lib/tasks/updaters.rake
namespace :dgidb do
  namespace :update do
    desc 'update CIViC'
    task civic: :environment do
      civic = Genome::Updaters::GetCivic.new
      if civic.is_current?
        puts('is current')
      else
        civic.to_tsv
        if DataModel::Source.where('lower(sources.source_db_name) = ?', 'civic').any?
          Utils::Database.delete_source('CIViC')
        end
        Genome::Importers::Civic.run(civic.default_savefile, civic.new_version)
      end
    end

    desc 'update DoCM'
    task docm: :environment do
      docm = Genome::Updaters::GetDocm.new
      if docm.is_current?
        puts('is current')
      else
        docm.to_tsv
        if DataModel::Source.where('lower(sources.source_db_name) = ?', 'docm').any?
          Utils::Database.delete_source('DoCM')
        end
        Genome::Importers::Docm.run(docm.default_savefile, docm.new_version)
      end
    end

    desc 'update GO'
    task go: :environment do
      go = Genome::Updaters::GetGo.new
      if go.is_current?
        puts('is current')
      else
        go.to_tsv
        if DataModel::Source.where('lower(sources.source_db_name) = ?', 'go').any?
          Utils::Database.delete_source('GO')
        end
        Genome::Importers::Go.run(go.default_savefile, go.new_version)
      end
    end

    desc 'update DrugBank' # TODO: Update DrugBank
    task drugbank: :environment do
      go = Genome::Updaters::GetGo.new
      if go.is_current?
        puts('is current')
      else
        go.to_tsv
        if DataModel::Source.where('lower(sources.source_db_name) = ?', 'go').any?
          Utils::Database.delete_source('GO')
        end
        Genome::Importers::Go.run(go.default_savefile, go.new_version)
      end
    end

    desc 'update Entrez'
    task entrez: :environment do
      entrez = Genome::Updaters::GetEntrez.new
      if entrez.is_current?
        puts('is current')
      else
        entrez.to_tsv
        if DataModel::Source.where('lower(sources.source_db_name) = ?', 'entrez').any?
          Utils::Database.delete_source('Entrez')
        end
        Genome::Importers::Entrez.run(entrez.local_path('gene_info.human'))
      end

    end

    desc 'update PubChem'
    task pubchem: :environment do
      # Unlike other importers, PubChem deletes records as part of updater
      Genome::Updaters::GetPubchem.run!
    end

    desc 'update all'
    task all: :environment do
      # Code for doing various updates
      # Entrez first
      puts 'Updating Entrez...'
      Rake::Task['dgidb:update:entrez'].execute

      # Other sources
      puts 'Updating CIViC...'
      Rake::Task['dgidb:update:civic'].execute
      puts 'Updating DoCM...'
      Rake::Task['dgidb:update:docm'].execute

      # TODO: Add GO
      # TODO: Add DrugBank
      # TODO: Add ChEMBL(?)

      # PubChem last
      puts 'Updating PubChem...'
      Rake::Task['dgidb:update:pubchem'].execute

      # Cleanup
      puts 'Grouping genes...'
      Genome::Groupers::GeneGrouper.run
      puts 'Importing pathways...'
      pathway_file = File.join(Rails.root, 'lib/genome/updaters/data/interactions.human')
      Genome::Importers::Entrez::EntrezGenePathwayImporter.new(pathway_file).import!
      puts 'Grouping drugs...'
      Genome::Groupers::DrugGrouper.run
      puts 'Removing undesired entries...'
      Utils::Database.destroy_common_aliases
      Utils::Database.destroy_na
      puts 'Populating source counters...'
      Genome::Normalizers::PopulateCounters.populate_source_counters
      puts 'Attempting to normalize drug types...'
      Genome::Normalizers::DrugTypeNormalizers.normalize_types
      puts 'Filling in source trust levels...'
      Genome::Normalizers::SourceTrustLevel.populate_trust_levels
      puts 'Attempting to normalize interaction types...'
      Genome::Normalizers::InteractionClaimType.normalize_types
      Rake::Task['dgidb:update:tsv']
      puts 'Exporting source TSVs...'
      Utils::TSV.update_druggable_gene_tsvs_archive
      puts 'Clearing cache...'
      Rails.cache.clear
    end

    desc 'update tsv files'
    task tsv: :environment do
      puts 'Exporting categories...'
      Utils::TSV.generate_categories_tsv
      puts 'Exporting interactions...'
      Utils::TSV.generate_interaction_claims_tsv
      puts 'Exporting genes...'
      Utils::TSV.generate_genes_tsv
      puts 'Exporting drugs...'
      Utils::TSV.generate_drugs_tsv
    end
    # desc 'generate a complete druggable categories tsv file'
    # task categories_tsv: :environment do
    #   Utils::TSV.generate_categories_tsv
    # end
  end
end
