bio-miga/miga

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lib/miga/remote_dataset.rb

Summary

Maintainability
D
1 day
Test Coverage
B
83%

Class has too many lines. [293/100]
Open

class MiGA::RemoteDataset < MiGA::MiGA
  include MiGA::RemoteDataset::Download

  # Class-level

Severity: Minor
Found in lib/miga/remote_dataset.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.

Assignment Branch Condition size for ncbi_asm_json_doc is too high. [57.06/15]
Open

  def ncbi_asm_json_doc
    return @_ncbi_asm_json_doc unless @_ncbi_asm_json_doc.nil?

    if db == :assembly && %i[ncbi gtdb seqcode].include?(universe)
      metadata[:ncbi_asm] ||= ids.first
Severity: Minor
Found in lib/miga/remote_dataset.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

Assignment Branch Condition size for use_ncbi_taxonomy_dump is too high. [37.71/15]
Open

    def use_ncbi_taxonomy_dump(path, cli = nil)
      raise "Directory doesn't exist: #{path}" unless File.directory?(path)

      # Structure: { TaxID => ["name", "rank", parent TaxID] }
      MiGA::MiGA.DEBUG "Loading NCBI Taxonomy dump: #{path}"
Severity: Minor
Found in lib/miga/remote_dataset.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

Assignment Branch Condition size for save_to is too high. [37.36/15]
Open

  def save_to(project, name = nil, is_ref = true, metadata_def = {})
    name ||= ids.join('_').miga_name
    project = MiGA::Project.new(project) if project.is_a? String
    MiGA::Dataset.exist?(project, name) and
      raise "Dataset #{name} exists in the project, aborting..."
Severity: Minor
Found in lib/miga/remote_dataset.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

Method has too many lines. [28/10]
Confirmed

  def get_type_status_ncbi_asm(metadata)
    from_type = nil

    # Try first from previously pulled NCBI metadata
    if metadata[:ncbi_dataset]
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Method has too many lines. [27/10]
Confirmed

    def use_ncbi_taxonomy_dump(path, cli = nil)
      raise "Directory doesn't exist: #{path}" unless File.directory?(path)

      # Structure: { TaxID => ["name", "rank", parent TaxID] }
      MiGA::MiGA.DEBUG "Loading NCBI Taxonomy dump: #{path}"
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Method has too many lines. [27/10]
Confirmed

  def ncbi_asm_json_doc
    return @_ncbi_asm_json_doc unless @_ncbi_asm_json_doc.nil?

    if db == :assembly && %i[ncbi gtdb seqcode].include?(universe)
      metadata[:ncbi_asm] ||= ids.first
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Assignment Branch Condition size for get_ncbi_taxonomy is too high. [29.56/15]
Open

  def get_ncbi_taxonomy
    tax_id = get_ncbi_taxid or return

    if self.class.ncbi_taxonomy_dump?
      return self.class.taxonomy_from_ncbi_dump(tax_id)
Severity: Minor
Found in lib/miga/remote_dataset.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

File remote_dataset.rb has 297 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'miga/taxonomy'
require 'miga/remote_dataset/download'

##
# MiGA representation of datasets with data in remote locations.
Severity: Minor
Found in lib/miga/remote_dataset.rb - About 3 hrs to fix

Method has too many lines. [22/10]
Confirmed

  def save_to(project, name = nil, is_ref = true, metadata_def = {})
    name ||= ids.join('_').miga_name
    project = MiGA::Project.new(project) if project.is_a? String
    MiGA::Dataset.exist?(project, name) and
      raise "Dataset #{name} exists in the project, aborting..."
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Method has too many lines. [20/10]
Confirmed

    def ncbi_asm_acc2id(acc, retrials = 3)
      return acc if acc =~ /^\d+$/

      search_doc = MiGA::Json.parse(
        download(:ncbi_search, :assembly, acc, :json),
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Cyclomatic complexity for ncbi_asm_json_doc is too high. [15/6]
Open

  def ncbi_asm_json_doc
    return @_ncbi_asm_json_doc unless @_ncbi_asm_json_doc.nil?

    if db == :assembly && %i[ncbi gtdb seqcode].include?(universe)
      metadata[:ncbi_asm] ||= ids.first
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Perceived complexity for ncbi_asm_json_doc is too high. [15/7]
Open

  def ncbi_asm_json_doc
    return @_ncbi_asm_json_doc unless @_ncbi_asm_json_doc.nil?

