Module: Buhos::SchemaCreation

Defined in:
lib/buhos/create_schema.rb

Overview

Module to create a blank, but usable schema for Buhos Used a on installer and to create clean schemas for testing

Example:

db=Sequel.connect('sqlite::memory:', :encoding => 'utf8',:reconnect=>false,:keep_reference=>false)
Buhos::SchemaCreation.create_db_from_scratch(db)

db should have a correct and usable version of Buhos.

Constant Summary collapse

VIEWS_BN = 
["sr_###_references_between_cd_rtr_n",
          "sr_###_resolutions_full_text",
          "sr_###_resolutions_references",
          "sr_###_resolutions_sta",
          "sr_###_references_between_cd_n",
          "sr_###_references_between_cd",
          "sr_###_bib_references",
          "sr_###_cd_id",
          "sr_###_record_id_table",
          "sr_###_reference_id_table",
          "sr_###_all_id_table"
]
BIBLIOGRAPHICAL_DATABASES = 
["scopus", "sage", "wos", "scielo", "ebscohost",
"refworks", "ieee", "generic", "pubmed", "lilacs",
"proquest", "bvs" ]

Insert bootstrap data collapse

Class Method Summary collapse

Class Method Details

.allocate_authorizations_to_roles(db) ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 436

def self.allocate_authorizations_to_roles(db)
  analyst_permits = ['review_view', 'review_analyze', 'message_view', 'message_edit', 'search_view', 'search_edit',
                     'record_view', 'record_edit', 'reference_view', 'reference_edit', 'file_view',
                     'canonical_document_view', 'group_view']
  analyst_permits.each do |auth|
    db[:authorizations_roles].replace(:authorization_id => auth, :role_id => 'analyst') if db[:authorizations_roles].where(:authorization_id => auth, :role_id => 'analyst').count==0
   end

  guest_permits = ['review_view', 'message_view', 'message_edit', 'search_view', 'record_view',
                   'reference_view', 'file_view', 'canonical_document_view', 'group_view']
  guest_permits.each do |auth|
    db[:authorizations_roles].replace(:authorization_id => auth, :role_id => 'guest') if db[:authorizations_roles].where(:authorization_id => auth, :role_id => 'guest').count==0
  end
end

.allocate_users_to_groups(db, id_admin, id_analyst, id_guest) ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 496

def self.allocate_users_to_groups(db, id_admin, id_analyst, id_guest)
  if db[:groups][id:1]
    group_id = 1
  else
    group_id = db[:groups].insert(:id=>1,:group_administrator => id_admin, :description => "First group, just for demostration", :name => "demo group")
  end
  insert_group_user_if_not_exists(db,group_id, id_admin)
  insert_group_user_if_not_exists(db,group_id, id_analyst)
  if db[:groups][id:2]
    group_guest = 2
  else
    group_guest = db[:groups].insert(:id=>2,:group_administrator => id_admin, :description => "Guest group", :name => "guest group")
  end

  insert_group_user_if_not_exists(db,group_guest, id_admin)
  insert_group_user_if_not_exists(db,group_guest, id_guest)

end

.create_authorizations(db) ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 451

def self.create_authorizations(db)
  authorizations = [
      'canonical_document_admin',
      'canonical_document_view',
      'crossref_query',
      'file_admin',
      'file_view',
      'group_admin',
      'group_view',
      'message_edit',
      'message_view',
      'pubmed_query',
      'record_edit',
      'record_view',
      'reference_edit',
      'reference_view',
      'reflection',
      'review_admin',
      'review_admin_view',
      'semantic_scholar_query',
      'review_analyze',
      'review_edit',
      'review_view',
      'role_admin',
      'role_view',
      'scale_admin',
      'institution_admin',
      'scopus_query',
      'search_edit',
      'search_view',
      'tag_edit',
      'user_admin'
  ]
  authorizations.each do |auth|
    db[:authorizations].insert(:id => auth) unless db[:authorizations][id:auth]
    #puts(db[:authorizations_roles].where(:authorization_id => auth, :role_id => 'administrator').count)
    db[:authorizations_roles].insert(:authorization_id => auth, :role_id => 'administrator') unless db[:authorizations_roles].where(:authorization_id => auth, :role_id => 'administrator').count>0
  end
end

.create_bootstrap_data(db, language = 'en') ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 345

def self.create_bootstrap_data(db,language='en')
  db.transaction do
    create_roles(db)
    id_admin, id_analyst, id_guest = create_users(db, language)
    create_authorizations(db)
    allocate_authorizations_to_roles(db)
    allocate_users_to_groups(db, id_admin, id_analyst, id_guest)
    insert_bib_db_data(db)
    insert_taxonomies_data(db)
    insert_basic_scales(db)
  end
end

.create_db_from_scratch(db_url, language = 'en', logger = nil) ⇒ Object

Create a usable db to work on Buhos

Parameters:

  • db_url —

    a [String] with a connection that Sequel.connect understand, or a Sequel::Database

  • language (defaults to: 'en') —

    used to assign default language for users

  • logger (defaults to: nil) —

    A Logger object could be attached to database.



