tsx delete mode 100644 react/src/components/SideBar.tsx create mode 100644 react/src/components/graph/AuthorshipGraph.tsx create mode 100644 react/src/components/graph/WorkGraph.tsx create mode 100644 react/src/components/pages/AuthorPage.tsx create mode 100644 react/src/components/pages/CustomQueryPage.tsx delete mode 100644 react/src/components/pages/InvestigationPage.tsx delete mode 100644 react/src/components/pages/InvestigationsPage.tsx create mode 100644 react/src/components/pages/WorkPage.tsx delete mode 100644 react/src/hooks/ADD_AUTHOR_WORKS.tsx delete mode 100644 react/src/hooks/ADD_CITATIONS.tsx delete mode 100644 react/src/hooks/ADD_REFERENCES.tsx delete mode 100644 react/src/hooks/CREATE_AUTHOR_NODE.tsx delete mode 100644 react/src/hooks/CREATE_INVESTIGATION.tsx delete mode 100644 react/src/hooks/CREATE_WORK_NODE.tsx delete mode 100644 react/src/hooks/UPDATE_WORK_NODE.tsx create mode 100644 react/src/hooks/useAuthorshipGraph.tsx delete mode 100644 react/src/hooks/useInvestigation.tsx delete mode 100644 react/src/hooks/useInvestigationGraph.tsx delete mode 100644 react/src/hooks/useInvestigations.tsx create mode 100644 react/src/hooks/useWorkGraph.tsx diff --git a/react/package-lock.json b/react/package-lock.json index c5a386e..742b53e 100644 --- a/react/package-lock.json +++ b/react/package-lock.json @@ -9,7 +9,10 @@ "version": "0.0.0", "dependencies": { "@apollo/client": "^3.10.8", + "@graphiql/react": "^0.28.2", "axios": "^1.6.8", + "d3-hierarchy": "^3.1.2", + "elkjs": "^0.9.3", "graphql": "^16.8.2", "react": "^18.2.0", "react-dom": "^18.2.0", @@ -2020,6 +2023,40 @@ "integrity": "sha512-0hYQ8SB4Db5zvZB4axdMHGwEaQjkZzFjQiN9LVYvIFB2nSUHW9tYpxWriPrWDASIxiaXax83REcLxuSdnGPZtw==", "dev": true }, + "node_modules/@codemirror/language": { + "version": "6.0.0", + "resolved": "https://registry.npmjs.org/@codemirror/language/-/language-6.0.0.tgz", + "integrity": "sha512-rtjk5ifyMzOna1c7PBu7J1VCt0PvA5wy3o8eMVnxMKb7z8KA7JFecvD04dSn14vj/bBaAbqRsGed5OjtofEnLA==", + "peer": true, + "dependencies": { + "@codemirror/state": "^6.0.0", + 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"dev": true }, + "meros": { + "version": "1.3.0", + "resolved": "https://registry.npmjs.org/meros/-/meros-1.3.0.tgz", + "integrity": "sha512-2BNGOimxEz5hmjUG2FwoxCt5HN7BXdaWyFqEwxPTrJzVdABtrL4TiHTcsWSFAxPQ/tOnEaQEJh3qWq71QRMY+w==", + "requires": {} + }, "micromatch": { "version": "4.0.8", "resolved": "https://registry.npmjs.org/micromatch/-/micromatch-4.0.8.tgz", @@ -18117,6 +20084,11 @@ "path-key": "^3.0.0" } }, + "nullthrows": { + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/nullthrows/-/nullthrows-1.1.1.tgz", + "integrity": "sha512-2vPPEi+Z7WqML2jZYddDIfy5Dqb0r2fze2zTxNNknZaFpVHU3mFB3R+DWeJWGVx0ecvttSGlJTI+WG+8Z4cDWw==" + }, "nwsapi": { "version": "2.2.12", "resolved": "https://registry.npmjs.org/nwsapi/-/nwsapi-2.2.12.tgz", @@ -18367,6 +20339,17 @@ } } }, + "popmotion": { + "version": "11.0.3", + "resolved": "https://registry.npmjs.org/popmotion/-/popmotion-11.0.3.tgz", + "integrity": "sha512-Y55FLdj3UxkR7Vl3s7Qr4e9m0onSnP8W7d/xQLsoJM40vs6UKHFdygs6SWryasTZYqugMjm3BepCF4CWXDiHgA==", + "requires": { + "framesync": "6.0.1", + "hey-listen": "^1.0.8", + "style-value-types": "5.0.0", + "tslib": "^2.1.0" + } + }, "postcss": { "version": "8.4.41", "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.41.tgz", @@ -18509,6 +20492,11 @@ "integrity": "sha512-vYt7UD1U9Wg6138shLtLOvdAu+8DsC/ilFtEVHcH+wydcSpNE20AfSOduf6MkRFahL5FY7X1oU7nKVZFtfq8Fg==", "dev": true }, + "punycode.js": { + "version": "2.3.1", + "resolved": "https://registry.npmjs.org/punycode.js/-/punycode.js-2.3.1.tgz", + "integrity": "sha512-uxFIHU0YlHYhDQtV4R9J6a52SLx28BCjT+4ieh7IGbgwVJWO+km431c4yRlREUAsAmt/uMjQUyQHNEPf0M39CA==" + }, "pure-rand": { "version": "6.1.0", "resolved": "https://registry.npmjs.org/pure-rand/-/pure-rand-6.1.0.tgz", @@ -18535,6 +20523,12 @@ "loose-envify": "^1.1.0" } }, + "react-compiler-runtime": { + "version": "19.0.0-beta-37ed2a7-20241206", + "resolved": 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+ "resolved": "https://registry.npmjs.org/style-value-types/-/style-value-types-5.0.0.tgz", + "integrity": "sha512-08yq36Ikn4kx4YU6RD7jWEv27v4V+PUsOGa4n/as8Et3CuODMJQ00ENeAVXAeydX4Z2j1XHZF1K2sX4mGl18fA==", + "requires": { + "hey-listen": "^1.0.8", + "tslib": "^2.1.0" + } + }, "sucrase": { "version": "3.35.0", "resolved": "https://registry.npmjs.org/sucrase/-/sucrase-3.35.0.tgz", @@ -19169,6 +21217,11 @@ "is-number": "^7.0.0" } }, + "toggle-selection": { + "version": "1.0.6", + "resolved": "https://registry.npmjs.org/toggle-selection/-/toggle-selection-1.0.6.tgz", + "integrity": "sha512-BiZS+C1OS8g/q2RRbJmy59xpyghNBqrr6k5L/uKBGRsTfxmu3ffiRnd8mlGPUVayg8pvfi5urfnu8TU7DVOkLQ==" + }, "tough-cookie": { "version": "4.1.4", "resolved": "https://registry.npmjs.org/tough-cookie/-/tough-cookie-4.1.4.tgz", @@ -19272,11 +21325,16 @@ "integrity": "sha512-Mtq29sKDAEYP7aljRgtPOpTvOfbwRWlS6dPRzwjdE+C0R4brX/GUyhHSecbHMFLNBLcJIPt9nl9yG5TZ1weH+Q==", "dev": true }, + "uc.micro": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/uc.micro/-/uc.micro-2.1.0.tgz", + "integrity": "sha512-ARDJmphmdvUk6Glw7y9DQ2bFkKBHwQHLi2lsaH6PPmz/Ka9sFOBsBluozhDltWmnv9u/cF6Rt87znRTPV+yp/A==" + }, "undici-types": { "version": "6.19.8", "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.19.8.tgz", "integrity": "sha512-ve2KP6f/JnbPBFyobGHuerC9g1FYGn/F8n1LWTwNxCEzd6IfqTwUQcNXgEtmmQ6DlRrC1hrSrBnCZPokRrDHjw==", - "dev": true + "devOptional": true }, "unicode-canonical-property-names-ecmascript": { "version": "2.0.0", @@ -19341,6 +21399,23 @@ "requires-port": "^1.0.0" } }, + "use-callback-ref": { + "version": "1.3.3", + "resolved": "https://registry.npmjs.org/use-callback-ref/-/use-callback-ref-1.3.3.tgz", + "integrity": "sha512-jQL3lRnocaFtu3V00JToYz/4QkNWswxijDaCVNZRiRTO3HQDLsdu1ZtmIUvV4yPp+rvWm5j0y0TG/S61cuijTg==", + "requires": { + "tslib": "^2.0.0" + } + }, + "use-sidecar": { + "version": "1.1.3", + "resolved": "https://registry.npmjs.org/use-sidecar/-/use-sidecar-1.1.3.tgz", + "integrity": "sha512-Fedw0aZvkhynoPYlA5WXrMCAMm+nSWdZt6lzJQ7Ok8S6Q+VsHmHpRWndVRJ8Be0ZbkfPc5LRYH+5XrzXcEeLRQ==", + "requires": { + "detect-node-es": "^1.1.0", + "tslib": "^2.0.0" + } + }, "use-sync-external-store": { "version": "1.2.2", "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.2.2.tgz", @@ -19382,6 +21457,17 @@ "rollup": "^4.20.0" } }, + "vscode-languageserver-types": { + "version": "3.17.5", + "resolved": "https://registry.npmjs.org/vscode-languageserver-types/-/vscode-languageserver-types-3.17.5.tgz", + "integrity": "sha512-Ld1VelNuX9pdF39h2Hgaeb5hEZM2Z3jUrrMgWQAu82jMtZp7p3vJT3BzToKtZI7NgQssZje5o0zryOrhQvzQAg==" + }, + "w3c-keyname": { + "version": "2.2.8", + "resolved": "https://registry.npmjs.org/w3c-keyname/-/w3c-keyname-2.2.8.tgz", + "integrity": "sha512-dpojBhNsCNN7T82Tm7k26A6G9ML3NkhDsnw9n/eoxSRlVBB4CEtIQ/KTCLI2Fwf3ataSXRhYFkQi3SlnFwPvPQ==", + "peer": true + }, "w3c-xmlserializer": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/w3c-xmlserializer/-/w3c-xmlserializer-4.0.0.tgz", diff --git a/react/package.json b/react/package.json index 391e320..65a21d5 100644 --- a/react/package.json +++ b/react/package.json @@ -12,7 +12,10 @@ }, "dependencies": { "@apollo/client": "^3.10.8", + "@graphiql/react": "^0.28.2", "axios": "^1.6.8", + "d3-hierarchy": "^3.1.2", + "elkjs": "^0.9.3", "graphql": "^16.8.2", "react": "^18.2.0", "react-dom": "^18.2.0", diff --git a/react/src/components/InvestigationCard.tsx b/react/src/components/InvestigationCard.tsx deleted file mode 100644 index 78f40e9..0000000 --- a/react/src/components/InvestigationCard.tsx +++ /dev/null @@ -1,34 +0,0 @@ -interface Props { - id: number; - name: string; - created_at: string; -} - -function InvestigationCard({ id, name, created_at }: Props) { - return ( - - -
-
- Investigation: {name} -
-