    if db == :assembly && %i[ncbi gtdb seqcode].include?(universe)
      metadata[:ncbi_asm] ||= ids.first
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Method has too many lines. [18/10]
Confirmed

  def get_metadata(metadata_def = {})
    metadata_def.each { |k, v| @metadata[k] = v }
    return @metadata if @metadata[:bypass_metadata]

    case universe
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Method ncbi_asm_json_doc has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

  def ncbi_asm_json_doc
    return @_ncbi_asm_json_doc unless @_ncbi_asm_json_doc.nil?

    if db == :assembly && %i[ncbi gtdb seqcode].include?(universe)
      metadata[:ncbi_asm] ||= ids.first
Severity: Minor
Found in lib/miga/remote_dataset.rb - About 2 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

Assignment Branch Condition size for get_type_status_ncbi_asm is too high. [21.79/15]
Open

  def get_type_status_ncbi_asm(metadata)
    from_type = nil

    # Try first from previously pulled NCBI metadata
    if metadata[:ncbi_dataset]
Severity: Minor
Found in lib/miga/remote_dataset.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

Method has too many lines. [15/10]
Confirmed

  def get_ncbi_taxonomy
    tax_id = get_ncbi_taxid or return

    if self.class.ncbi_taxonomy_dump?
      return self.class.taxonomy_from_ncbi_dump(tax_id)
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Method has too many lines. [14/10]
Confirmed

  def get_gtdb_taxonomy
    gtdb_genome = metadata[:gtdb_assembly] or return

    doc = MiGA::Json.parse(
      MiGA::RemoteDataset.download(
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Method has too many lines. [14/10]
Confirmed

  def save_assembly_to(project, name, udb)
    dir = MiGA::Dataset.RESULT_DIRS[:assembly]
    base = "#{project.path}/data/#{dir}/#{name}"
    l_ctg = "#{base}.LargeContigs.fna"
    a_ctg = "#{base}.AllContigs.fna"
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Assignment Branch Condition size for get_ncbi_taxid_from_ncbi is too high. [19.62/15]
Open

  def get_ncbi_taxid_from_ncbi
    # Try first from Assembly data
    return get_ncbi_taxid_from_web if db == :assembly

    # Try from previously pulled NCBI data
Severity: Minor
Found in lib/miga/remote_dataset.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

Assignment Branch Condition size for save_assembly_to is too high. [19.75/15]
Open

  def save_assembly_to(project, name, udb)
    dir = MiGA::Dataset.RESULT_DIRS[:assembly]
    base = "#{project.path}/data/#{dir}/#{name}"
    l_ctg = "#{base}.LargeContigs.fna"
    a_ctg = "#{base}.AllContigs.fna"
Severity: Minor
Found in lib/miga/remote_dataset.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

Cyclomatic complexity for get_ncbi_taxonomy is too high. [10/6]
Open

  def get_ncbi_taxonomy
    tax_id = get_ncbi_taxid or return

    if self.class.ncbi_taxonomy_dump?
      return self.class.taxonomy_from_ncbi_dump(tax_id)
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Cyclomatic complexity for get_type_status_ncbi_asm is too high. [10/6]
Open

  def get_type_status_ncbi_asm(metadata)
    from_type = nil

    # Try first from previously pulled NCBI metadata
    if metadata[:ncbi_dataset]
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Assignment Branch Condition size for get_metadata is too high. [19.31/15]
Open

  def get_metadata(metadata_def = {})
    metadata_def.each { |k, v| @metadata[k] = v }
    return @metadata if @metadata[:bypass_metadata]

    case universe
Severity: Minor
Found in lib/miga/remote_dataset.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

Perceived complexity for get_ncbi_taxonomy is too high. [10/7]
Open

  def get_ncbi_taxonomy
    tax_id = get_ncbi_taxid or return

    if self.class.ncbi_taxonomy_dump?
      return self.class.taxonomy_from_ncbi_dump(tax_id)
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Assignment Branch Condition size for initialize is too high. [17.92/15]
Open

  def initialize(ids, db, universe)
    ids = [ids] unless ids.is_a? Array
    @ids = (ids.is_a?(Array) ? ids : [ids])
    @db = db.to_sym
    @universe = universe.to_sym
Severity: Minor
Found in lib/miga/remote_dataset.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

