Method delete_source has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def self.delete_source(source_db_name)
      source_id = DataModel::Source.where('lower(sources.source_db_name) = ?',
        source_db_name.downcase).pluck(:id).first

      if source_id

Function eatStr has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        eatStr: function (str, side, bite_size, fill) {
            var length = str.length,
                key = utils.eatStr.generateKey.apply(null, arguments),
                half_length,
                half_bite_size;

Method import_claims has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def import_claims
      CSV.foreach(file_path, :headers => true, :col_sep => ",") do |row|
        next if row['Highest_status'] == 'Terminated' || row['Highest_status'] == 'Withdrawn from market' || row['Highest_status'].match(/Discontinued/) || row['Highest_status'] == 'Investigative'

        gene_name, gene_abbreviation = row['Target_Name'].split(' (', 2)

Method each_row has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

      def self.each_row(row_delimiter)
        f = File.open(@tsv_path)
        if @tsv_path.to_s.ends_with?('.tsv.gz')
          f = Zlib::GzipReader(f)
        end

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Method unpack_locals has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def unpack_locals(params)
    @preset_fda = (params[:approved_drug] == "checked" ? "Approved" : "")
    @preset_neo = (params[:anti_neoplastic] == "checked" ? "Anti-neoplastics" : "")
    @preset_immuno = (params[:immunotherapy] == "checked" ? "Immunotherapies" : "")
    @preset_clin = (params[:clinically_actionable] == "checked" ? "Clinically Actionable" : "")

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Method print_interaction_claim_row has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def self.print_interaction_claim_row(file_handle, interaction_claim)
      row = [
        interaction_claim.gene ? interaction_claim.gene.name : "",
        interaction_claim.gene_claim.name,
        interaction_claim.gene ? interaction_claim.gene.entrez_id : "",

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Function parse has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def parse(self):
        self.rows = []
        go_ids = [':'.join((x['go_id'][:2], x['go_id'][2:])) for x in self.dgidb_go_terms]
        category_lookup = {x['go_id']: x['human_readable'].upper() for x in self.dgidb_go_terms}

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Method create_gene_claims has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

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

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Method create_interaction_claims has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def create_interaction_claims
      CSV.foreach(file_path, :headers => true, :col_sep => "\t") do |row|
        next if row['Association'] == 'not associated' || row['Association'] == 'ambiguous'
        if row['Entity1_type'] == 'Gene' and row['Entity2_type'] == 'Chemical'
          gene_name = row['Entity1_name']

Method uniquify_gene_claims has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def self.uniquify_gene_claims
      DataModel::GeneClaim.find_each do |gc|
        all_matching_claims = DataModel::GeneClaim.where(name: gc.name, nomenclature: gc.nomenclature, source_id: gc.source_id).all
        next if all_matching_claims.length == 1

Method sort_value has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def self.sort_value(sortval)
    case sortval
      when 'CIViC'
        1
      when 'DoCM'

Method uniquify_drug_claims has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def self.uniquify_drug_claims
      DataModel::DrugClaim.find_each do |dc|
        all_matching_claims = DataModel::DrugClaim.where(name: dc.name, nomenclature: dc.nomenclature, source_id: dc.source_id).all
        next if all_matching_claims.length == 1

Method initialize has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def initialize
        @term_to_matches_dict = {}
        @term_to_record_dict = {}
        @valid_chembl_ids = []
        @invalid_chembl_ids = []

Method import_claims has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def import_claims
      CSV.foreach(file_path, :col_sep => "\t", :headers => true) do |row|
        drug_claim = create_drug_claim(row['drug_id'].upcase, row['drug_name'], 'DrugBank Drug Identifier')

        create_drug_claim_alias(drug_claim, row['drug_name'].upcase, 'DrugBank Drug Name')

Method match_search_terms_to_objects has 34 lines of code (exceeds 25 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])

Consider simplifying this complex logical expression.

Open

        elsif val == 'inhibitory immune response' || val == 'car-t-cell-therapy(dual specific)' || val == 'immunomodulator' || val == 'immunomodulator (immunostimulant)' || val == 'immune response agent' || val == 'car-t-cell-therapy' || val == 'immune response agent' || val == 'immunostimulant'
          'immunotherapy'
        elsif val == 'component of'
          'product of'
        elsif val == 'opener'

Function cookie has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    var config = $.cookie = function (key, value, options) {

        // write
        if (value !== undefined) {
            options = $.extend({}, config.defaults, options);

Method uniquify_interaction_claims has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def self.uniquify_interaction_claims
      DataModel::InteractionClaim.find_each do |ic|
        all_matching_claims = DataModel::InteractionClaim.where(drug_claim_id: ic.drug_claim_id, gene_claim_id: ic.gene_claim_id, source_id: ic.source_id).all
        next if all_matching_claims.length == 1

Method add_member has a Cognitive Complexity of 11 (exceeds 5 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

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

Open

  def validate_interaction_request(params)
    if params[:search_mode].nil?
      if params[:genes]
        params[:search_mode] = 'genes'
      elsif params[:drugs]

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