- Hey this here is some investigation description text beep beep lorem - ipsum nice -

-

- Created at: {created_at} -

-
- - ); -} - -export default InvestigationCard; diff --git a/react/src/components/SideBar.tsx b/react/src/components/SideBar.tsx deleted file mode 100644 index 0ccf529..0000000 --- a/react/src/components/SideBar.tsx +++ /dev/null @@ -1,107 +0,0 @@ -import { gql, useMutation } from "@apollo/client"; -import { useState } from "react"; -import { USE_INVESTIGATION_GRAPH } from "../hooks/useInvestigationGraph.tsx"; -import { useParams } from "react-router"; -import { CREATE_WORK_NODE } from "../hooks/CREATE_WORK_NODE.tsx"; -import { CREATE_NOTE_NODE } from "../hooks/CREATE_NOTE_NODE.tsx"; -import { CREATE_AUTHOR_NODE } from "../hooks/CREATE_AUTHOR_NODE.tsx"; - -function SideBar() { - const { investigationId } = useParams(); - const [doiSearch, setDoiSearch] = useState(""); - const [openalexAuthorSearch, setOpenalexAuthorSearch] = useState(""); - const [noteBodyText, setNoteBodyText] = useState(""); - - // const [addAuthor] = useMutation(CREATE_AUTHOR_NODE, { - // errorPolicy: "ignore", - // variables: { - // openalexId: openalexAuthorSearch, - // investigationId: investigationId, - // }, - // onCompleted: (data) => {}, - // onError: (data) => { - // console.log(data); - // }, - // refetchQueries: [USE_INVESTIGATION_GRAPH], - // }); - - const [createWorkNode] = useMutation(CREATE_WORK_NODE, { - errorPolicy: "ignore", - variables: { - doi: doiSearch, - investigationId: investigationId, - }, - onCompleted: (data) => { - { - { - window.location.reload(); - } - } - }, - onError: (data) => { - console.log(data); - }, - // refetchQueries: [USE_INVESTIGATION_GRAPH], - }); - - let doiInputHandler = (e) => { - setDoiSearch(e.target.value); - }; - - let authorInputHandler = (e) => { - setOpenalexAuthorSearch(e.target.value); - }; - - let noteTextInputHandler = (e) => { - setNoteBodyText(e.target.value); - }; - - const [addNote] = useMutation(CREATE_NOTE_NODE, { - variables: { - bodyText: noteBodyText, - investigationId: investigationId, - }, - onCompleted: (data) => { - { - { - window.location.reload(); - } - } - }, - onError: (data) => { - console.log(data); - }, - // refetchQueries: [USE_INVESTIGATION_GRAPH], - }); - - return ( - <> - - - -