Perceived complexity for get_type_status_ncbi_asm is too high. [9/7]
Open

  def get_type_status_ncbi_asm(metadata)
    from_type = nil

    # Try first from previously pulled NCBI metadata
    if metadata[:ncbi_dataset]
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Method has too many lines. [12/10]
Confirmed

  def get_ncbi_taxid_from_ncbi
    # Try first from Assembly data
    return get_ncbi_taxid_from_web if db == :assembly

    # Try from previously pulled NCBI data
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Method has too many lines. [11/10]
Confirmed

  def initialize(ids, db, universe)
    ids = [ids] unless ids.is_a? Array
    @ids = (ids.is_a?(Array) ? ids : [ids])
    @db = db.to_sym
    @universe = universe.to_sym
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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

Cyclomatic complexity for get_metadata is too high. [7/6]
Open

  def get_metadata(metadata_def = {})
    metadata_def.each { |k, v| @metadata[k] = v }
    return @metadata if @metadata[:bypass_metadata]

    case universe
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Cyclomatic complexity for save_to is too high. [7/6]
Confirmed

  def save_to(project, name = nil, is_ref = true, metadata_def = {})
    name ||= ids.join('_').miga_name
    project = MiGA::Project.new(project) if project.is_a? String
    MiGA::Dataset.exist?(project, name) and
      raise "Dataset #{name} exists in the project, aborting..."
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Method get_type_status_ncbi_asm has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

  def get_type_status_ncbi_asm(metadata)
    from_type = nil

    # Try first from previously pulled NCBI metadata
    if metadata[:ncbi_dataset]
Severity: Minor
Found in lib/miga/remote_dataset.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 use_ncbi_taxonomy_dump has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

    def use_ncbi_taxonomy_dump(path, cli = nil)
      raise "Directory doesn't exist: #{path}" unless File.directory?(path)

      # Structure: { TaxID => ["name", "rank", parent TaxID] }
      MiGA::MiGA.DEBUG "Loading NCBI Taxonomy dump: #{path}"
Severity: Minor
Found in lib/miga/remote_dataset.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 get_ncbi_taxonomy has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

  def get_ncbi_taxonomy
    tax_id = get_ncbi_taxid or return

    if self.class.ncbi_taxonomy_dump?
      return self.class.taxonomy_from_ncbi_dump(tax_id)
Severity: Minor
Found in lib/miga/remote_dataset.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 get_type_status_ncbi_asm has 28 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def get_type_status_ncbi_asm(metadata)
    from_type = nil

    # Try first from previously pulled NCBI metadata
    if metadata[:ncbi_dataset]
Severity: Minor
Found in lib/miga/remote_dataset.rb - About 1 hr to fix

Method ncbi_asm_acc2id has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def ncbi_asm_acc2id(acc, retrials = 3)
      return acc if acc =~ /^\d+$/

      search_doc = MiGA::Json.parse(
        download(:ncbi_search, :assembly, acc, :json),
Severity: Minor
Found in lib/miga/remote_dataset.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 ncbi_asm_json_doc has 27 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def ncbi_asm_json_doc
    return @_ncbi_asm_json_doc unless @_ncbi_asm_json_doc.nil?

    if db == :assembly && %i[ncbi gtdb seqcode].include?(universe)
      metadata[:ncbi_asm] ||= ids.first
Severity: Minor
Found in lib/miga/remote_dataset.rb - About 1 hr to fix

Method use_ncbi_taxonomy_dump has 27 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def use_ncbi_taxonomy_dump(path, cli = nil)
      raise "Directory doesn't exist: #{path}" unless File.directory?(path)

      # Structure: { TaxID => ["name", "rank", parent TaxID] }
      MiGA::MiGA.DEBUG "Loading NCBI Taxonomy dump: #{path}"
Severity: Minor
Found in lib/miga/remote_dataset.rb - About 1 hr to fix

Method save_to has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def save_to(project, name = nil, is_ref = true, metadata_def = {})
    name ||= ids.join('_').miga_name
    project = MiGA::Project.new(project) if project.is_a? String
    MiGA::Dataset.exist?(project, name) and
      raise "Dataset #{name} exists in the project, aborting..."
Severity: Minor
Found in lib/miga/remote_dataset.rb - About 55 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 get_ncbi_taxid_from_ncbi has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def get_ncbi_taxid_from_ncbi
    # Try first from Assembly data
    return get_ncbi_taxid_from_web if db == :assembly

    # Try from previously pulled NCBI data
Severity: Minor
Found in lib/miga/remote_dataset.rb - About 25 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

FIXME found
Open

    # FIXME: Part of the +map_to+ support:
Severity: Minor
Found in lib/miga/remote_dataset.rb by fixme

Unnecessary spacing detected.
Open

    ln  = doc.grep(%r{^\s+/db_xref="taxon:}).first
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks for extra/unnecessary whitespace.

