Complex method AccessionService#submit (99.9) Open
def submit(user, *accessionables) # rubocop:todo Metrics/CyclomaticComplexity
ActiveRecord::Base.transaction do
submission = Accessionable::Submission.new(self, user, *accessionables)
errors = submission.all_accessionables.map(&:errors).flatten
- Read upRead up
- Exclude checks
Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.
You can read more about ABC metrics or the flog tool
Method submit
has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring. Open
def submit(user, *accessionables) # rubocop:todo Metrics/CyclomaticComplexity
ActiveRecord::Base.transaction do
submission = Accessionable::Submission.new(self, user, *accessionables)
errors = submission.all_accessionables.map(&:errors).flatten
- Read upRead up
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
Complex method AccessionService#post_files (43.5) Open
def post_files(file_params) # rubocop:todo Metrics/CyclomaticComplexity
rc = rest_client_resource
if configatron.disable_web_proxy == true
RestClient.proxy = nil
- Read upRead up
- Exclude checks
Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.
You can read more about ABC metrics or the flog tool
Method submit
has 52 lines of code (exceeds 25 allowed). Consider refactoring. Open
def submit(user, *accessionables) # rubocop:todo Metrics/CyclomaticComplexity
ActiveRecord::Base.transaction do
submission = Accessionable::Submission.new(self, user, *accessionables)
errors = submission.all_accessionables.map(&:errors).flatten
Complex method AccessionService#accession_submission_xml (37.5) Open
def accession_submission_xml(submission, accession_number) # rubocop:todo Metrics/AbcSize
xml = Builder::XmlMarkup.new
xml.instruct!
xml.SUBMISSION(
'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
- Read upRead up
- Exclude checks
Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.
You can read more about ABC metrics or the flog tool
Method accession_submission_xml
has 28 lines of code (exceeds 25 allowed). Consider refactoring. Open
def accession_submission_xml(submission, accession_number) # rubocop:todo Metrics/AbcSize
xml = Builder::XmlMarkup.new
xml.instruct!
xml.SUBMISSION(
'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
Method accession_submission_xml
has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring. Open
def accession_submission_xml(submission, accession_number) # rubocop:todo Metrics/AbcSize
xml = Builder::XmlMarkup.new
xml.instruct!
xml.SUBMISSION(
'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
- Read upRead up
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 post_files
has 27 lines of code (exceeds 25 allowed). Consider refactoring. Open
def post_files(file_params) # rubocop:todo Metrics/CyclomaticComplexity
rc = rest_client_resource
if configatron.disable_web_proxy == true
RestClient.proxy = nil
AccessionService#submit refers to 'acc' more than self (maybe move it to another class?) Open
file = Tempfile.open("#{acc.schema_type}_file")
files << file
file.puts(acc.xml)
file.open # reopen for read
- Read upRead up
- Exclude checks
Feature Envy occurs when a code fragment references another object more often than it references itself, or when several clients do the same series of manipulations on a particular type of object.
Feature Envy reduces the code's ability to communicate intent: code that "belongs" on one class but which is located in another can be hard to find, and may upset the "System of Names" in the host class.
Feature Envy also affects the design's flexibility: A code fragment that is in the wrong class creates couplings that may not be natural within the application's domain, and creates a loss of cohesion in the unwilling host class.
Feature Envy often arises because it must manipulate other objects (usually its arguments) to get them into a useful form, and one force preventing them (the arguments) doing this themselves is that the common knowledge lives outside the arguments, or the arguments are of too basic a type to justify extending that type. Therefore there must be something which 'knows' about the contents or purposes of the arguments. That thing would have to be more than just a basic type, because the basic types are either containers which don't know about their contents, or they are single objects which can't capture their relationship with their fellows of the same type. So, this thing with the extra knowledge should be reified into a class, and the utility method will most likely belong there.
Example
Running Reek on:
class Warehouse
def sale_price(item)
(item.price - item.rebate) * @vat
end
end
would report:
Warehouse#total_price refers to item more than self (FeatureEnvy)
since this:
(item.price - item.rebate)
belongs to the Item class, not the Warehouse.
AccessionService#accession_submission_xml has approx 13 statements Open
def accession_submission_xml(submission, accession_number) # rubocop:todo Metrics/AbcSize
- Read upRead up
- Exclude checks
A method with Too Many Statements
is any method that has a large number of lines.
Too Many Statements
warns about any method that has more than 5 statements. Reek's smell detector for Too Many Statements
counts +1 for every simple statement in a method and +1 for every statement within a control structure (if
, else
, case
, when
, for
, while
, until
, begin
, rescue
) but it doesn't count the control structure itself.
So the following method would score +6 in Reek's statement-counting algorithm:
def parse(arg, argv, &error)
if !(val = arg) and (argv.empty? or /\A-/ =~ (val = argv[0]))
return nil, block, nil # +1
end
opt = (val = parse_arg(val, &error))[1] # +2
val = conv_arg(*val) # +3
if opt and !arg
argv.shift # +4
else
val[0] = nil # +5
end
val # +6
end
(You might argue that the two assigments within the first @if@ should count as statements, and that perhaps the nested assignment should count as +2.)
AccessionService#submit has approx 33 statements Open
def submit(user, *accessionables) # rubocop:todo Metrics/CyclomaticComplexity
- Read upRead up
- Exclude checks
A method with Too Many Statements
is any method that has a large number of lines.
