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lib/seek/data/bio_samples.rb

Summary

Maintainability
F
1 wk
Test Coverage

File bio_samples.rb has 800 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require "libxml"

module Seek
  module Data
    class BioSamples
Severity: Major
Found in lib/seek/data/bio_samples.rb - About 1 day to fix

    Method populate_sample has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.
    Open

        def populate_sample sample_json, specimen, assay=nil


        sample_title = sample_json["title"]
        sample_type = sample_json["type"]
    Severity: Minor
    Found in lib/seek/data/bio_samples.rb - About 5 hrs 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

    Class BioSamples has 33 methods (exceeds 20 allowed). Consider refactoring.
    Open

        class BioSamples

    attr_reader :investigation, :study, :assay, :assay_class, :assay_type,
                :units, :treatments, :organisms, :strains, :culture_growth_type, :tissue_and_cell_types,
                :specimens, :samples,  :specimen_names, :sample_names, :treatments,:treatments_text,
    Severity: Minor
    Found in lib/seek/data/bio_samples.rb - About 4 hrs to fix

      Method build_all_bio_sample_json has 92 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          def build_all_bio_sample_json sheet

      # population order should NOT change, DB is populated only if @to_populate is set to be true

      # probing number of rows with data in sheet
      Severity: Major
      Found in lib/seek/data/bio_samples.rb - About 3 hrs to fix

        Method populate_specimen has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
        Open

            def populate_specimen specimen_json

      specimen_title = specimen_json["title"]
      sex = specimen_json["sex"]
      age = specimen_json["age"]
        Severity: Minor
        Found in lib/seek/data/bio_samples.rb - About 3 hrs 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 populate_treatment has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
        Open

            def populate_treatment treatment_json, specimen=nil, sample=nil

        start_value = treatment_json["start value"]
        end_value = treatment_json["end value"]
        standard_deviation = treatment_json["standard deviation"]
        Severity: Minor
        Found in lib/seek/data/bio_samples.rb - About 3 hrs 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 populate_specimen has 86 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

            def populate_specimen specimen_json

      specimen_title = specimen_json["title"]
      sex = specimen_json["sex"]
      age = specimen_json["age"]
        Severity: Major
        Found in lib/seek/data/bio_samples.rb - About 3 hrs to fix

          Method populate_sample has 78 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

              def populate_sample sample_json, specimen, assay=nil


        sample_title = sample_json["title"]
        sample_type = sample_json["type"]
          Severity: Major
          Found in lib/seek/data/bio_samples.rb - About 3 hrs to fix

            Method initialize has 58 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                def initialize file, xml=nil, to_populate=true, institution_id = nil
      @file = file

      @investigation = nil
      @study = nil
            Severity: Major
            Found in lib/seek/data/bio_samples.rb - About 2 hrs to fix

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

                  def initialize file, xml=nil, to_populate=true, institution_id = nil
      @file = file

      @investigation = nil
      @study = nil
              Severity: Minor
              Found in lib/seek/data/bio_samples.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 populate_db has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
              Open

                  def populate_db data

      assay = nil
      assay_json = data["assay"]
              Severity: Minor
              Found in lib/seek/data/bio_samples.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 build_all_bio_sample_json has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
              Open

                  def build_all_bio_sample_json sheet

      # population order should NOT change, DB is populated only if @to_populate is set to be true

      # probing number of rows with data in sheet
              Severity: Minor
              Found in lib/seek/data/bio_samples.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 build_assay_mock_json has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
              Open

                  def build_assay_mock_json sheet

      if @assay_mapping[:parsing_direction] == "horizontal"
        mapped_field_hunter = method(:hunt_for_horizontal_field_value_mapped)
      else
              Severity: Minor
              Found in lib/seek/data/bio_samples.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 populate_treatment has 41 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  def populate_treatment treatment_json, specimen=nil, sample=nil

        start_value = treatment_json["start value"]
        end_value = treatment_json["end value"]
        standard_deviation = treatment_json["standard deviation"]
              Severity: Minor
              Found in lib/seek/data/bio_samples.rb - About 1 hr to fix

                Method populate_assay has 35 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                    def populate_assay assay_json, filename

      investigation_title = assay_json["investigation title"]
      assay_type_title = assay_json["assay type title"]
      study_title = assay_json["study title"]
                Severity: Minor
                Found in lib/seek/data/bio_samples.rb - About 1 hr to fix

                  Consider simplifying this complex logical expression.
                  Open

                            unless sample.specimen == specimen &&
              sample.sample_type == sample_type &&
              (sample.tissue_and_cell_types.member?(tissue_and_cell_type) || tissue_and_cell_type_title == "") &&
              sample.donation_date == Time.zone.parse(donation_date).utc &&
              sample.institution == institution &&
                  Severity: Critical
                  Found in lib/seek/data/bio_samples.rb - About 1 hr to fix

                    Method populate_db has 32 lines of code (exceeds 25 allowed). Consider refactoring.
                    Open

                        def populate_db data

      assay = nil
      assay_json = data["assay"]
                    Severity: Minor
                    Found in lib/seek/data/bio_samples.rb - About 1 hr to fix

                      Method extract_from_document has 28 lines of code (exceeds 25 allowed). Consider refactoring.
                      Open

                          def extract_from_document doc
      doc.root.namespaces.default_prefix = "ss"


      template_sheet = nil
                      Severity: Minor
                      Found in lib/seek/data/bio_samples.rb - About 1 hr to fix