Example:

# good if AllowForAlignment is true
name      = "RuboCop"
# Some comment and an empty line

website  += "/bbatsov/rubocop" unless cond
puts        "rubocop"          if     debug

# bad for any configuration
set_app("RuboCop")
website  = "https://github.com/bbatsov/rubocop"

Do not prefix reader method names with get_.
Open

  def get_ncbi_taxonomy
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop makes sure that accessor methods are named properly.

Example:

# bad
def set_attribute(value)
end

# good
def attribute=(value)
end

# bad
def get_attribute
end

# good
def attribute
end

Use alias get_ncbi_taxid_from_seqcode get_ncbi_taxid_from_ncbi instead of alias :get_ncbi_taxid_from_seqcode :get_ncbi_taxid_from_ncbi.
Open

  alias :get_ncbi_taxid_from_seqcode :get_ncbi_taxid_from_ncbi
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop enforces the use of either #alias or #alias_method depending on configuration. It also flags uses of alias :symbol rather than alias bareword.

Example: EnforcedStyle: prefer_alias (default)

# bad
alias_method :bar, :foo
alias :bar :foo

# good
alias bar foo

Example: EnforcedStyle: preferaliasmethod

# bad
alias :bar :foo
alias bar foo

# good
alias_method :bar, :foo

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

        '%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

Align the operands of a condition in an if statement spanning multiple lines.
Open

         metadata[:ncbi_nuccore] && !metadata[:ncbi_wgs]
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks the indentation of the right hand side operand in binary operations that span more than one line.

Example:

# bad
if a +
b
  something
end

# good
if a +
   b
  something
end

Do not prefix reader method names with get_.
Open

  def get_gtdb_taxonomy
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop makes sure that accessor methods are named properly.

Example:

# bad
def set_attribute(value)
end

# good
def attribute=(value)
end

# bad
def get_attribute
end

# good
def attribute
end

Provide an exception class and message as arguments to raise.
Open

        raise MiGA::RemoteDataMissingError.new(
          "NCBI Assembly Accession not found: #{acc}"
        )
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks the args passed to fail and raise. For exploded style (default), it recommends passing the exception class and message to raise, rather than construct an instance of the error. It will still allow passing just a message, or the construction of an error with more than one argument.

The exploded style works identically, but with the addition that it will also suggest constructing error objects when the exception is passed multiple arguments.

Example: EnforcedStyle: exploded (default)

# bad
raise StandardError.new("message")

# good
raise StandardError, "message"
fail "message"
raise MyCustomError.new(arg1, arg2, arg3)
raise MyKwArgError.new(key1: val1, key2: val2)

Example: EnforcedStyle: compact

# bad
raise StandardError, "message"
raise RuntimeError, arg1, arg2, arg3

# good
raise StandardError.new("message")
raise MyCustomError.new(arg1, arg2, arg3)
fail "message"

Do not prefix reader method names with get_.
Open

  def get_ncbi_taxid_from_web
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop makes sure that accessor methods are named properly.

Example:

# bad
def set_attribute(value)
end

# good
def attribute=(value)
end

# bad
def get_attribute
end

# good
def attribute
end

Use alias get_ncbi_taxid_from_gtdb get_ncbi_taxid_from_ncbi instead of alias :get_ncbi_taxid_from_gtdb :get_ncbi_taxid_from_ncbi.
Open

  alias :get_ncbi_taxid_from_gtdb :get_ncbi_taxid_from_ncbi
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop enforces the use of either #alias or #alias_method depending on configuration. It also flags uses of alias :symbol rather than alias bareword.