-

-

- - {/* - */} - - {/* - */} - - ); -} - -export default SideBar; diff --git a/react/src/components/graph/AuthorshipGraph.tsx b/react/src/components/graph/AuthorshipGraph.tsx new file mode 100644 index 0000000..bc1dd02 --- /dev/null +++ b/react/src/components/graph/AuthorshipGraph.tsx @@ -0,0 +1,104 @@ +import { useMemo, } from "react"; +import ReactFlow, { useNodesState, useEdgesState, MarkerType, useReactFlow } from "reactflow"; +import "reactflow/dist/style.css"; +import WorkNode from "./nodes/WorkNode.tsx"; +import AuthorNode from "./nodes/AuthorNode.tsx"; +import AuthorshipEdge from "./edges/AuthorshipEdge.tsx"; +import { stratify, tree, hierarchy } from 'd3-hierarchy'; + + +interface Props { + authorshipData: JSON; +} + +const getLayoutedElements = (nodes, edges) => { + const { width, height } = document + .querySelector(`[data-id="${nodes[0].id}"]`) + ?.getBoundingClientRect() || { width: 100, height: 100 }; + + const radius = Math.min(width, height) / 2; + + const g = tree() + .size([2 * Math.PI, radius]) + .separation((a, b) => (a.parent == b.parent ? 1 : 2) / a.depth); + + const hierarchy = stratify() + .id((node) => node.id) + .parentId((node) => edges.find((edge) => edge.target === node.id)?.source); + + const root = g(hierarchy(nodes)); + const layout = g.nodeSize([width * 2, height * 2])(root); + + return { + nodes: layout + .descendants() + .map((node) => ({ ...node.data, position: { x: node.x, y: node.y } })), + edges, + }; +}; + +function AuthorshipGraph({ + authorshipData +}: Props) { + + const nodeTypes = useMemo( + () => ({ + work: WorkNode, + author: AuthorNode, + }), + [] + ); + + const initialNodes = []; + const initialEdges = []; + + for (let i = 0; i <= authorshipData.works.length - 1; i++) { + initialNodes.push({ + id: `work-${authorshipData.works[i].id}`, + data: { + workData: authorshipData.works[i], + }, + type: "work", + }); + + initialEdges.push({ + source: `author-${authorshipData.id}`, + target: `work-${authorshipData.works[i].id}`, + id: `authorshipedge-${authorshipData.id}-${authorshipData.works[i].id}`, + label: "authored", + style: { + strokeWidth: 4, + stroke: "#008000", + }, + }); + } + + initialNodes.push({ + id: `author-${authorshipData.id}`, + data: { + authorData: authorshipData, + }, + type: "author" + }) + + const layoutedElements = getLayoutedElements(initialNodes, initialEdges); + + const [nodes, setNodes, onNodesChange] = useNodesState(layoutedElements.nodes); + const [edges, setEdges, onEdgesChange] = useEdgesState(layoutedElements.edges); + + return ( +
+ +
+ ); +} + +export default AuthorshipGraph; diff --git a/react/src/components/graph/WorkGraph.tsx b/react/src/components/graph/WorkGraph.tsx new file mode 100644 index 0000000..e4688e2 --- /dev/null +++ b/react/src/components/graph/WorkGraph.tsx @@ -0,0 +1,28 @@ +import { useMemo, } from "react"; +import ReactFlow, { useNodesState, useEdgesState, MarkerType, useReactFlow } from "reactflow"; +import "reactflow/dist/style.css"; +import WorkNode from "./nodes/WorkNode.tsx"; +import AuthorNode from "./nodes/AuthorNode.tsx"; +import AuthorshipEdge from "./edges/AuthorshipEdge.tsx"; +import { stratify, tree, hierarchy } from 'd3-hierarchy'; + +interface Props { + workData: JSON; +} + +function WorkGraph({ + workData +}: Props) { + const nodeTypes = useMemo( + () => ({ + work: WorkNode, + author: AuthorNode, + }), + [] + ); + + return (<> + ) +} + +export default WorkGraph; \ No newline at end of file diff --git a/react/src/components/graph/nodes/AuthorDetails.tsx b/react/src/components/graph/nodes/AuthorDetails.tsx index f5c1f7a..d5a9933 100644 --- a/react/src/components/graph/nodes/AuthorDetails.tsx +++ b/react/src/components/graph/nodes/AuthorDetails.tsx @@ -1,20 +1,19 @@ interface Props { - name: string; + displayName: string; orcid: string; - openalexId: string; - hIndex: number; - i10Index: number; - citedByCount: number; + authorOpenalexId: string; worksCount: number; + citedByCount: number; + lastKnownInstitution: string; } function AuthorDetails({ + displayName, orcid, - openalexId, - hIndex, - i10Index, - citedByCount, + authorOpenalexId, worksCount, + citedByCount, + lastKnownInstitution, }: Props) { return ( <> @@ -28,15 +27,7 @@ function AuthorDetails({ OpenAlexId - {openalexId} - - - h-Index - {hIndex} - - - i10 Index - {i10Index} + {authorOpenalexId} Cited By Count @@ -46,6 +37,11 @@ function AuthorDetails({ Works Count {worksCount} + + Last Known Institution + {lastKnownInstitution} + + ); diff --git a/react/src/components/graph/nodes/AuthorNode.tsx b/react/src/components/graph/nodes/AuthorNode.tsx index 33234ab..3087703 100644 --- a/react/src/components/graph/nodes/AuthorNode.tsx +++ b/react/src/components/graph/nodes/AuthorNode.tsx @@ -1,9 +1,6 @@ import { Handle, Position } from "reactflow"; -import { useMutation } from "@apollo/client"; import { useParams } from "react-router"; import "./author-node.css"; -import { USE_INVESTIGATION_GRAPH } from "../../../hooks/useInvestigationGraph"; -import { ADD_AUTHOR_WORKS } from "../../../hooks/ADD_AUTHOR_WORKS"; import { useCallback, useEffect, useRef, useState } from "react"; import AuthorDetails from "./AuthorDetails"; @@ -23,48 +20,19 @@ function AuthorNode({ data }) { setIsExpanded((isExpanded) => !isExpanded); }, []); - const [addAuthorWorks] = useMutation(ADD_AUTHOR_WORKS, { - errorPolicy: "ignore", - onCompleted: (data) => { - { - { - window.location.reload(); - } - } - }, - onError: (data) => { - console.log(data); - }, - // refetchQueries: [USE_INVESTIGATION_GRAPH], - }); - useEffect(() => { if (ref.current) { setContentHeight(ref.current["clientHeight"]); } }, []); - console.log(data); return (
- +
- -

