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

  def create
    @snp_comment = SnpComment.new(comment_params)
    if @snp_comment.comment_text.index(/\A(\@\#\d*\:)/) == nil
      @snp_comment.reply_to_id = -1
    else
Severity: Minor
Found in app/controllers/snp_comments_controller.rb - About 1 hr to fix

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

      def feed
    @phenotype = Phenotype.find(params[:id])
    @user_phenotypes = @phenotype.user_phenotypes
    @genotypes = []
    @user_phenotypes.each do |up|
    Severity: Minor
    Found in app/controllers/phenotypes_controller.rb and 1 other location - About 1 hr to fix
    app/controllers/picture_phenotypes_controller.rb on lines 98..111

    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 47.

    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 feed
    @phenotype = PicturePhenotype.find(params[:id])
    @user_phenotypes = @phenotype.user_picture_phenotypes
    @genotypes = []
    @user_phenotypes.each do |up|
    Severity: Minor
    Found in app/controllers/picture_phenotypes_controller.rb and 1 other location - About 1 hr to fix
    app/controllers/phenotypes_controller.rb on lines 110..123

    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 47.

    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 perform has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

      def perform(mendeley_paper_id)
     mendeley_paper = MendeleyPaper.find_by_id(mendeley_paper_id.to_i)
     return if mendeley_paper.nil?

     key_handle = File.open(::Rails.root.to_s+"/key_mendeley.txt")
    Severity: Minor
    Found in app/workers/mendeley_details.rb - About 55 mins 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

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

      def check_and_award_new_phenotypes(amount, achievement_string)
    @achievement = Achievement.find_by_award(achievement_string)
    if current_user.phenotype_creation_counter >= amount and UserAchievement.find_by_achievement_id_and_user_id(@achievement.id,current_user.id) == nil

      UserAchievement.create(achievement_id: @achievement.id, user_id: current_user.id)
    Severity: Minor
    Found in app/controllers/picture_phenotypes_controller.rb and 1 other location - About 50 mins to fix
    app/controllers/phenotypes_controller.rb on lines 225..231

    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 43.

    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

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

      def check_and_award_new_phenotypes(amount, achievement_string)
    @achievement = Achievement.find_by_award(achievement_string)
    if current_user.phenotype_creation_counter >= amount and UserAchievement.find_by_achievement_id_and_user_id(@achievement.id,current_user.id) == nil

      UserAchievement.create(achievement_id: @achievement.id, user_id: current_user.id)
    Severity: Minor
    Found in app/controllers/phenotypes_controller.rb and 1 other location - About 50 mins to fix
    app/controllers/picture_phenotypes_controller.rb on lines 129..135

    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 43.

    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

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

      def check_and_award_additional_phenotypes(amount, achievement_string)
    @achievement = Achievement.find_by_award(achievement_string)
    if current_user.phenotype_count >= amount and UserAchievement.find_by_achievement_id_and_user_id(@achievement.id,current_user.id) == nil
      UserAchievement.create(user_id: current_user.id, achievement_id: @achievement.id)
      flash[:achievement] = %(Congratulations! You've unlocked an achievement: <a href="#{url_for(@achievement)}">#{@achievement.award}</a>).html_safe
    Severity: Minor
    Found in app/controllers/phenotypes_controller.rb and 1 other location - About 50 mins to fix
    app/controllers/picture_phenotypes_controller.rb on lines 138..143

    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 43.

    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

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

      def check_and_award_additional_phenotypes(amount, achievement_string)
    @achievement = Achievement.find_by_award(achievement_string)
    if current_user.phenotype_count >= amount and UserAchievement.find_by_achievement_id_and_user_id(@achievement.id,current_user.id) == nil
      UserAchievement.create(user_id: current_user.id, achievement_id: @achievement.id)
      flash[:achievement] = %(Congratulations! You've unlocked an achievement: <a href="#{url_for(@achievement)}">#{@achievement.award}</a>).html_safe
    Severity: Minor
    Found in app/controllers/picture_phenotypes_controller.rb and 1 other location - About 50 mins to fix
    app/controllers/phenotypes_controller.rb on lines 234..239

    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 43.