Example: EnforcedStyle: prefer_alias (default)

# bad
alias_method :bar, :foo
alias :bar :foo

# good
alias bar foo

Example: EnforcedStyle: preferaliasmethod

# bad
alias :bar :foo
alias bar foo

# good
alias_method :bar, :foo

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

        '%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop is designed to help upgrade to Ruby 3.0. It will add the comment # frozen_string_literal: true to the top of files to enable frozen string literals. Frozen string literals may be default in Ruby 3.0. The comment will be added below a shebang and encoding comment. The frozen string literal comment is only valid in Ruby 2.3+.

Example: EnforcedStyle: when_needed (default)

# The `when_needed` style will add the frozen string literal comment
# to files only when the `TargetRubyVersion` is set to 2.3+.
# bad
module Foo
  # ...
end

# good
# frozen_string_literal: true

module Foo
  # ...
end

Example: EnforcedStyle: always

# The `always` style will always add the frozen string literal comment
# to a file, regardless of the Ruby version or if `freeze` or `<<` are
# called on a string literal.
# bad
module Bar
  # ...
end

# good
# frozen_string_literal: true

module Bar
  # ...
end

Example: EnforcedStyle: never

# The `never` will enforce that the frozen string literal comment does
# not exist in a file.
# bad
# frozen_string_literal: true

module Baz
  # ...
end

# good
module Baz
  # ...
end

Do not prefix reader method names with get_.
Open

  def get_ncbi_taxid_from_ncbi
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop makes sure that accessor methods are named properly.

Example:

# bad
def set_attribute(value)
end

# good
def attribute=(value)
end

# bad
def get_attribute
end

# good
def attribute
end

Use a guard clause instead of wrapping the code inside a conditional expression.
Open

      if retrials <= 0
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

Use a guard clause instead of wrapping the code inside a conditional expression

Example:

# bad
def test
  if something
    work
  end
end

# good
def test
  return unless something
  work
end

# also good
def test
  work if something
end

# bad
if something
  raise 'exception'
else
  ok
end

# good
raise 'exception' if something
ok

Do not prefix reader method names with get_.
Open

  def get_ncbi_taxid_from_ebi
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop makes sure that accessor methods are named properly.

Example:

# bad
def set_attribute(value)
end

# good
def attribute=(value)
end

# bad
def get_attribute
end

# good
def attribute
end

Operator = should be surrounded by a single space.
Open

    ln  = doc.grep(%r{^\s+/db_xref="taxon:}).first
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

Checks that operators have space around them, except for ** which should not have surrounding space.

Example:

# bad
total = 3*4
"apple"+"juice"
my_number = 38/4
a ** b

# good
total = 3 * 4
"apple" + "juice"
my_number = 38 / 4
a**b

Avoid when branches without a body.
Open

    when nil
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks for the presence of when branches without a body.

Example:

# bad

case foo
when bar then 1
when baz then # nothing
end

Example:

# good

case foo
when bar then 1
when baz then 2
end

Do not prefix reader method names with get_.
Open

  def get_ncbi_taxid
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop makes sure that accessor methods are named properly.

Example:

# bad
def set_attribute(value)
end

# good
def attribute=(value)
end

# bad
def get_attribute
end

# good
def attribute
end

Omit parentheses for ternary conditions.
Open

      (@ncbi_taxonomy_names ||= nil) ? true : false
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks for the presence of parentheses around ternary conditions. It is configurable to enforce inclusion or omission of parentheses using EnforcedStyle. Omission is only enforced when removing the parentheses won't cause a different behavior.

Example: EnforcedStyle: requirenoparentheses (default)

# bad
foo = (bar?) ? a : b
foo = (bar.baz?) ? a : b
foo = (bar && baz) ? a : b

# good
foo = bar? ? a : b
foo = bar.baz? ? a : b
foo = bar && baz ? a : b

Example: EnforcedStyle: require_parentheses

# bad
foo = bar? ? a : b
foo = bar.baz? ? a : b
foo = bar && baz ? a : b

# good
foo = (bar?) ? a : b
foo = (bar.baz?) ? a : b
foo = (bar && baz) ? a : b

Example: EnforcedStyle: requireparentheseswhen_complex

# bad
foo = (bar?) ? a : b
foo = (bar.baz?) ? a : b
foo = bar && baz ? a : b

# good
foo = bar? ? a : b
foo = bar.baz? ? a : b
foo = (bar && baz) ? a : b

Line is too long. [96/80]
Open

      doc = self.class.download(:ncbi_fetch, :nuccore, metadata[:ncbi_nuccore], :gb).split(/\n/)
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

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