@@ -77,13 +45,12 @@ function AuthorNode({ data }) { >
diff --git a/react/src/components/graph/nodes/NoteNode.tsx b/react/src/components/graph/nodes/NoteNode.tsx index 4d6a8f9..b7e443f 100644 --- a/react/src/components/graph/nodes/NoteNode.tsx +++ b/react/src/components/graph/nodes/NoteNode.tsx @@ -1,7 +1,6 @@ import { Handle, Position } from 'reactflow' import { useMutation } from '@apollo/client' import { useParams } from 'react-router' -import { USE_INVESTIGATION_GRAPH } from '../../../hooks/useInvestigationGraph' import './note-node.css' import { DELETE_NOTE_NODE } from '../../../hooks/DELETE_NOTE_NODE' diff --git a/react/src/components/graph/nodes/WorkDetails.tsx b/react/src/components/graph/nodes/WorkDetails.tsx index 7cd22d6..d7f1980 100644 --- a/react/src/components/graph/nodes/WorkDetails.tsx +++ b/react/src/components/graph/nodes/WorkDetails.tsx @@ -1,125 +1,75 @@ -import { useMutation } from "@apollo/client"; import { useParams } from "react-router"; -import { USE_INVESTIGATION_GRAPH } from "../../../hooks/useInvestigationGraph"; -import { CREATE_AUTHOR_NODE } from "../../../hooks/CREATE_AUTHOR_NODE"; interface Props { + title: string; doi: string; - keywords: string[]; - language: string; publicationYear: number; - title: string; - topics: string[]; - authors: string[]; - isOpenAccess: boolean; - openAccessUrl: string; - openalexId: string; - abstract: string; + publicationDate: number; + workType: string; + citedByCount: number; + isRetracted: boolean; + isParatext: boolean; + language: string; + // isOpenAccess: boolean; + workOpenalexId: string; + // abstract: string; } function WorkDetails({ + title, doi, - keywords, - language, publicationYear, - title, - topics, - authors, - isOpenAccess, - openAccessUrl, - openalexId, - abstract, + publicationDate, + workType, + citedByCount, + isRetracted, + isParatext, + language }: Props) { - const { investigationId } = useParams(); - const [addAuthor] = useMutation(CREATE_AUTHOR_NODE, { - errorPolicy: "ignore", - onCompleted: (data) => { - { - { - window.location.reload(); - } - } - }, - onError: (data) => { - console.log(data); - }, - // refetchQueries: [USE_INVESTIGATION_GRAPH], - }); return ( <> - + + - - {authors && authors.map((author: any) => )} + + - - {authors && - authors.map((author: any) => ( - - ))} + + - - {topics && topics.map((topic: any) => )} + + - - + + - - - - - - {keywords.map((keyword: any) => ( - - ))} + + - - + + - - + + +
- {abstract} - Title{title}
Authors{author.name}DOI{doi}
ORCID - {author.orcid} -

- - 		Publication Year{publicationYear}
Topics{topic}Publication Date{publicationDate}
DOI{doi}Work Type{workType}
Language {language}
Publication Year{publicationYear}
Keywords{keyword}Cited By Count{citedByCount}
Is Open Access?{isOpenAccess ? "Yes" : "No"}Is Retracted?{isRetracted}
Open Access Url{openAccessUrl}Is Paratext?{isParatext}
); diff --git a/react/src/components/graph/nodes/WorkNode.tsx b/react/src/components/graph/nodes/WorkNode.tsx index 90ba04f..d928de5 100644 --- a/react/src/components/graph/nodes/WorkNode.tsx +++ b/react/src/components/graph/nodes/WorkNode.tsx @@ -1,13 +1,8 @@ import { Handle, Position } from "reactflow"; -import { useMutation } from "@apollo/client"; import { useParams } from "react-router"; import "./work-node.css"; import { useState, useCallback, useRef, useEffect } from "react"; -import { USE_INVESTIGATION_GRAPH } from "../../../hooks/useInvestigationGraph"; import WorkDetails from "./WorkDetails"; -import { ADD_REFERENCES } from "../../../hooks/ADD_REFERENCES"; -import { ADD_CITATIONS } from "../../../hooks/ADD_CITATIONS"; -import { UPDATE_WORK_NODE } from "../../../hooks/UPDATE_WORK_NODE"; interface WorkNode { id: number; @@ -21,67 +16,11 @@ function WorkNode({ data }) { const ref = useRef(null); const noderef = useRef(null); const [contentHeight, setContentHeight] = useState(0); - const [xCoordinate, setXCoordinate] = useState(data.workData.xCoordinate); - const [yCoordinate, setYCoordinate] = useState(data.workData.yCoordinate); - const { investigationId } = useParams(); - - const [updateNode] = useMutation(UPDATE_WORK_NODE, { - variables: { - workNodeId: data.workData.id.toString(), - xCoordinate: xCoordinate, - yCoordinate: yCoordinate, - visible: true, - }, - }); - - useEffect(() => { - const interval = setInterval(() => { - let translateMatrix = - noderef.current.parentElement.style.transform.split(", "); - let x = Number(translateMatrix[0].split("(")[1].split("px")[0]); - let y = Number(translateMatrix[1].split("px")[0]); - setXCoordinate(x); - setYCoordinate(y); - updateNode(); - }, 10000); - - return () => clearInterval(interval); - }, []); const toggleIsExpanded = useCallback(() => { setIsExpanded((isExpanded) => !isExpanded); }, []); - const [addReferences] = useMutation(ADD_REFERENCES, { - variables: { - openalexId: data.workData.work.openalexId, - investigationId: investigationId, - }, - onCompleted: (data) => { - { - { - window.location.reload(); - } - } - }, - // refetchQueries: [USE_INVESTIGATION_GRAPH], - }); - - const [addCitations] = useMutation(ADD_CITATIONS, { - variables: { - openalexId: data.workData.work.openalexId, - investigationId: investigationId, - }, - onCompleted: (data) => { - { - { - window.location.reload(); - } - } - }, - // refetchQueries: [USE_INVESTIGATION_GRAPH], - }); - useEffect(() => { if (ref.current) { setContentHeight(ref.current.clientHeight); @@ -92,19 +31,13 @@ function WorkNode({ data }) {
- - -