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# File 'lib/buhos/create_schema.rb', line 64

def self.create_db_from_scratch(db_url, language='en',logger=nil)
  require 'sequel'
  if db_url.is_a? Sequel::Database
    db=db_url
  else
    db=Sequel.connect(db_url, :encoding => 'utf8',:reconnect=>true)
  end
  db.logger=logger if logger
  Buhos::SchemaCreation.create_schema(db)
  Sequel.extension :migration
  Sequel::Migrator.run(db, "db/migrations")
  Buhos::SchemaCreation.create_bootstrap_data(db,language)
  Buhos::SchemaCreation.delete_views(db,language)
  db
end

.create_roles(db) ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 387

def self.create_roles(db)

  db[:roles].insert(:id => 'administrator', :description => 'App administrator') unless db[:roles][id:'administrator']
  db[:roles].insert(:id => 'analyst', :description => 'App analyst') unless db[:roles][id:'analyst']
  db[:roles].insert(:id => 'guest', :description => 'Guest') unless db[:roles][id:'guest']
end

.create_schema(db) ⇒ Object

Create basis schema to run Buhos. Updates to database are stored on /db/migrations, so don’t forget later to run migrations.

See Also:

  • {self{self.create_db_from_scratch}


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# File 'lib/buhos/create_schema.rb', line 83

def self.create_schema(db)
  # Sequel try to create an already created table even in table exists

  begin
    db.create_table? :roles do
      String :id, :size => 50, :primary_key => true
      String :description
    end

    db.create_table? :users do
      primary_key :id
      String :login, :size => 255, :null => false
      String :name, :size => 255
      String :password, :size => 255, :null => false
      foreign_key :role_id, :roles, :type => String, :size => 50, :null => false, :key => [:id]
      TrueClass :active, :default=>true, :null=>false
    end


    db.create_table? :groups do
      primary_key :id
      foreign_key :group_administrator, :users, :null => false, :key => [:id]
      String :description, :text => true
      String :name, :size => 255, :null => false
    end

    db.create_join_table?(:user_id => :users, :group_id=> :groups)


    db.create_table? :systematic_reviews do
      primary_key :id
      String :name, :size => 255
      Date :date_creation
      String :description, :text => true
      String :objectives, :text => true
      Integer :year_start
      Integer :year_end
      String :keywords, :text =>true
      foreign_key :group_id, :groups, :null => false, :key => [:id]
      foreign_key :sr_administrator, :users, :key => [:id]
      TrueClass :active, :default => true, :null => false
      String :stage, :default => "search", :size => 32, :null => false

      index [:sr_administrator], :name => :sr_administrator_index
      index [:group_id], :name => :group_id_i
    end

    # Systematic review taxonomies

    db.create_table? :sr_taxonomies do
      primary_key :id
      String :name # Should be included on locale later
      String :description, :text=>true # Should be included on locale later
    end

    db.create_table? :sr_taxonomy_categories do
      primary_key :id
      foreign_key :srt_id, :sr_taxonomies, :null => false, :key => [:id]
      String :name, :size=>50 # Should be included on locale later
      String :description # Should be included on locale later
      index [:name]
    end


    db.create_table? :systematic_review_srtcs do
      foreign_key :srtc_id, :sr_taxonomy_categories, :null => false, :key => [:id]
      foreign_key :sr_id, :systematic_reviews, :null => false, :key => [:id]
      primary_key [:srtc_id, :sr_id]
    end



    db.create_table? :bibliographic_databases do
      primary_key :id
      String :name, :size => 255
      String :description, :text => true
    end


    db.create_table? :canonical_documents do
      primary_key :id
      String :type, :size => 255
      String :title, :text => true
      String :author, :text => true
      String :date, :size => 255
      String :journal, :text => true
      String :volume, :size => 255
      String :number, :size => 255
      String :pages, :size => 255
      String :book_name, :text => true
      String :editors, :text => true
      String :proceedings, :text => true
      String :place, :size => 255
      String :editorial, :size => 255
      String :doi, :size => 255
      String :pubmed, :size => 255
      Integer :year, :null => false
      String :journal_abbr, :size => 255
      longtext :abstract
      Integer :duplicated
      String :url, :text => true
      String :wos_id, :size => 32
      String :scopus_id, :size => 255
      String :ebscohost_id, :size => 255
      String :scielo_id, :size => 255
      String :refworks_id, :size => 255
    end

