Method match_search_terms_to_objects has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def self.match_search_terms_to_objects(search_terms, scope, filter)
    search_terms = search_terms.dup
    results_to_gene_groups = search_terms.each_with_object({}) { |term, h| h[term] = [] }

    unfiltered_gene_results = DataModel::Gene.send(scope).where(["genes.name in (?) or entrez_id in (?)", search_terms, search_terms.map {|x| Integer(x) rescue nil }.compact])

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Method trust_level_map has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def self.trust_level_map
      {
        'Expert curated' =>
          [
            'MyCancerGenome',

Method interaction_search_results has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def interaction_search_results
    if !params[:name].nil?
      params[:search_mode] = 'drugs'
      params[:identifiers] = params[:name]
      params[:gene_categories] = DataModel::GeneClaimCategory.all_category_names unless params[:gene_categories]

Method run has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def self.run(tsv_path)
        blank_filter = ->(x) { x.blank? || x == "''" || x == '""' }
        upcase = ->(x) {x.upcase}
        downcase = ->(x) {x.downcase}
        known = ->() {if :action_type.blank?

Method create_interaction_claims has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def create_interaction_claims
      api_client = ApiClient.new
      genes = get_genes(api_client)
      drugs = get_drugs(api_client)
      api_client.variants.each do |variant|

Method categories has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def categories
      {
        "KINASE" => "0016301",
        "TYROSINE KINASE" => "0004713",
        "SERINE THREONINE KINASE" => "0004674",

Method run has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def self.run(tsv_path)
        na_filter = ->(x) { x.upcase == 'N/A' }
        TSVImporter.import tsv_path, PharmgkbRow, source_info do
          interaction known_action_type: 'unknown' do
            attribute 'Interaction Type', name: 'n/a'

Method process_pubchem_file has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

      def process_pubchem_file(pubchem_file)
        alternate_names = []
        current_id = nil
        lines_processed = 0
        Zlib::GzipReader.new(pubchem_file).each_line do |line|

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Method add_drug_claim_attributes_to_drug has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

      def add_drug_claim_attributes_to_drug(drug_claim, drug)
        drug_attributes = drug.drug_attributes.pluck(:name, :value)
                              .map { |drug_attribute| drug_attribute.map(&:upcase) }
                              .to_set
        drug_claim.drug_claim_attributes.each do |drug_claim_attribute|

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Method add_member has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def self.add_member(interaction_claim)
        drug = interaction_claim.drug_claim.drug
        gene = interaction_claim.gene_claim.gene
        interaction = DataModel::Interaction.where(drug_id: drug.id, gene_id: gene.id).first_or_create
        interaction_claim.interaction = interaction

Method ambiguous_matches has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def ambiguous_matches
    unless @ambiguous_matches
      @ambiguous_matches = []
      results = ambiguous_result_presenters.uniq{|r| r.gene_categories}
      results.each do |result|

Method match_objects_to_drugs has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def self.match_objects_to_drugs(unfiltered_results, filtered_results, search_terms)
    results_to_drug_groups = search_terms.each_with_object({}) { |term, h| h[term] = [] }
    ids_to_results = filtered_results.each_with_object({}) { |result, h| h[result.id] = result}
    unfiltered_results.each do |unfiltered_result|
      result = ids_to_results[unfiltered_result.id]

Method create_interaction_claims has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def create_interaction_claims
      api_client = ApiClient.new
      api_client.genes.each do |gene|
        gene_claim = create_gene_claim(gene['geneName'], 'CKB Gene Name')
        create_gene_claim_aliases(gene_claim, gene)

Method create_gene_claims has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def create_gene_claims
      api_client = ApiClient.new
      categories.each do |category|
        start = 0
        count = 100

Method add_drug_claim_attributes_to_drug has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def add_drug_claim_attributes_to_drug(drug_claim, drug)
        drug_attributes = drug.drug_attributes.pluck(:name, :value)
                              .map { |drug_attribute| drug_attribute.map(&:upcase) }
                              .to_set
        drug_claim.drug_claim_attributes.each do |drug_claim_attribute|

Consider simplifying this complex logical expression.

Open

        elsif val == 'neutralizer' || val == 'reducer' || val == 'metabolizer' || val == 'acetylation' || val == 'chelator' || val == 'cross-linking/alkylation' || val == 'regulator'
          'modulator'
        elsif val == 'positive allosteric modulator' || val == 'regulator (upregulator)' || val == 'enhancer' || val == 'modulator (allosteric modulator)'
          'positive modulator'
        elsif val == 'inhibitor, competitive' || val == 'gating inhibitor' || val == 'inhibitor; antagonist; blocker' || val == 'inhibitor (gating inhibitor)' || val == 'growth_inhibition' || val == 'inhibition' || val == 'weak inhibitor' || val == 'aggregation inhibitor' || val == 'inhibition of synthesis' || val == "translocation inhibitor" || val == 'inhibits downstream inflammation cascades' || val == 'inactivator'

Method partition has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def partition
    if has_results?
      if is_ambiguous? && has_interactions?
          :ambiguous
      elsif is_ambiguous? && !has_interactions?

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Method sorted_claims has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def sorted_claims
    drug_claims.sort_by{ |d| [(d.drug_claim_attributes.empty? ? 1 : 0), (DrugClaimPresenter.new(d).publications.empty? ? 1 : 0), (d.drug_claim_aliases.empty? ? 1 : 0), d.sort_value] }
  end

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Method create_interaction_claims has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def create_interaction_claims
      api_client = ApiClient.new
      genes = get_genes(api_client)
      drugs = get_drugs(api_client)
      api_client.variants.each do |variant|

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Method sorted_claims has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def sorted_claims
    gene_claims.sort_by{ |g| [(g.gene_claim_attributes.empty? ? 1 : 0), (GeneClaimPresenter.new(g).publications.empty? ? 1 : 0), (g.gene_claim_aliases.empty? ? 1 : 0), g.sort_value] }
  end

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