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GlobalNamesArchitecture/dwca-hunter

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Showing 91 of 144 total issues

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

    def get_classification
      DwcaHunter.logger_write(object_id, "Building classification...")
      open(@nodes_file, "r:utf-8").each_with_index do |line, i|
        DwcaHunter.logger_write(object_id, "Collected %s nodes..." % i) if i > 0 && i % BATCH_SIZE == 0
        line = line.split("|").map { |l| cleanup(l) }
Severity: Minor
Found in lib/dwca_hunter/resources/ncbi.rb - About 1 hr to fix

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

        def collect_names
      @names_index = {}
      file = CSV.open(File.join(@download_dir, find_csv_file),
        headers: true)
      file.each do |row|
    Severity: Minor
    Found in lib/dwca_hunter/resources/disc_life_bees.rb - About 1 hr to fix

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

          def collect_names
      @names_index = {}
      file = CSV.open(File.join(@download_dir, "globalnames_classification.csv"),
                      headers: true)
      Severity: Minor
      Found in lib/dwca_hunter/resources/arctos.rb - About 1 hr to fix

        Method generate_dwca has 34 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/algaebase.rb - About 1 hr to fix

          Method initialize has 34 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

              def initialize(opts = {})
      @command = "open-tree"
      @title = "Open Tree of Life Reference Taxonomy"
      @uuid = "e10865e2-cdd9-4f97-912f-08f3d5ef49f7"
      @data = []
          Severity: Minor
          Found in lib/dwca_hunter/resources/opentree.rb - About 1 hr to fix

            Method generate_dwca has 34 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/acceptedNameUsageID",
            Severity: Minor
            Found in lib/dwca_hunter/resources/lpsn_bacteria.rb - About 1 hr to fix

              Method organize_data has 34 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  def organize_data
      DwcaHunter::logger_write(self.object_id,
                               "Organizing data")
      path = File.join(__dir__, "..",
                       "..", "files", "reptile_checklist_2014_12.csv")
              Severity: Minor
              Found in lib/dwca_hunter/resources/reptiles_checklist.rb - About 1 hr to fix

                Method collect_names has 33 lines of code (exceeds 25 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

                  Method collect_names has 33 lines of code (exceeds 25 allowed). Consider refactoring.
                  Open

                      def collect_names
      @names_index = {}
      latin1 = File.read(File.join(@download_dir, find_csv_file))
      w = File.open(File.join(@download_dir, "data.tsv"), "w:utf-8")
      w.write(latin1.force_encoding("iso-8859-1").encode("UTF-8"))
                  Severity: Minor
                  Found in lib/dwca_hunter/resources/lcvp.rb - About 1 hr to fix

                    Method generate_dwca has 33 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://globalnames.org/terms/localID",
                    Severity: Minor
                    Found in lib/dwca_hunter/resources/ictv.rb - About 1 hr to fix

                      Method collect_names has 32 lines of code (exceeds 25 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

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

                            def collect_names
      @names_index = {}
      file = CSV.open(File.join(@download_dir, "taxon.txt"),
                      headers: true, col_sep: "\t", quote_char: "\b")
      file.each_with_index do |row, i|
                        Severity: Minor
                        Found in lib/dwca_hunter/resources/worms.rb - About 1 hr to fix

                          Method collect_genera has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
                          Open

                              def collect_genera
      puts "Processing genera"
      file = CSV.open(File.join(@download_dir, "genus_groups.tsv"),
                      headers: true, col_sep: "\t")
                          Severity: Minor
                          Found in lib/dwca_hunter/resources/wikidata.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 11 (exceeds 5 allowed). Consider refactoring.
                          Open

                              def organize_data
      DwcaHunter::logger_write(self.object_id,
                               "Organizing data")
      path = File.join(__dir__, "..",
                       "..", "files", "reptile_checklist_2014_12.csv")
                          Severity: Minor
                          Found in lib/dwca_hunter/resources/reptiles_checklist.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 generate_dwca has 31 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/paleobiodb.rb - About 1 hr to fix

                            Method collect_names has 30 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/clements.rb - About 1 hr to fix

                              Method collect_names has 30 lines of code (exceeds 25 allowed). Consider refactoring.
                              Open

                                  def collect_names
      @names_index = {}
      file = CSV.open(File.join(@download_dir, find_csv_file),
                      headers: true)
      file.each do |row|
                              Severity: Minor
                              Found in lib/dwca_hunter/resources/mammal_divdb.rb - About 1 hr to fix

                                Method get_names has 30 lines of code (exceeds 25 allowed). Consider refactoring.
                                Open

                                    def get_names
      puts "Processing names"
      file = CSV.open(@download_path, headers: true)

      file.each_with_index do |row, i|
                                Severity: Minor
                                Found in lib/dwca_hunter/resources/lpsn_bacteria.rb - About 1 hr to fix

                                  Method collect_names has 29 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/index-fungorum.rb - About 1 hr to fix

                                    Method generate_dwca has 29 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/ruhoff.rb - About 1 hr to fix
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