Class GeneCategorySearchResultsPresenter has 22 methods (exceeds 20 allowed). Consider refactoring.

Open

class GeneCategorySearchResultsPresenter
  include Genome::Extensions
  attr_reader :search_results

  def initialize(search_results, params, start_time, view_context)

Function fnUpdate has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

        "fnUpdate": function ( oSettings, fnDraw ) {
            var iListLength = 5;
            var oPaging = oSettings.oInstance.fnPagingInfo();
            var an = oSettings.aanFeatures.p;
            var i, j, sClass, iStart, iEnd, iHalf=Math.floor(iListLength/2);

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Method interaction_search_results has a Cognitive Complexity of 17 (exceeds 5 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]

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Function parse has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

    def parse(self):
        self.rows = []
        with open(os.path.join(self.download_path, 'gene_info.human')) as f:
            fieldnames = ['tax_id', 'entrez_id', 'entrez_gene_symbol', 'locus_tag',
                         'entrez_gene_synonyms', 'dbXrefs', 'chromosome', 'map_loc',

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File get_drugbank.py has 257 lines of code (exceeds 250 allowed). Consider refactoring.

Open

__author__ = 'Kelsy C Cotto'

import zipfile
import os
import sys

Class InteractionSearchResultApiV1Presenter has 21 methods (exceeds 20 allowed). Consider refactoring.

Open

class InteractionSearchResultApiV1Presenter
  def initialize(search_result, identifier, interactions)
    @result = search_result
    @identifier = identifier
    @interactions = interactions.flat_map(&:interaction_claims).map{|i| InteractionWrapper.new(i)}

Method dgidb_go_terms has 52 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def dgidb_go_terms
        @dgidb_go_terms ||= [{short_name: "Kinase", full_go_name: "KinaseActivity",
                           human_readable: "Kinase", go_id: "GO0016301"},
                          {short_name: "TyrosineKinase", full_go_name: "ProteinTyrosineKinaseActivity",
                           human_readable: "Tyrosine Kinase", go_id: "GO0004713"},

Consider simplifying this complex logical expression.

Open

        elsif val =~ /other/ || val =~ /unknown/ || val == 'protector' || val == 'oxidizer' || val == 'coating agent' || val == 'dilator' || val == 'deoxidizer' || val == 'diffusing substance'|| val == 'vesicant' || val == 'gene replacement'
          'other/unknown'
        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)'

Function truncate has 48 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function truncate() {
        var data = this.data('trunk8'),
            settings = data.settings,
            width = settings.width,
            side = settings.side,

Method get_normalized_record_for_chembl_match has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

      def get_normalized_record_for_chembl_match(chembl_match)
        records = chembl_match['records']
        if records.size == 1
          return get_normalized_record_or_drug_for_chembl_id(records.first['concept_identifier'])
        else

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Method get_normalized_record_for_multi_matches has 47 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def get_normalized_record_for_multi_matches(matches)
        #2. a.
        matches_with_chembl_id = matches.select{|t, m| chembl_ids_for_records(m['records']).size > 0}
        if matches_with_chembl_id.size == 0
          matches_with_chembl_id = matches

Method match_objects_to_drugs has a Cognitive Complexity of 14 (exceeds 5 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]

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Method create_interaction_claims has a Cognitive Complexity of 14 (exceeds 5 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']

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Function fnUpdate has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        "fnUpdate": function ( oSettings, fnDraw ) {
            var iListLength = 5;
            var oPaging = oSettings.oInstance.fnPagingInfo();
            var an = oSettings.aanFeatures.p;
            var i, j, sClass, iStart, iEnd, iHalf=Math.floor(iListLength/2);

Method to_tsv has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def to_tsv
        # entrez = Genome::Updaters::GetEntrez.new
        # f = open(entrez.local_path('gene_info.gz'))
        check_files
        f = File.open(local_path('gene_info.gz'))

Method name_normalizer has 40 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def self.name_normalizer(val)
        val = val.downcase.strip
        if val == 'na' || val == 'n/a'
          'n/a'
        elsif val =~ /other/ || val =~ /unknown/ || val == 'protector' || val == 'oxidizer' || val == 'coating agent' || val == 'dilator' || val == 'deoxidizer' || val == 'diffusing substance'|| val == 'vesicant' || val == 'gene replacement'

Method uniquify_interaction_claims has a Cognitive Complexity of 13 (exceeds 5 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

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Method query_drug_claim_aliases has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

      def query_drug_claim_aliases(drug_claim_aliases)
        record = nil
        drug_claim_aliases.each do |a|
          normalized_record = find_normalized_record_for_term(a.alias)
          unless normalized_record.nil?

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Method original_data_source_url has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def original_data_source_url
      base_url = self.source.base_url
      name = self.name
      case self.source.source_db_name
        when 'DrugBank'

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

Open

      def process_drug(current_id, alternate_names)
        if alternate_names.any? { |name| existing_drugs[name.upcase.strip] }
          pubchem_primary_name = alternate_names.first.upcase.strip
          drug_claim = DataModel::DrugClaim.create(
            {