    db.create_table? :canonical_authors do
      primary_key :id
      String :surname, :size => 255
      String :family_name, :size => 255
      String :email, :size => 255
      String :scopus_id, :size => 255
      String :wos_id, :size => 255
    end

    db.create_table? :canonical_document_authors do
      foreign_key :canonical_document_id, :canonical_documents, :null => false, :key => [:id]
      foreign_key :canonical_author_id, :canonical_authors, :null => false, :key => [:id]
      String :affiliation, :size => 255
      String :email, :size => 255
      index [:canonical_author_id], :name => :canonical_author_id_index
      primary_key [:canonical_document_id, :canonical_author_id]
    end

    db.create_table? :searches do
      primary_key :id
      foreign_key :systematic_review_id, :systematic_reviews, :null => false, :key => [:id]
      foreign_key :bibliographic_database_id, :bibliographic_databases, :null => false, :key => [:id]
      Date :date_creation
      String :search_criteria, :text => true
      String :description, :text => true
      File   :file_body, size: :long
      String :filetype, :size => 50
      String :filename, :size => 128

      index [:bibliographic_database_id], :name => :bibliographic_database_id_index
      index [:date_creation]
      index [:systematic_review_id]
    end

    db.create_table? :records do
      primary_key :id
      foreign_key :bibliographic_database_id , :bibliographic_databases, :null => false, :key => [:id]
      String :uid, :text => true
      String :type, :size => 255
      String :title, :text => true
      String :author, :text => true
      String :date, :size => 255
      String :journal, :text => true
      String :volume, :size => 255
      String :number, :size => 255
      String :pages, :size => 255
      String :book_name, :text => true
      String :editors, :text => true
      String :proceedings, :text => true
      String :place, :size => 255
      String :publisher, :size => 255
      String :doi, :size => 255
      String :pmid, :size => 255
      String :arxiv_id, :size => 255
      foreign_key :canonical_document_id, :canonical_documents, :key => [:id]
      String :journal_abbr, :size => 128
      Integer :year
      longtext :abstract
      String :url, :text => true

      index [:bibliographic_database_id]
      index [:canonical_document_id]
    end

    db.create_table? :bib_references do
      String :id, :primary_key => true
      String :text, :text => true
      String :doi, :size => 255
      foreign_key :canonical_document_id, :canonical_documents, :key => [:id]
      index [:canonical_document_id]
    end

    db.create_join_table?(:search_id => :searches, :record_id => :records)


    db.create_join_table?({:reference_id => {:table => :bib_references, :type => String}, :record_id => :records}, {:name=>:records_references})

    db.create_table? :authorizations do
      String :id, :size => 50, :primary_key => true
      String :description, :size => 255
    end


    db.create_table? :configurations do
      String :id, :primary_key => true
      String :value , :text => true
    end

    db.create_table? :authorizations_roles do
      foreign_key :authorization_id, :authorizations, :type => String, :size => 50, :null => false, :key => [:id]
      foreign_key :role_id, :roles, :type => String, :size => 50, :null => false, :key => [:id]

      primary_key [:authorization_id, :role_id]

      index [:role_id]
    end


    db.create_table? :crossref_queries do
      String :id, :size => 100, :primary_key => true
      String :query, :text => true
      longtext  :json
    end


    db.create_table? :crossref_dois do
      String :doi, :size => 100, :primary_key => true
      String :bibtex, :text => true
      longtext :json
    end

    db.create_table? :scopus_abstracts do
      String :id, :primary_key => true
      longtext :xml
      String :doi, :size => 255
    end

    db.create_table? :decisions do
      foreign_key :systematic_review_id, :systematic_reviews, :null => false, :key => [:id]
      foreign_key :canonical_document_id, :canonical_documents, :null => false, :key => [:id]
      foreign_key :user_id, :users, :null => false, :key => [:id]
      String :stage, :size => 32, :null => false
      String :decision, :size => 255
      String :commentary, :text => true

      primary_key [:systematic_review_id, :user_id, :canonical_document_id, :stage]

      index [:canonical_document_id]
      index [:systematic_review_id]
      index [:systematic_review_id, :user_id, :stage]
      index [:user_id]
    end
    db.create_table? :resolutions do
      foreign_key :systematic_review_id, :systematic_reviews, :null => false, :key => [:id]
      foreign_key :canonical_document_id, :canonical_documents, :null => false, :key => [:id]
      foreign_key :user_id, :users, :null => false, :key => [:id]
      String :stage, :size => 32, :null => false
      String :resolution, :size => 255
      String :commentary, :text => true

