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yannickwurm/sequenceserver

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lib/sequenceserver/blast/report.rb

Summary

Maintainability
A
45 mins
Test Coverage

Class has too many lines. [191/150]
Open

    class Report < Report
      def initialize(job)
        super do
          @querydb = job.databases
        end
Severity: Minor
Found in lib/sequenceserver/blast/report.rb by rubocop

This cop checks if the length a class exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

You can set literals you want to fold with CountAsOne. Available are: 'array', 'hash', and 'heredoc'. Each literal will be counted as one line regardless of its actual size.

Example: CountAsOne: ['array', 'heredoc']

class Foo
  ARRAY = [         # +1
    1,
    2
  ]

  HASH = {          # +3
    key: 'value'
  }

  MSG = <<~HEREDOC  # +1
    Heredoc
    content.
  HEREDOC
end                 # 5 points

NOTE: This cop also applies for Struct definitions.

Method parse_advanced has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

      def parse_advanced(param_line)
        param_list = (param_line || '').split(' ')
        res = {}

        param_list.each_with_index do |word, i|
Severity: Minor
Found in lib/sequenceserver/blast/report.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

Assignment Branch Condition size for extract_params is too high. [<6, 18, 2> 19.08/17]
Open

      def extract_params
        # Parse/get params from the job first.
        job_params = parse_advanced(job.advanced)
        # Old jobs from beta releases may not have the advanced key but they
        # will have the deprecated advanced_params key.
Severity: Minor
Found in lib/sequenceserver/blast/report.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric and https://en.wikipedia.org/wiki/ABC_Software_Metric.

Interpreting ABC size:

  • <= 17 satisfactory
  • 18..30 unsatisfactory
  • > 30 dangerous

You can have repeated "attributes" calls count as a single "branch". For this purpose, attributes are any method with no argument; no attempt is meant to distinguish actual attr_reader from other methods.

Example: CountRepeatedAttributes: false (default is true)

# `model` and `current_user`, refenced 3 times each,
 # are each counted as only 1 branch each if
 # `CountRepeatedAttributes` is set to 'false'

 def search
   @posts = model.active.visible_by(current_user)
             .search(params[:q])
   @posts = model.some_process(@posts, current_user)
   @posts = model.another_process(@posts, current_user)

   render 'pages/search/page'
 end

This cop also takes into account IgnoredMethods (defaults to [])

Assignment Branch Condition size for to_json is too high. [<3, 22, 3> 22.41/17]
Open

      def to_json(*_args)
        %i[querydb program program_version params stats
           queries].inject({}) do |h, k|
          h[k] = send(k)
          h
Severity: Minor
Found in lib/sequenceserver/blast/report.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric and https://en.wikipedia.org/wiki/ABC_Software_Metric.

Interpreting ABC size:

  • <= 17 satisfactory
  • 18..30 unsatisfactory
  • > 30 dangerous

You can have repeated "attributes" calls count as a single "branch". For this purpose, attributes are any method with no argument; no attempt is meant to distinguish actual attr_reader from other methods.

Example: CountRepeatedAttributes: false (default is true)

# `model` and `current_user`, refenced 3 times each,
 # are each counted as only 1 branch each if
 # `CountRepeatedAttributes` is set to 'false'

 def search
   @posts = model.active.visible_by(current_user)
             .search(params[:q])
   @posts = model.some_process(@posts, current_user)
   @posts = model.another_process(@posts, current_user)

   render 'pages/search/page'
 end

This cop also takes into account IgnoredMethods (defaults to [])

Assignment Branch Condition size for query_hits is too high. [<7, 29, 4> 30.1/17]
Open

      def query_hits(xml_ir, tsv_ir, query)
        return [] if xml_ir == ["\n"] # => No hits.

        xml_ir.map do |n|
          # If hit comes from a non -parse_seqids database, then id (n[1]) is a
Severity: Minor
Found in lib/sequenceserver/blast/report.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric and https://en.wikipedia.org/wiki/ABC_Software_Metric.

Interpreting ABC size:

  • <= 17 satisfactory
  • 18..30 unsatisfactory
  • > 30 dangerous

You can have repeated "attributes" calls count as a single "branch". For this purpose, attributes are any method with no argument; no attempt is meant to distinguish actual attr_reader from other methods.

Example: CountRepeatedAttributes: false (default is true)

# `model` and `current_user`, refenced 3 times each,
 # are each counted as only 1 branch each if
 # `CountRepeatedAttributes` is set to 'false'

 def search
   @posts = model.active.visible_by(current_user)
             .search(params[:q])
   @posts = model.some_process(@posts, current_user)
   @posts = model.another_process(@posts, current_user)

   render 'pages/search/page'
 end

This cop also takes into account IgnoredMethods (defaults to [])

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