openSNP/snpr

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Showing 71 of 71 total issues

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

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

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

      def parse_iyg(rows)
        db_snp_names = {
          "MT-T3027C" => "rs199838004", "MT-T4336C" => "rs41456348",
          "MT-G4580A" => "rs28357975", "MT-T5004C" => "rs41419549",
          "MT-C5178a" => "rs28357984", "MT-A5390G" => "rs41333444",
    Severity: Minor
    Found in app/workers/parsing.rb - About 1 hr to fix

      Method perform has 26 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        def perform(phenotype_id, variation, target_address)
          @user_phenotypes = UserPhenotype
            .where(phenotype_id: phenotype_id)
            .search(variation)
          @genotyping_files = []
      Severity: Minor
      Found in app/workers/zipgenotypingfiles.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_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 231..236

        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_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 222..228

        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

        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

        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

          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 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

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

              def zip_genotype_files(genotypes, zipfile)
                genotypes.each do |gen_file|
                  yob = gen_file.user.yearofbirth
                  sex = gen_file.user.sex
                  to_zip_file = "#{Rails.root}/public/data/#{gen_file.fs_filename}"
            Severity: Minor
            Found in app/workers/zipfulldata.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_user_csv has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
            Open

              def create_user_csv(genotypes, zipfile)
                phenotypes = Phenotype.all
                csv_file_name = "#{tmp_dir}/dump#{time_str}.csv"
                csv_head = %w(user_id genotype_filename date_of_birth chrom_sex openhumans_name)
                csv_head.concat(phenotypes.map(&:characteristic))
            Severity: Minor
            Found in app/workers/zipfulldata.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

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