genome/dgi-db

module DataModel
  class GeneClaim < ::ActiveRecord::Base
    include Genome::Extensions::UUIDPrimaryKey
    belongs_to :gene
    has_and_belongs_to_many :gene_claim_categories, :join_table => 'gene_claim_categories_gene_claims'
    has_many :gene_claim_aliases, inverse_of: :gene_claim, dependent: :delete_all
    has_many :gene_claim_attributes, inverse_of: :gene_claim, dependent: :delete_all
    belongs_to :source, inverse_of: :gene_claims, counter_cache: true
    has_many :interaction_claims, inverse_of: :gene_claim
    has_many :drug_claims, through: :interaction_claims

    def self.for_search
      eager_load(gene: [gene_claims: {interaction_claims: { source: [], drug_claim: [:source], interaction_claim_types: [], gene_claim: [gene: [gene_claims: [:gene_claim_categories]]]}}])
    end

    def self.for_gene_categories
      eager_load(gene: [gene_claims: [:source, :gene_claim_categories]])
    end

    def self.for_show
      eager_load(:gene, :source, :gene_claim_aliases, :gene_claim_attributes)
    end

    def self.for_gene_id_mapping
      eager_load(gene: [gene_claims: [:source]])
    end

    def self.for_tsv
      includes(:gene, :source)
    end

    def source_db_name
      self.source.source_db_name
    end

    def sort_value
      GeneClaimSortOrder.sort_value(self.source_db_name)
    end

    def original_data_source_url
      base_url = self.source.base_url
      name = self.name
      case self.source.source_db_name
        when 'DrugBank'
          [base_url, 'biodb', 'bio_entities', name].join('/')
        when 'CIViC'
          [base_url, 'links', 'entrez_name', name].join('/')
        when 'PharmGKB'
          pharmgkb_id = self.gene_claim_aliases.find{|a| a.nomenclature == 'PharmGKB ID'}.alias
          [base_url, 'gene', pharmgkb_id].join('/')
        when 'TTD'
          ttd_id = self.gene_claim_aliases.find{|a| a.nomenclature == 'TTD Target ID'}.alias
          [base_url, 'data', 'target',  'details', ttd_id].join('/')
        when 'JAX-CKB'
          entrez_id = self.gene_claim_aliases.select{|a| a.nomenclature == 'CKB Entrez Id'}.first.alias
          base_url + entrez_id
        when 'GO'
          uniprot_alias = self.gene_claim_aliases.select{|a| a.nomenclature == 'UniProtKB ID'}.first
          if uniprot_alias.nil?
            'http://amigo.geneontology.org/amigo/search/bioentity?q=' + name
          else
            entrez_id = uniprot_alias.alias
            base_url + entrez_id
          end
        when 'OncoKB'
          'http://oncokb.org/#/gene/' + name
        when 'ChemblInteractions'
          'https://www.ebi.ac.uk/chembl/g/#search_results/all/query=' + name
        when 'Pharos'
          'https://pharos.nih.gov/targets?q=' + name
        when 'GuideToPharmacologyInteractions', 'GuideToPharmacologyGenes'
          'http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=' + name
        when 'MyCancerGenome', 'CancerCommons', 'ClearityFoundationBiomarkers', 'ClearityFoundationClinicalTrial',
            'MyCancerGenomeClinicalTrial', 'MskImpact', 'CarisMolecularIntelligence', 'CGI', 'FDA', 'NCI',
            'HingoraniCasas', 'TALC', 'Tempus', 'FoundationOneGenes', 'DoCM', 'COSMIC', 'Oncomine'
          base_url
        else
          base_url + name
      end
    end
  end
end