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GlobalNamesArchitecture/dwca-hunter

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Showing 144 of 144 total issues

Method collect_names has 36 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/algaebase.rb - About 1 hr to fix

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

        def rank(name_string) 
      res = ""
      parsed = @parser.parse(name_string)
      if parsed[:parsed]
        if parsed[:cardinality] == 2
    Severity: Major
    Found in lib/dwca_hunter/resources/algaebase.rb and 1 other location - About 1 hr to fix
    lib/dwca_hunter/resources/wcvp.rb on lines 75..92

    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 60.

    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 rank(name_string)
      res = ""
      parsed = @parser.parse(name_string)
      if parsed[:parsed]
        return "species" if parsed[:cardinality] == 2
    Severity: Major
    Found in lib/dwca_hunter/resources/wcvp.rb and 1 other location - About 1 hr to fix
    lib/dwca_hunter/resources/algaebase.rb on lines 95..116

    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 60.

    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 enrich_data has 35 lines of code (exceeds 25 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

      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
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