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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" : "")
Severity: Minor
Found in app/controllers/interaction_claims_controller.rb - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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}
Severity: Minor
Found in lib/genome/updaters/get_go.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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']
Severity: Minor
Found in lib/genome/importers/pharmgkb/new_pharmgkb.rb - About 1 hr to fix

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

      def group_map(drug)
    hash = drug_claims.each_with_object({}) do |drug_claim, h|
      source_db_name = drug_claim.source.source_db_name
      names = drug_claim.drug_claim_aliases.map{|a| a.alias} << drug_claim.name
      names.each do |name|
    Severity: Major
    Found in app/presenters/drug_presenter.rb and 1 other location - About 1 hr to fix
    app/presenters/gene_presenter.rb on lines 72..84

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 59.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

      def group_map(gene)
    hash = gene_claims.each_with_object({}) do |gene_claim, h|
      source_db_name = gene_claim.source.source_db_name
      names = gene_claim.gene_claim_aliases.map{|a| a.alias} << gene_claim.name
      names.each do |name|
    Severity: Major
    Found in app/presenters/gene_presenter.rb and 1 other location - About 1 hr to fix
    app/presenters/drug_presenter.rb on lines 17..29

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 59.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    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
    Severity: Minor
    Found in lib/utils/uniquify_claims.rb - About 1 hr to fix

      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')
      Severity: Minor
      Found in lib/genome/importers/drug_bank/new_drug_bank.rb - About 1 hr to fix

        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'
        Severity: Minor
        Found in app/sort_orders/interaction_result_sort_order.rb - About 1 hr to fix

          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])
          Severity: Minor
          Found in app/searches/lookup_genes.rb - About 1 hr to fix

            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 = []
            Severity: Minor
            Found in lib/genome/groupers/drug_grouper.rb - About 1 hr to fix

              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
              Severity: Minor
              Found in lib/utils/uniquify_claims.rb - About 1 hr to fix

                Similar blocks of code found in 2 locations. Consider refactoring.
                Open

                            drug_name = row['Entity1_name']
            pharmgkb_drug_id = row['Entity1_id']
            gene_name = row['Entity2_name']
            pharmgkb_gene_id = row['Entity2_id']
            drug_claim = create_drug_claim(drug_name, drug_name, 'PharmGKB Drug Name')
                Severity: Major
                Found in lib/genome/importers/pharmgkb/new_pharmgkb.rb and 1 other location - About 1 hr to fix
                lib/genome/importers/pharmgkb/new_pharmgkb.rb on lines 48..59

                Duplicated Code

                Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                Tuning

                This issue has a mass of 58.

                We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                Refactorings

                Further Reading

                Similar blocks of code found in 2 locations. Consider refactoring.
                Open

                          gene_name = row['Entity1_name']
          pharmgkb_gene_id = row['Entity1_id']
          drug_name = row['Entity2_name']
          pharmgkb_drug_id = row['Entity2_id']
          drug_claim = create_drug_claim(drug_name, drug_name, 'PharmGKB Drug Name')
                Severity: Major
                Found in lib/genome/importers/pharmgkb/new_pharmgkb.rb and 1 other location - About 1 hr to fix
                lib/genome/importers/pharmgkb/new_pharmgkb.rb on lines 63..74

                Duplicated Code

                Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                Tuning

                This issue has a mass of 58.

                We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                Refactorings

                Further Reading

                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'
                Severity: Critical
                Found in lib/genome/normalizers/interaction_claim_type.rb - About 1 hr to fix

                  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);
                  Severity: Minor
                  Found in app/assets/javascripts/jquery.cookie.js - About 1 hr to fix

                    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
                    Severity: Minor
                    Found in lib/utils/uniquify_claims.rb - About 1 hr to fix

                      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]
                      Severity: Minor
                      Found in app/controllers/application_controller.rb - About 1 hr to fix

                      Cognitive Complexity

                      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                      A method's cognitive complexity is based on a few simple rules:

                      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                      • Code is considered more complex for each "break in the linear flow of the code"
                      • Code is considered more complex when "flow breaking structures are nested"

                      Further reading

                      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
                      Severity: Minor
                      Found in lib/genome/groupers/interaction_grouper.rb - About 1 hr to fix

                      Cognitive Complexity

                      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                      A method's cognitive complexity is based on a few simple rules:

                      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                      • Code is considered more complex for each "break in the linear flow of the code"
                      • Code is considered more complex when "flow breaking structures are nested"

                      Further reading

                      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])
                      Severity: Minor
                      Found in app/searches/lookup_genes.rb - About 1 hr to fix

                      Cognitive Complexity

                      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                      A method's cognitive complexity is based on a few simple rules:

                      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                      • Code is considered more complex for each "break in the linear flow of the code"
                      • Code is considered more complex when "flow breaking structures are nested"

                      Further reading

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

                            def self.trust_level_map
      {
        'Expert curated' =>
          [
            'MyCancerGenome',
                      Severity: Minor
                      Found in lib/genome/normalizers/source_trust_level.rb - About 1 hr to fix
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