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GlobalNamesArchitecture/dwca-hunter

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Showing 144 of 144 total issues

Method generate_dwca has 51 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def generate_dwca
      DwcaHunter.logger_write(object_id,
                              "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
                "http://rs.tdwg.org/dwc/terms/parentNameUsageID",
Severity: Major
Found in lib/dwca_hunter/resources/itis.rb - About 2 hrs to fix

    Method generate_dwca has 50 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def generate_dwca
      DwcaHunter.logger_write(object_id, "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
                "http://rs.tdwg.org/dwc/terms/scientificName",
                "http://rs.tdwg.org/dwc/terms/kingdom",
    Severity: Minor
    Found in lib/dwca_hunter/resources/tpt.rb - About 2 hrs to fix

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

          def enrich_data
      DwcaHunter.logger_write(object_id,
                              "Extracting data from xml file...")
      Dir.chdir(@download_dir)
      f = open("data.xml", "r:utf-8")
      Severity: Minor
      Found in lib/dwca_hunter/resources/wikispecies.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 collect_names has 47 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          def collect_names
      file = CSV.open(File.join(@download_dir, "data.csv"),
                      headers: true)
      file.each_with_index do |row, i|
        kingdom = "Animalia"
      Severity: Minor
      Found in lib/dwca_hunter/resources/how-moore-birds.rb - About 1 hr to fix

        Method generate_dwca has 47 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

            def generate_dwca
      DwcaHunter.logger_write(object_id,
                              "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
                "http://rs.tdwg.org/dwc/terms/scientificName",
        Severity: Minor
        Found in lib/dwca_hunter/resources/how-moore-birds.rb - About 1 hr to fix

          Method generate_dwca has 43 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

              def generate_dwca
      DwcaHunter.logger_write(object_id,
                              "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
                "http://rs.tdwg.org/dwc/terms/scientificName",
          Severity: Minor
          Found in lib/dwca_hunter/resources/mcz.rb - About 1 hr to fix

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

                def generate_dwca
      DwcaHunter.logger_write(object_id, "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonId",
                "http://rs.tdwg.org/dwc/terms/parentNameUsageId",
                "http://rs.tdwg.org/dwc/terms/scientificName",
            Severity: Major
            Found in lib/dwca_hunter/resources/tropicos.rb and 1 other location - About 1 hr to fix
            lib/dwca_hunter/resources/ruhoff.rb on lines 81..112

            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 67.

            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 generate_dwca
      DwcaHunter.logger_write(object_id, "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
                "http://rs.tdwg.org/dwc/terms/scientificName",
                "http://rs.tdwg.org/dwc/terms/kingdom",
            Severity: Major
            Found in lib/dwca_hunter/resources/ruhoff.rb and 1 other location - About 1 hr to fix
            lib/dwca_hunter/resources/tropicos.rb on lines 74..113

            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 67.

            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 collect_names has 41 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                def collect_names
      tpt_dir = "tpt-taxonomy-main"
      tpt_path = File.join(@download_dir, tpt_dir)
      @names_index = {}
      files = Dir.entries(tpt_path)
            Severity: Minor
            Found in lib/dwca_hunter/resources/tpt.rb - About 1 hr to fix

              Method generate_dwca has 40 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  def generate_dwca
      DwcaHunter.logger_write(object_id,
                              "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
                "http://rs.tdwg.org/dwc/terms/scientificName",
              Severity: Minor
              Found in lib/dwca_hunter/resources/freebase.rb - About 1 hr to fix

                Method get_names has 40 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                    def get_names
      # 0    tsn serial not null
      # 1    unit_ind1 char(1)
      # 2    unit_name1 char(35) not null
      # 3    unit_ind2 char(1)
                Severity: Minor
                Found in lib/dwca_hunter/resources/itis.rb - About 1 hr to fix

                  Method collect_names has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
                  Open

                      def collect_names
      @names_index = {}
      file = CSV.open(File.join(@download_dir, find_csv_file),
                      headers: true, col_sep: "|", quote_char: "\b")
      file.each do |row|
                  Severity: Minor
                  Found in lib/dwca_hunter/resources/wcvp.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 collect_names has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
                  Open

                      def collect_names
      @names_index = {}
      file = CSV.open(File.join(@download_dir, "data.tsv"),
                      headers: true, col_sep: "\t", quote_char: "\b")
      file.each_with_index do |row, i|
                  Severity: Minor
                  Found in lib/dwca_hunter/resources/fungal_names.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 organize_data has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
                  Open

                      def organize_data
      @data = JSON.load(open(@download_path, "r:utf-8").read)
      @data.each do |d|
        scientific_name = d["scientific_name"].to_s
        id = d["id"]
                  Severity: Minor
                  Found in lib/dwca_hunter/resources/freebase.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 process_hierarchy has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
                  Open

                      def process_hierarchy(rec)
      parent_id = @clades["Mammalia"][:id]
      is_row_rank = false
      %i[order suborder infraorder superfamily family
         subfamily tribe genus subgenus species subspecies].each do |rank|
                  Severity: Minor
                  Found in lib/dwca_hunter/resources/mammal_species.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 collect_names has 38 lines of code (exceeds 25 allowed). Consider refactoring.
                  Open

                      def collect_names
      @names_index = {}
      file = CSV.open(File.join(@download_dir, "data.csv"),
                      headers: true)
      file.each_with_index do |row, _i|
                  Severity: Minor
                  Found in lib/dwca_hunter/resources/aos-birds.rb - About 1 hr to fix

                    Method generate_dwca has 37 lines of code (exceeds 25 allowed). Consider refactoring.
                    Open

                        def generate_dwca
      DwcaHunter.logger_write(object_id,
                              "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
                "http://rs.tdwg.org/dwc/terms/scientificName",
                    Severity: Minor
                    Found in lib/dwca_hunter/resources/ion.rb - About 1 hr to fix

                      Method generate_dwca has 37 lines of code (exceeds 25 allowed). Consider refactoring.
                      Open

                          def generate_dwca
      DwcaHunter.logger_write(object_id, "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonId",
                "http://rs.tdwg.org/dwc/terms/parentNameUsageId",
                "http://rs.tdwg.org/dwc/terms/scientificName",
                      Severity: Minor
                      Found in lib/dwca_hunter/resources/tropicos.rb - About 1 hr to fix

                        Method generate_dwca has 36 lines of code (exceeds 25 allowed). Consider refactoring.
                        Open

                            def generate_dwca
      DwcaHunter.logger_write(object_id, "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
                "http://rs.tdwg.org/dwc/terms/scientificName",
                "http://rs.tdwg.org/dwc/terms/acceptedNameUsageID",
                        Severity: Minor
                        Found in lib/dwca_hunter/resources/disc_life_bees.rb - About 1 hr to fix

                          Method generate_dwca has 36 lines of code (exceeds 25 allowed). Consider refactoring.
                          Open

                              def generate_dwca
      DwcaHunter.logger_write(object_id, "Creating DarwinCore Archive file")
      @core = [["http://rs.tdwg.org/dwc/terms/taxonID",
                "http://rs.tdwg.org/dwc/terms/scientificName",
                "http://rs.tdwg.org/dwc/terms/taxonRank",
                          Severity: Minor
                          Found in lib/dwca_hunter/resources/nom-zoologicus.rb - About 1 hr to fix
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