                        Method populate_assay has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
                        Open

                            def populate_assay assay_json, filename

      investigation_title = assay_json["investigation title"]
      assay_type_title = assay_json["assay type title"]
      study_title = assay_json["study title"]
                        Severity: Minor
                        Found in lib/seek/data/bio_samples.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 hunt_for_field_values_mapped has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
                        Open

                            def hunt_for_field_values_mapped sheet, field_name, mapping, probing_num_rows = false
      field_values = hunt_for_field_values sheet, mapping[field_name][:column], probing_num_rows
      if field_values && !field_values.empty?

        if probing_num_rows
                        Severity: Minor
                        Found in lib/seek/data/bio_samples.rb - About 45 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 extract_from_document has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
                        Open

                            def extract_from_document doc
      doc.root.namespaces.default_prefix = "ss"


      template_sheet = nil
                        Severity: Minor
                        Found in lib/seek/data/bio_samples.rb - About 45 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

                        Similar blocks of code found in 3 locations. Consider refactoring.
                        Open

                            def set_treatments sheet, treatment_protocol, treatment_attribute_names         # not used anymore
      sheet_name = sheet.attributes["name"]

      row = treatment_protocol.attributes["row"].to_i
      col = treatment_protocol.attributes["column"].to_i
                        Severity: Major
                        Found in lib/seek/data/bio_samples.rb and 2 other locations - About 1 hr to fix
                        lib/seek/data/bio_samples.rb on lines 562..575
                        lib/seek/data/bio_samples.rb on lines 578..591

                        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 68.

                        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 3 locations. Consider refactoring.
                        Open

                            def set_sequencing sheet, sequencing_protocol, sequencing_attribute_names   # not used anymore
      sheet_name = sheet.attributes["name"]

      row = sequencing_protocol.attributes["row"].to_i
      col = sequencing_protocol.attributes["column"].to_i
                        Severity: Major
                        Found in lib/seek/data/bio_samples.rb and 2 other locations - About 1 hr to fix
                        lib/seek/data/bio_samples.rb on lines 546..559
                        lib/seek/data/bio_samples.rb on lines 562..575

                        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 68.

                        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 3 locations. Consider refactoring.
                        Open

                            def set_rna_extractions sheet, rna_extraction_protocol, rna_attribute_names       # not used anymore
      sheet_name = sheet.attributes["name"]

      row = rna_extraction_protocol.attributes["row"].to_i
      col = rna_extraction_protocol.attributes["column"].to_i
                        Severity: Major
                        Found in lib/seek/data/bio_samples.rb and 2 other locations - About 1 hr to fix
                        lib/seek/data/bio_samples.rb on lines 546..559
                        lib/seek/data/bio_samples.rb on lines 578..591

                        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 68.

                        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

                                  samples_data = sample_titles.zip(sample_types, sample_donation_dates, sample_comments, sample_organism_parts, tissue_and_cell_types, sop_titles, institution_titles, specimen_titles).map do |sample_title, sample_type, sample_donation_date, sample_comment, sample_organism_part, tissue_and_cell_type, sop_title, institution_title, specimen_title|
            {:sample_title => sample_title, :sample_type => sample_type, :sample_donation_date => sample_donation_date, :sample_comment => sample_comment, :sample_organism_part => sample_organism_part,
             :tissue_and_cell_type => tissue_and_cell_type, :sop_title => sop_title, :institution_title => institution_title, :specimen_title => specimen_title}
                        Severity: Minor
                        Found in lib/seek/data/bio_samples.rb and 1 other location - About 30 mins to fix
                        lib/seek/data/bio_samples.rb on lines 377..384

                        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 33.

                        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

                                specimen_data = specimen_titles.
        zip(specimen_sexes, specimen_ages, specimen_age_units,
            specimen_comments, organism_titles, strain_titles, genotype_titles, genotype_modifications).
        map do |specimen_title, specimen_sex, specimen_age, specimen_age_unit,
            specimen_comment, organism_title, strain_title, genotype_title, genotype_modification |
                        Severity: Minor
                        Found in lib/seek/data/bio_samples.rb and 1 other location - About 30 mins to fix
                        lib/seek/data/bio_samples.rb on lines 412..414

                        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 33.

                        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 find_samples_sheet doc
      #sheet = doc.find_first("//ss:sheet[@name='SDRF']")
      #sheet = doc.find_first("//ss:sheet[@name='sdrf']") if sheet.nil?
      #sheet = doc.find_first("//ss:sheet[@name='Sdrf']") if sheet.nil?
      #sheet = hunt_for_sheet(doc, "SDRF") if sheet.nil?
                        Severity: Minor
                        Found in lib/seek/data/bio_samples.rb and 1 other location - About 30 mins to fix
                        lib/seek/data/bio_samples.rb on lines 140..154

                        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 32.

                        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 find_template_sheet doc
      #sheet = doc.find_first("//ss:sheet[@name='IDF']")
      #sheet = doc.find_first("//ss:sheet[@name='idf']") if sheet.nil?
      #sheet = doc.find_first("//ss:sheet[@name='Idf']") if sheet.nil?
      #sheet = hunt_for_sheet(doc, "IDF") if sheet.nil?
                        Severity: Minor
                        Found in lib/seek/data/bio_samples.rb and 1 other location - About 30 mins to fix
                        lib/seek/data/bio_samples.rb on lines 158..172

                        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 32.

                        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

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