    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

    Avoid deeply nested control flow statements.
    Open

          if l.strip.split(",").length == 6
        file_is_ok = true
        logger.info "file is decodeme and is ok!"
      end
    Severity: Major
    Found in app/workers/preparsing.rb - About 45 mins to fix

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

            var pictureReplyButtonCallback = function (event) {
        event.preventDefault();
        sendCommentId(document.new_comment.picture_phenotype_comment_comment_text, '@#' + this.id);
        return false;
      };
      Severity: Minor
      Found in app/assets/javascripts/script.js and 1 other location - About 45 mins to fix
      app/assets/javascripts/script.js on lines 65..69

      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 50.

      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

      Avoid deeply nested control flow statements.
      Open

          elsif genotype.filetype == "ftdna-illumina"
      # first line is of length 4
      if l.strip.split(",").length == 4
        file_is_ok = true
        logger.info "file is ftdna and is ok!"
      Severity: Major
      Found in app/workers/preparsing.rb - About 45 mins to fix

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

              var snpReplyButtonCallback = function (event) {
        event.preventDefault();
        sendCommentId(document.new_comment.snp_comment_comment_text, '@#' + this.id);
        return false;
      };
        Severity: Minor
        Found in app/assets/javascripts/script.js and 1 other location - About 45 mins to fix
        app/assets/javascripts/script.js on lines 59..63

        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 50.

        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 new
    @user_phenotype = UserPhenotype.new
    @title = 'Add variation'

    if params[:phenotype]
        Severity: Minor
        Found in app/controllers/user_phenotypes_controller.rb and 1 other location - About 40 mins to fix
        app/controllers/user_picture_phenotypes_controller.rb on lines 5..20

        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 38.

        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 new
    @user_phenotype = UserPicturePhenotype.new
    @title = 'Add variation'

    if params[:phenotype]
        Severity: Minor
        Found in app/controllers/user_picture_phenotypes_controller.rb and 1 other location - About 40 mins to fix
        app/controllers/user_phenotypes_controller.rb on lines 5..20

        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 38.

        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 show has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

          def show
    @snp = Snp.includes(:snp_comments).
      where(name: params[:id].downcase).first || not_found

    if params[:format] == 'json'
        Severity: Minor
        Found in app/controllers/snps_controller.rb - About 35 mins 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 build_user_picture_phenotype_row has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

            def build_user_picture_phenotype_row(user, picture_phenotypes, picture_zip)
      user_picture_phenotypes = user
                                .user_picture_phenotypes
                                .index_by(&:picture_phenotype_id)
        Severity: Minor
        Found in app/services/data_zipper_service/zip_user_picture_phenotypes.rb - About 35 mins 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 has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

          def create
    @genotype = Genotype.create(genotype_params)
    @genotype.user = current_user
    if @genotype.valid? && @genotype.save
      Preparsing.perform_async(@genotype.id)
        Severity: Minor
        Found in app/controllers/genotypes_controller.rb - About 35 mins 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 sortable has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
        Open

          def sortable(column, title = nil)
    title ||= column.titleize
    css_class = column == sort_column ? "current #{sort_direction}" : nil
    direction = column == sort_column && sort_direction == 'asc' ? 'desc' : 'asc'
    link_to title, { sort: column, direction: direction }, class: css_class
        Severity: Minor
        Found in app/helpers/application_helper.rb - About 25 mins 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 responses has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
        Open

          def responses
    begin
      @position = params[:pos].to_i
      @chromosome = params[:chrom]
      @allele = params[:allele].upcase
        Severity: Minor
        Found in app/controllers/beacon_controller.rb - About 25 mins 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

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

                               @snps.each do |s|
                           # there is only one user_snp for each snps
                           if @types != []
                             @single_user_snp = s.user_snps.find_by_genotype_id(@genotype.id)
                             if @types.include? @single_user_snp.local_genotype
        Severity: Minor
        Found in app/controllers/das_controller.rb and 1 other location - About 25 mins to fix
        app/controllers/das_controller.rb on lines 46..54

        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 30.

        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

        Severity
        Category
        Status
        Source
        Language