- -

+ @@ -117,17 +50,16 @@ function WorkNode({ data }) { >
diff --git a/react/src/components/pages/AuthorPage.tsx b/react/src/components/pages/AuthorPage.tsx new file mode 100644 index 0000000..6c947cf --- /dev/null +++ b/react/src/components/pages/AuthorPage.tsx @@ -0,0 +1,33 @@ +import { useParams } from "react-router"; +import Header from "../Header.tsx"; +import AuthorshipGraph from "../graph/AuthorshipGraph.tsx"; +import { useAuthorshipGraph } from "../../hooks/useAuthorshipGraph.tsx"; + +type AuthorPageParams = { + orcid: string; +}; + +function AuthorPage() { + const { orcid } = useParams(); + const { error, data, loading } = useAuthorshipGraph(orcid); + + if (loading) return
loading....
; + if (error) return
uh oh error...
; + + return ( + <> +
+
+
+
+ +
+
+
+ + ); +} + +export default AuthorPage; diff --git a/react/src/components/pages/CustomQueryPage.tsx b/react/src/components/pages/CustomQueryPage.tsx new file mode 100644 index 0000000..cbb0805 --- /dev/null +++ b/react/src/components/pages/CustomQueryPage.tsx @@ -0,0 +1,11 @@ +import Header from "../Header.tsx"; + +function CustomQueryPage() { + return ( + <> + eyy i'm a placeholder for a graphql interface + + ) +} + +export default CustomQueryPage; \ No newline at end of file diff --git a/react/src/components/pages/InvestigationPage.tsx b/react/src/components/pages/InvestigationPage.tsx deleted file mode 100644 index 32bf10f..0000000 --- a/react/src/components/pages/InvestigationPage.tsx +++ /dev/null @@ -1,47 +0,0 @@ -import { useParams } from "react-router"; -import SideBar from "../SideBar.tsx"; -import InvestigationGraph from "../graph/InvestigationGraph.tsx"; -import Header from "../Header.tsx"; -import { useInvestigationGraph } from "../../hooks/useInvestigationGraph.tsx"; - -interface Props { - name: string; - created_at: string; -} - -type InvestigationParams = { - investigationId: string; -}; - -function InvestigationPage() { - const { investigationId } = useParams(); - const { error, data, loading } = useInvestigationGraph(investigationId); - - if (loading) return
loading....
; - if (error) return
uh oh error...
; - - return ( - <> -
-

Investigation: {data.investigation.name}

-
-
-
- -
-
- -
-
-
- - ); -} - -export default InvestigationPage; diff --git a/react/src/components/pages/InvestigationsPage.tsx b/react/src/components/pages/InvestigationsPage.tsx deleted file mode 100644 index d3ab41d..0000000 --- a/react/src/components/pages/InvestigationsPage.tsx +++ /dev/null @@ -1,70 +0,0 @@ -import { useMutation } from "@apollo/client"; -import { useState } from "react"; -import InvestigationCard from "../InvestigationCard.tsx"; -import { - useInvestigations, - GET_INVESTIGATIONS, -} from "../../hooks/useInvestigations.tsx"; -import Header from "../Header.tsx"; -import { useNavigate } from "react-router-dom"; -import { CREATE_INVESTIGATION } from "../../hooks/CREATE_INVESTIGATION.tsx"; - -function InvestigationsPage() { - const { error, data, loading } = useInvestigations(); - const [newInvestigationName, setNewInvestigationName] = useState(""); - const navigate = useNavigate(); - - const [createInvestigation, createInvestigationResult] = useMutation( - CREATE_INVESTIGATION, - { - variables: { - name: newInvestigationName, - }, - onCompleted: (data) => { - navigate(`/investigations/${data.createInvestigation.id}`); - }, - refetchQueries: [GET_INVESTIGATIONS], - } - ); - - let newInvestigationNameHandler = (e) => { - setNewInvestigationName(e.target.value); - }; - - if (loading) return
loading....
; - if (error) return
uh oh error...
; - - if (!localStorage.getItem("email")) { - return ( - <> -

Please sign in!

