Avoid deeply nested control flow statements.

Open

                        if isinstance(datum, tuple):
                            datum = ';'.join(str(x) for x in datum)
                        datum = str(datum).replace("\t", '')

Method initialize has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def initialize(collection, request, item_presenter_type, pagination_presenter_type, additional_meta = {}, page_state_param_names = [])

Avoid deeply nested control flow statements.

Open

                        if species == '9606':  # Grab human only
                            wf.write(line_ascii)

Method import has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

      def self.import(tsv_path, rowtype, source_info, header = true, row_delimiter = "\t",  &block)

Method uniquify_gene_claims has a Cognitive Complexity of 8 (exceeds 5 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

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Method uniquify_drug_claims has a Cognitive Complexity of 8 (exceeds 5 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

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Method create_gene_claim_aliases has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def create_gene_claim_aliases (gene_claim, line)
      create_gene_claim_alias(gene_claim, line['target'], 'GuideToPharmacology Name') unless blank?(line['target'])
      unless blank?(line['target_ensembl_gene_id'])
        line['target_ensembl_gene_id'].split('|').each do |ensembl_id|
          create_gene_claim_alias(gene_claim, ensembl_id, 'Ensembl ID')

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Avoid deeply nested control flow statements.

Open

                  if records_with_trade_name.size == 1
                    return records_with_trade_name.first
                  elsif records_with_trade_name.size == 0
                    return get_normalized_record_or_drug_for_chembl_id(get_min_chembl_id(chembl_ids_for_records(records_with_highest_max_phase)))
                  else

Avoid deeply nested control flow statements.

Open

                        if identifier.find('entry:resource',ns).text == 'HUGO Gene Nomenclature Committee (HGNC)':
                            hgnc_gene_acc = identifier.find('entry:identifier', ns).text
                            # Some identifiers are incorrectly labeled by DrugBank
                            r = re.compile(r'^\d+$')
                            if hgnc_gene_acc.startswith('GNC:'):

Method parse_interaction_information has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def parse_interaction_information(variant)
      return [] unless variant.include?('meta')
      drug_data = variant['meta'].find { |table| table.include?('Drug Interaction Data') }
      return [] unless drug_data.present?
      fields = drug_data['Drug Interaction Data']['fields']

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Method add_interaction_claim_publications has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def add_interaction_claim_publications(interaction_claim, source_string)
      if source_string.include?(';')
        source_string.split(';').each do |value|
          value.split(/[^\d]/).each do |pmid|
            unless pmid.nil? || pmid == ''

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Avoid deeply nested control flow statements.

Open

                        if not datum or datum == 'None':
                            datum = 'N/A'
                        out.append(datum)

Method add_interaction_claim_publications has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def add_interaction_claim_publications(interaction_claim, source_string)
      if source_string.include?(';')
        source_string.split(';').each do |value|
          value.split(/[^\d]/).each do |pmid|
            unless pmid.nil? || pmid == ''

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Consider simplifying this complex logical expression.

Open

        elsif val == 'incorporation into and destabilization' || val == 'intercalation' || val == 'desensitize the target' || val == 'disrupter' || val == 'intercalator' || val == 'downregulator'
          'negative modulator'
        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'

Consider simplifying this complex logical expression.

Open

          unless pmid.nil? || pmid == "" || pmid == '""' || pmid == "''" || pmid[0] =='-' || pmid =='15288657'
            create_interaction_claim_publication(interaction_claim, pmid)
          end

Method validate_search_request has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

  def validate_search_request(params)
    bad_request("Please enter at least one gene to search!") if params[:genes].blank?
    params[:gene_categories] = DataModel::GeneClaimCategory.all_category_names unless params[:gene_categories]
    params[:sources] = DataModel::Source.potentially_druggable_source_names unless params[:sources]
    params[:source_trust_levels] = DataModel::SourceTrustLevel.all_trust_levels unless params[:source_trust_levels]

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Method create_entries_for_evidence_item has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def create_entries_for_evidence_item(variant, ei, source)
      ei['drugs'].select { |d| valid_drug?(d) }.each do |drug|
        gc = create_gene_claim(variant['entrez_name'], 'Entrez Gene Symbol')
        create_gene_claim_aliases(gc, variant)
        if ei['clinical_significance'] == 'Resistance'

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Function extract has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def extract(self, file):
        with gzip.open(file, 'rb') as rf:
            with open(os.path.join(self.download_path, file.rsplit('.', 1)[0] + '.human'), 'w') as wf:
                for i, line in enumerate(rf):
                    line_ascii = line.decode('utf-8')

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Method create_drug_claims has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def create_drug_claims(row, gene_claim, fusion_protein)
      if row['Drug'].include?(',')
        combination_therapy = row['Drug']
        row['Drug'].split(',').each do |drug|
          drug_claim = create_drug_claim(drug, drug, 'FDA Drug Name')

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Avoid too many return statements within this method.

Open

                return get_normalized_record_or_drug_for_chembl_id(get_min_chembl_id(chembl_ids_for_records(records_with_trade_name)))