      primary_key [:systematic_review_id, :canonical_document_id, :stage]

      index [:canonical_document_id]
      index [:systematic_review_id]
      index [:systematic_review_id, :canonical_document_id]
    end
  end

end

.create_users(db, language) ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 375

def self.create_users(db, language)
  id_admin = (db, 'admin')
  id_admin ||= db[:users].insert(:login => 'admin', :name => 'Administrator', :password => ::Digest::SHA1.hexdigest('admin'), :role_id => 'administrator', :active => 1, :language => language)

  id_analyst = (db, 'analyst')
  id_analyst ||= db[:users].insert(:login => 'analyst', :name => 'Analyst', :password => ::Digest::SHA1.hexdigest('analyst'), :role_id => 'analyst', :active => 1, :language => language)

  id_guest = (db, 'guest')
  id_guest ||= db[:users].insert(:login => 'guest', :name => 'Guest', :password => ::Digest::SHA1.hexdigest('guest'), :role_id => 'guest', :active => 1, :language => language)
  return id_admin, id_analyst, id_guest
end

.delete_views(db, language = 'en') ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 358

def self.delete_views(db,language='en')
#require 'logger'
#db.loggers << Logger.new($stdout)
  db[:systematic_reviews].each do |rev|
    rev_id=rev[:id]
      VIEWS_BN.each do  |view_n|
        table_name=view_n.gsub("###", rev_id.to_s)
        if db.table_exists?(table_name.to_sym)
          db.transaction do
            db.drop_view(table_name.to_sym)
          end
        end
      end
  end
end

.get_id_user_by_login(db, login) ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 340

def self.(db,)
  user=db[:users][:login=>]
  user ? user[:id] :nil
end

.insert_basic_scales(db) ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 421

def self.insert_basic_scales(db)
  scales = {
      1=>{-99=>'not_applicable', -98=>'cant_say', 0=>'No', 1=>'Yes'},
      2=>{-99=>'not_applicable', -98=>'cant_say', 0=>'No', 1=>'Partial', 2=>'Complete'}
  }

    db[:scales].insert(:id=>1, :name=>::I18n::t("scales.dichomotic"), :description=>::I18n::t('scales.dichotomic_description')) unless db[:scales][id:1]
    db[:scales].insert(:id=>2, :name=>::I18n::t("scales.three_values"), :description=>::I18n::t('scales.three_values_description'))  unless db[:scales][id:2]

  scales.each_pair do |scale_id, values|
    values.each_pair do |value, name|
      db[:scales_items].insert(scale_id:scale_id, value:value, name: ::I18n::t("scales.#{name}")) if db[:scales_items].where(scale_id:scale_id, value:value).count==0
    end
  end
end

.insert_bib_db_data(db) ⇒ Object

Insert data for bibliographic databases



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# File 'lib/buhos/create_schema.rb', line 415

def self.insert_bib_db_data(db)
  BIBLIOGRAPHICAL_DATABASES.each do |bib_db|
    bib_db_o=db[:bibliographic_databases][:name=>bib_db]
    db[:bibliographic_databases].insert(:name => bib_db) unless bib_db_o
  end
end

.insert_group_user_if_not_exists(db, group_id, user_id) ⇒ Object 



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# File 'lib/buhos/create_schema.rb', line 491

def self.insert_group_user_if_not_exists(db, group_id, user_id)
  if db[:groups_users].where(:group_id => group_id, :user_id => user_id).count==0
    db[:groups_users].insert(:group_id => group_id, :user_id => user_id)
  end
end

.insert_taxonomies_data(db) ⇒ Object

Insert data for taxonomies



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# File 'lib/buhos/create_schema.rb', line 395

def self.insert_taxonomies_data(db)
  taxonomies = {
      "focus" => ["practice_or_application", "theory", "research_methods", "research_results"],
      "objectives" => ["critical", "main_themes", "integration"],
      "perspective" => ["neutral", "adoption_of_posture"],
      "coverage" => ["exhaustive", "exhaustive_with_selection", "representative", "essential"],
      "organization" => ["methodology", "conceptual", "historical"],
      "receiver" => ["academics_specialist", "academics_general", "practicians_politics", "general_public"]

  }

  taxonomies.each_pair do |category, values|
    f_id = db[:sr_taxonomies][:name=>category] && db[:sr_taxonomies][:name=>category][:id]
    f_id = db[:sr_taxonomies].insert(:name => category) unless f_id
    values.each do |name|
      db[:sr_taxonomy_categories].insert(:srt_id => f_id, :name => name) if  db[:sr_taxonomy_categories].where(:srt_id => f_id, :name => name).empty?
    end
  end
end