- - ); - } - - return ( - <> -
- - - {data.investigations.length == 0 &&

No Investigations Found :(

} - {data.investigations.map((investigation: any) => ( - - ))} - - ); -} - -export default InvestigationsPage; diff --git a/react/src/components/pages/WorkPage.tsx b/react/src/components/pages/WorkPage.tsx new file mode 100644 index 0000000..c245bce --- /dev/null +++ b/react/src/components/pages/WorkPage.tsx @@ -0,0 +1,35 @@ +import { useParams } from "react-router"; +import Header from "../Header.tsx"; +import WorkGraph from "../graph/WorkGraph.tsx" +import { useWorkGraph } from "../../hooks/useWorkGraph.tsx"; + +type WorkPageParams = { + doi: string; +} + +function WorkPage() { + const { doi } = useParams(); + const { error, data, loading } = useWorkGraph(doi); + + if (loading) return
loading....
; + if (error) return
uh oh error...
; + + console.log(data) + + return ( + <> +
+
+
+
+ +
+
+
+ + ); +} + +export default WorkPage; \ No newline at end of file diff --git a/react/src/hooks/ADD_AUTHOR_WORKS.tsx b/react/src/hooks/ADD_AUTHOR_WORKS.tsx deleted file mode 100644 index e488779..0000000 --- a/react/src/hooks/ADD_AUTHOR_WORKS.tsx +++ /dev/null @@ -1,16 +0,0 @@ -import { gql } from "@apollo/client"; - -export const ADD_AUTHOR_WORKS = gql` - mutation ($openalexId: String!, $investigationId: String!) { - addAuthorWorks( - input: { openalexId: $openalexId, investigationId: $investigationId } - ) { - xCoordinate - yCoordinate - work { - openalexId - doi - } - } - } -`; diff --git a/react/src/hooks/ADD_CITATIONS.tsx b/react/src/hooks/ADD_CITATIONS.tsx deleted file mode 100644 index 47c414d..0000000 --- a/react/src/hooks/ADD_CITATIONS.tsx +++ /dev/null @@ -1,16 +0,0 @@ -import { gql } from "@apollo/client"; - -export const ADD_CITATIONS = gql` - mutation ($openalexId: String!, $investigationId: String!) { - addCitations( - input: { openalexId: $openalexId, investigationId: $investigationId } - ) { - xCoordinate - yCoordinate - visible - work { - openalexId - } - } - } -`; diff --git a/react/src/hooks/ADD_REFERENCES.tsx b/react/src/hooks/ADD_REFERENCES.tsx deleted file mode 100644 index 44f07b1..0000000 --- a/react/src/hooks/ADD_REFERENCES.tsx +++ /dev/null @@ -1,16 +0,0 @@ -import { gql } from "@apollo/client"; - -export const ADD_REFERENCES = gql` - mutation ($openalexId: String!, $investigationId: String!) { - addReferences( - input: { openalexId: $openalexId, investigationId: $investigationId } - ) { - xCoordinate - yCoordinate - visible - work { - openalexId - } - } - } -`; diff --git a/react/src/hooks/CREATE_AUTHOR_NODE.tsx b/react/src/hooks/CREATE_AUTHOR_NODE.tsx deleted file mode 100644 index 68f702c..0000000 --- a/react/src/hooks/CREATE_AUTHOR_NODE.tsx +++ /dev/null @@ -1,24 +0,0 @@ -import { gql } from "@apollo/client"; - -export const CREATE_AUTHOR_NODE = gql` - mutation ( - $authorOpenalexId: String! - $workOpenalexId: String! - $investigationId: String! - ) { - createAuthorNode( - input: { - authorOpenalexId: $authorOpenalexId - workOpenalexId: $workOpenalexId - investigationId: $investigationId - } - ) { - xCoordinate - yCoordinate - visible - author { - name - } - } - } -`; diff --git a/react/src/hooks/CREATE_INVESTIGATION.tsx b/react/src/hooks/CREATE_INVESTIGATION.tsx deleted file mode 100644 index 77972e5..0000000 --- a/react/src/hooks/CREATE_INVESTIGATION.tsx +++ /dev/null @@ -1,10 +0,0 @@ -import { gql } from "@apollo/client"; - -export const CREATE_INVESTIGATION = gql` - mutation ($name: String!) { - createInvestigation(input: { name: $name }) { - id - name - } - } -`; diff --git a/react/src/hooks/CREATE_WORK_NODE.tsx b/react/src/hooks/CREATE_WORK_NODE.tsx deleted file mode 100644 index 33f9fd1..0000000 --- a/react/src/hooks/CREATE_WORK_NODE.tsx +++ /dev/null @@ -1,15 +0,0 @@ -import { gql } from "@apollo/client"; - -export const CREATE_WORK_NODE = gql` - mutation ($doi: String!, $investigationId: String!) { - createWorkNode(input: { doi: $doi, investigationId: $investigationId }) { - id - xCoordinate - yCoordinate - visible - work { - title - } - } - } -`; diff --git a/react/src/hooks/UPDATE_WORK_NODE.tsx b/react/src/hooks/UPDATE_WORK_NODE.tsx deleted file mode 100644 index 97b38e3..0000000 --- a/react/src/hooks/UPDATE_WORK_NODE.tsx +++ /dev/null @@ -1,24 +0,0 @@ -import { useMutation, gql } from "@apollo/client"; - -export const UPDATE_WORK_NODE = gql` - mutation ( - $workNodeId: String! - $xCoordinate: Int - $yCoordinate: Int - $visible: Boolean - ) { - updateWorkNode( - input: { - workNodeId: $workNodeId - xCoordinate: $xCoordinate - yCoordinate: $yCoordinate - visible: $visible - } - ) { - id - xCoordinate - yCoordinate - visible - } - } -`; diff --git a/react/src/hooks/useAuthorshipGraph.tsx b/react/src/hooks/useAuthorshipGraph.tsx new file mode 100644 index 0000000..1e8ca8c --- /dev/null +++ b/react/src/hooks/useAuthorshipGraph.tsx @@ -0,0 +1,42 @@ +import { useQuery, gql } from "@apollo/client"; + +export const USE_AUTHORSHIP_GRAPH = gql` +query AuthorshipGraph($orcid: String!) { + authorByOrcid(orcid: $orcid) { + id + displayName + orcid + authorOpenalexId + worksCount + citedByCount + lastKnownInstitution + works { + id + title + doi + workOpenalexId + publicationYear + publicationDate + workType + citedByCount + isRetracted + isParatext + language + } + } +} +`; + +export const useAuthorshipGraph = (orcid: string) => { + const { loading, error, data } = useQuery(USE_AUTHORSHIP_GRAPH, { + variables: { + orcid, + }, + }); + + return { + error, + data, + loading, + }; +}; diff --git a/react/src/hooks/useInvestigation.tsx b/react/src/hooks/useInvestigation.tsx deleted file mode 100644 index 2b129d3..0000000 --- a/react/src/hooks/useInvestigation.tsx +++ /dev/null @@ -1,24 +0,0 @@ -import { useQuery, gql } from "@apollo/client"; - -const GET_INVESTIGATION = gql` - query GetInvestigation($id: ID!) { - investigation(id: $id) { - id - name - } - } -`; - -export const useInvestigation = (id: string) => { - const { loading, error, data } = useQuery(GET_INVESTIGATION, { - variables: { - id, - }, - }); - - return { - error, - data, - loading, - }; -}; diff --git a/react/src/hooks/useInvestigationGraph.tsx b/react/src/hooks/useInvestigationGraph.tsx deleted file mode 100644 index 875f477..0000000 --- a/react/src/hooks/useInvestigationGraph.tsx +++ /dev/null @@ -1,90 +0,0 @@ -import { useQuery, gql } from "@apollo/client"; - -export const USE_INVESTIGATION_GRAPH = gql` - query UseInvestigationGraph($id: ID!) { - investigation(id: $id) { - workNodes { - id - xCoordinate - yCoordinate - visible - work { - id - doi - title - openalexId - language - publicationYear - keywords - topics - isOpenAccess - abstract - authors { - name - id - orcid - openalexId - } - citations { - id - } - references { - id - } - } - } - authorNodes { - id - xCoordinate - yCoordinate - visible - author { - name - orcid - openalexId - hIndex - i10Index - citedByCount - worksCount - } - } - noteNodes { - id - } - workEdges { - id - visible - citationNode { - id - } - referenceNode { - id - } - } - authorshipEdges { - id - visible - authorNode { - id - } - workNode { - id - } - } - } - } -`; - -export const useInvestigationGraph = (id: string) => { - const { loading, error, data } = useQuery(USE_INVESTIGATION_GRAPH, { - variables: { - id, - }, - }); - - return { - error, - data, - loading, - }; -}; diff --git a/react/src/hooks/useInvestigations.tsx b/react/src/hooks/useInvestigations.tsx deleted file mode 100644 index 4eee984..0000000 --- a/react/src/hooks/useInvestigations.tsx +++ /dev/null @@ -1,20 +0,0 @@ -import { useQuery, gql } from "@apollo/client"; - -export const GET_INVESTIGATIONS = gql` - query { - investigations { - id - name - } - } -`; - -export const useInvestigations = () => { - const { loading, error, data } = useQuery(GET_INVESTIGATIONS); - - return { - error, - data, - loading, - }; -}; diff --git a/react/src/hooks/useWorkGraph.tsx b/react/src/hooks/useWorkGraph.tsx new file mode 100644 index 0000000..a97dbe1 --- /dev/null +++ b/react/src/hooks/useWorkGraph.tsx @@ -0,0 +1,25 @@ +import { useQuery, gql } from "@apollo/client"; + +export const USE_WORK_GRAPH = gql` +query WorkGraph($doi: String!) { + workByDoi(doi: $doi) { + id + displayName + } +} +`; + +export const useWorkGraph = (doi: string) => { + const { loading, error, data } = useQuery(USE_WORK_GRAPH, { + variables: { + doi + }, + }); + + return { + error, + data, + loading, + } +}; + diff --git a/react/src/main.tsx b/react/src/main.tsx index bb4886a..7789a40 100644 --- a/react/src/main.tsx +++ b/react/src/main.tsx @@ -10,8 +10,9 @@ import { BrowserRouter as Router, Routes, Route } from "react-router-dom"; import Root from "./root.tsx"; import "./index.css"; -import InvestigationsPage from "./components/pages/InvestigationsPage.tsx"; -import InvestigationPage from "./components/pages/InvestigationPage.tsx"; +import AuthorPage from "./components/pages/AuthorPage.tsx"; +import WorkPage from "./components/pages/WorkPage.tsx"; +import CustomQueryPage from "./components/pages/CustomQueryPage.tsx"; import RegistrationPage from "./components/pages/RegistrationPage.tsx"; import SignInPage from "./components/pages/SignInPage.tsx"; import { setContext } from "@apollo/client/link/context"; @@ -44,10 +45,17 @@ ReactDOM.createRoot(document.getElementById("root")!).render( } /> - } /> } + path="/author/:orcid" + element={} + /> + } + /> + } /> } /> } /> diff --git a/react/src/root.tsx b/react/src/root.tsx index bda764d..fa74015 100644 --- a/react/src/root.tsx +++ b/react/src/root.tsx @@ -8,8 +8,6 @@ export default function Root() { Register
Sign In -
- My investigations ); } From 0d8490f8001c6df6f5858509a62be8a0a064a4fe Mon Sep 17 00:00:00 2001 From: Alex Boyd Date: Thu, 16 Jan 2025 19:43:26 +0000 Subject: [PATCH 44/44] misc other fixes for loading openalex snapshot version --- rails/Dockerfile | 1 + rails/README.md | 0 rails/app/graphql/types/author_type.rb | 15 +++++++++- ...stitutions_associated_institutions_type.rb | 12 -------- rails/app/graphql/types/query_type.rb | 28 +++++++++++-------- rails/app/graphql/types/topic_type.rb | 6 +++- rails/app/graphql/types/work_type.rb | 5 ++++ .../graphql/types/works_authorship_type.rb | 14 ---------- rails/app/models/author.rb | 3 ++ rails/config/database.yml | 6 ++-- rails/config/environments/development.rb | 2 ++ rails/db/seeds.rb | 8 +++--- rails/lib/tasks/load_works.rake | 2 +- rails/package-lock.json | 2 +- 14 files changed, 56 insertions(+), 48 deletions(-) create mode 100644 rails/README.md delete mode 100644 rails/app/graphql/types/institutions_associated_institutions_type.rb delete mode 100644 rails/app/graphql/types/works_authorship_type.rb diff --git a/rails/Dockerfile b/rails/Dockerfile index adc752b..e43cb51 100644 --- a/rails/Dockerfile +++ b/rails/Dockerfile @@ -9,6 +9,7 @@ WORKDIR /rails # Set production environment ENV RAILS_ENV="production" \ + RAILS_MASTER_KEY=$RAILS_MASTER_KEY \ BUNDLE_DEPLOYMENT="1" \ BUNDLE_PATH="/usr/local/bundle" \ BUNDLE_WITHOUT="development" diff --git a/rails/README.md b/rails/README.md new file mode 100644 index 0000000..e69de29 diff --git a/rails/app/graphql/types/author_type.rb b/rails/app/graphql/types/author_type.rb index 7dde100..9b8ae07 100644 --- a/rails/app/graphql/types/author_type.rb +++ b/rails/app/graphql/types/author_type.rb @@ -12,11 +12,24 @@ class AuthorType < Types::BaseObject field :last_known_institution, String field :works_api_url, String - field :authors_ids, Types::AuthorsIdsType field :works, [Types::WorkType] + def works + object.works + end + field :authors_ids, Types::AuthorsIdsType def authors_ids object.authors_ids end + + field :institutions, [Types::InstitutionType] + def institutions + object.institutions.uniq # move this to the Author model probably + end + + field :authors_counts_by_year, [Types::AuthorsCountsByYearType] + def authors_counts_by_year + object.authors_counts_by_year + end end end diff --git a/rails/app/graphql/types/institutions_associated_institutions_type.rb b/rails/app/graphql/types/institutions_associated_institutions_type.rb deleted file mode 100644 index 2d5d95e..0000000 --- a/rails/app/graphql/types/institutions_associated_institutions_type.rb +++ /dev/null @@ -1,12 +0,0 @@ -# frozen_string_literal: true - -module Types - class InstitutionsAssociatedInstitutionsType < Types::BaseObject - field :id, ID, null: false - field :institution_openalex_id, String - field :associated_institution_openalex_id, String - field :relationship, String - field :created_at, GraphQL::Types::ISO8601DateTime, null: false - field :updated_at, GraphQL::Types::ISO8601DateTime, null: false - end -end diff --git a/rails/app/graphql/types/query_type.rb b/rails/app/graphql/types/query_type.rb index 50768ec..f19f70d 100644 --- a/rails/app/graphql/types/query_type.rb +++ b/rails/app/graphql/types/query_type.rb @@ -24,15 +24,16 @@ def nodes(ids:) ids.map { |id| context.schema.object_from_id(id, context) } end - field :institution_by_openalex_id, - Types::InstitutionType, - null: true, - description: 'Fetches an institution by institution_openalex_id' do - argument :institution_openalex_id, String, required: true - end - def institution(institution_openalex_id:) - Institution.find_by(institution_openalex_id: institution_openalex_id) - end + # need to index institutions by openalex id + # field :institution_by_openalex_id, + # Types::InstitutionType, + # null: true, + # description: 'Fetches an institution by institution_openalex_id' do + # argument :institution_openalex_id, String, required: true + # end + # def institution_by_openalex_id(institution_openalex_id:) + # Institution.find_by(institution_openalex_id: institution_openalex_id) + # end field :institution_by_ror, Types::InstitutionType, @@ -40,7 +41,7 @@ def institution(institution_openalex_id:) description: 'Fetches an institution by ROR' do argument :ror, String, required: true end - def institution(institution_openalex_id:) + def institution_by_ror(ror:) Institution.find_by(ror: ror) end @@ -63,7 +64,12 @@ def author_by_openalex_id(author_openalex_id:) argument :orcid, String, required: true end def author_by_orcid(orcid:) - Author.find_by(orcid: orcid) + # do some error handling for invalid entries + if "https://orcid.org/".in? orcid + Author.find_by(orcid: orcid) + else + Author.find_by(orcid: "https://orcid.org/" + orcid) + end end # work entry points diff --git a/rails/app/graphql/types/topic_type.rb b/rails/app/graphql/types/topic_type.rb index e9f7b07..fe00d44 100644 --- a/rails/app/graphql/types/topic_type.rb +++ b/rails/app/graphql/types/topic_type.rb @@ -12,12 +12,16 @@ class TopicType < Types::BaseObject field :openalex_domain_id, Integer field :openalex_domain_display_name, String field :description, String - field :keywords, String field :works_api_url, String field :wikipedia_id, String field :works_count, Integer field :cited_by_count, Integer field :created_at, GraphQL::Types::ISO8601DateTime, null: false field :updated_at, GraphQL::Types::ISO8601DateTime, null: false + + field :keywords, [String] + def keywords + object.keywords + end end end diff --git a/rails/app/graphql/types/work_type.rb b/rails/app/graphql/types/work_type.rb index 01898da..e4260fd 100644 --- a/rails/app/graphql/types/work_type.rb +++ b/rails/app/graphql/types/work_type.rb @@ -53,5 +53,10 @@ def works_biblio def topics object.topics end + + field :works_ids, Types::WorksIdsType + def works_ids + object.works_ids + end end end diff --git a/rails/app/graphql/types/works_authorship_type.rb b/rails/app/graphql/types/works_authorship_type.rb deleted file mode 100644 index f9054fb..0000000 --- a/rails/app/graphql/types/works_authorship_type.rb +++ /dev/null @@ -1,14 +0,0 @@ -# frozen_string_literal: true - -module Types - class WorksAuthorshipType < Types::BaseObject - field :id, ID, null: false - field :work_openalex_id, String - field :author_position, String - field :author_openalex_id, String - field :institution_openalex_id, String - field :raw_affiliation_string, String - field :created_at, GraphQL::Types::ISO8601DateTime, null: false - field :updated_at, GraphQL::Types::ISO8601DateTime, null: false - end -end diff --git a/rails/app/models/author.rb b/rails/app/models/author.rb index dc90a79..33ca809 100644 --- a/rails/app/models/author.rb +++ b/rails/app/models/author.rb @@ -4,12 +4,15 @@ class Author < ApplicationRecord has_one :authors_ids, primary_key: :author_openalex_id, foreign_key: :author_openalex_id + has_many :authors_counts_by_year, primary_key: :author_openalex_id, foreign_key: :author_openalex_id + has_many :works_authorships, primary_key: :author_openalex_id, foreign_key: :author_openalex_id + has_many :institutions, through: :works_authorships has_many :works, through: :works_authorships end diff --git a/rails/config/database.yml b/rails/config/database.yml index f25e8af..886144f 100644 --- a/rails/config/database.yml +++ b/rails/config/database.yml @@ -3,17 +3,17 @@ default: &default encoding: unicode username: bookworm # password: <%= ENV["POSTGRES_PASSWORD"] %> - password: password pool: 5 development: - host: localhost <<: *default + host: localhost + password: password database: bookworm_development test: - host: localhost <<: *default + host: localhost database: bookworm_test password: password diff --git a/rails/config/environments/development.rb b/rails/config/environments/development.rb index e183944..1a8bd5c 100644 --- a/rails/config/environments/development.rb +++ b/rails/config/environments/development.rb @@ -3,6 +3,8 @@ require 'active_support/core_ext/integer/time' Rails.application.configure do + config.hosts << 'ec2-34-215-107-32.us-west-2.compute.amazonaws.com:3000' + config.hosts << 'ec2-35-94-47-108.us-west-2.compute.amazonaws.com:3000' config.log_level = :debug # Settings specified here will take precedence over those in config/application.rb. diff --git a/rails/db/seeds.rb b/rails/db/seeds.rb index e734a64..93e2845 100644 --- a/rails/db/seeds.rb +++ b/rails/db/seeds.rb @@ -98,7 +98,7 @@ # end # # create initial work node -# BookWormApiSchema.execute( +# BookWormSchema.execute( # sign_in_mutation, # variables: { # email: user_1.email, @@ -107,7 +107,7 @@ # ) # work_node_response = -# BookWormApiSchema.execute( +# BookWormSchema.execute( # create_work_node_mutation, # variables: { # investigationId: investigation_1.id.to_s, @@ -122,7 +122,7 @@ # work_node_response['data']['createWorkNode']['work']['openalexId'] # response = -# BookWormApiSchema.execute( +# BookWormSchema.execute( # add_references_mutation, # variables: { # openalexId: work_node_openalex_id, @@ -134,7 +134,7 @@ # ).to_h # investigation_response = -# BookWormApiSchema.execute( +# BookWormSchema.execute( # investigation_query, # variables: { # id: investigation_1.id diff --git a/rails/lib/tasks/load_works.rake b/rails/lib/tasks/load_works.rake index 49c0aa3..76a891b 100644 --- a/rails/lib/tasks/load_works.rake +++ b/rails/lib/tasks/load_works.rake @@ -30,7 +30,7 @@ namespace :data_import do language: row[12] } - if works.count >= 5000 + if works.count >= 10000 Work.insert_all(works) works = [] end diff --git a/rails/package-lock.json b/rails/package-lock.json index ae03999..9a251e4 100644 --- a/rails/package-lock.json +++ b/rails/package-lock.json @@ -1,5 +1,5 @@ { - "name": "bookworm", + "name": "rails", "lockfileVersion": 2, "requires": true, "packages": {