Too Many Statements
warns about any method that has more than 5 statements. Reek's smell detector for Too Many Statements
counts +1 for every simple statement in a method and +1 for every statement within a control structure (if
, else
, case
, when
, for
, while
, until
, begin
, rescue
) but it doesn't count the control structure itself.
So the following method would score +6 in Reek's statement-counting algorithm:
def parse(arg, argv, &error)
if !(val = arg) and (argv.empty? or /\A-/ =~ (val = argv[0]))
return nil, block, nil # +1
end
opt = (val = parse_arg(val, &error))[1] # +2
val = conv_arg(*val) # +3
if opt and !arg
argv.shift # +4
else
val[0] = nil # +5
end
val # +6
end
(You might argue that the two assigments within the first @if@ should count as statements, and that perhaps the nested assignment should count as +2.)
AccessionService has at least 18 methods Open
class AccessionService # rubocop:todo Metrics/ClassLength
- Read upRead up
- Exclude checks
Too Many Methods
is a special case of LargeClass
.
Example
Given this configuration
TooManyMethods:
max_methods: 3
and this code:
class TooManyMethods
def one; end
def two; end
def three; end
def four; end
end
Reek would emit the following warning:
test.rb -- 1 warning:
[1]:TooManyMethods has at least 4 methods (TooManyMethods)
AccessionService#post_files has approx 16 statements Open
def post_files(file_params) # rubocop:todo Metrics/CyclomaticComplexity
- Read upRead up
- Exclude checks
A method with Too Many Statements
is any method that has a large number of lines.
Too Many Statements
warns about any method that has more than 5 statements. Reek's smell detector for Too Many Statements
counts +1 for every simple statement in a method and +1 for every statement within a control structure (if
, else
, case
, when
, for
, while
, until
, begin
, rescue
) but it doesn't count the control structure itself.
So the following method would score +6 in Reek's statement-counting algorithm:
def parse(arg, argv, &error)
if !(val = arg) and (argv.empty? or /\A-/ =~ (val = argv[0]))
return nil, block, nil # +1
end
opt = (val = parse_arg(val, &error))[1] # +2
val = conv_arg(*val) # +3
if opt and !arg
argv.shift # +4
else
val[0] = nil # +5
end
val # +6
end
(You might argue that the two assigments within the first @if@ should count as statements, and that perhaps the nested assignment should count as +2.)
Method post_files
has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def post_files(file_params) # rubocop:todo Metrics/CyclomaticComplexity
rc = rest_client_resource
if configatron.disable_web_proxy == true
RestClient.proxy = nil
- Read upRead up
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
AccessionService#submit calls 'Rails.logger' 2 times Open
Rails.logger.debug { file.each_line.to_a.join("\n") }
{ name: acc.schema_type.upcase, local_name: file.path, remote_name: acc.file_name }
end
)
- Read upRead up
- Exclude checks
Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.
Reek implements a check for Duplicate Method Call.
Example
Here's a very much simplified and contrived example. The following method will report a warning:
def double_thing()
@other.thing + @other.thing
end
One quick approach to silence Reek would be to refactor the code thus:
def double_thing()
thing = @other.thing
thing + thing
end
A slightly different approach would be to replace all calls of double_thing
by calls to @other.double_thing
:
class Other
def double_thing()
thing + thing
end
end
The approach you take will depend on balancing other factors in your code.
AccessionService#submit calls 'Rails.logger.debug' 2 times Open
Rails.logger.debug { file.each_line.to_a.join("\n") }
{ name: acc.schema_type.upcase, local_name: file.path, remote_name: acc.file_name }
end
)
- Read upRead up
- Exclude checks
Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.
Reek implements a check for Duplicate Method Call.
Example
Here's a very much simplified and contrived example. The following method will report a warning:
def double_thing()
@other.thing + @other.thing
end
One quick approach to silence Reek would be to refactor the code thus:
def double_thing()
thing = @other.thing
thing + thing
end
A slightly different approach would be to replace all calls of double_thing
by calls to @other.double_thing
:
class Other
def double_thing()
thing + thing
end
end
The approach you take will depend on balancing other factors in your code.
AccessionService#submit calls 'submission.all_accessionables' 3 times Open
errors = submission.all_accessionables.map(&:errors).flatten
raise AccessionServiceError, errors.join("\n") unless errors.empty?
files = [] # maybe not necessary, but just to be sure that the tempfile still exists when they are sent
- Read upRead up
- Exclude checks
Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.
Reek implements a check for Duplicate Method Call.
Example
Here's a very much simplified and contrived example. The following method will report a warning:
def double_thing()
@other.thing + @other.thing
end
One quick approach to silence Reek would be to refactor the code thus:
def double_thing()
thing = @other.thing
thing + thing
end
A slightly different approach would be to replace all calls of double_thing
by calls to @other.double_thing
:
class Other
def double_thing()
thing + thing
end
end
The approach you take will depend on balancing other factors in your code.
AccessionService#accession_submission_xml calls 'submission[:source]' 2 times Open
xml.ADD(source: submission[:source], schema: submission[:schema])
else
xml.MODIFY(source: submission[:source], target: '')
- Read upRead up
- Exclude checks
Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.
Reek implements a check for Duplicate Method Call.
Example
Here's a very much simplified and contrived example. The following method will report a warning:
def double_thing()
@other.thing + @other.thing
end
One quick approach to silence Reek would be to refactor the code thus:
def double_thing()
thing = @other.thing
thing + thing
end
A slightly different approach would be to replace all calls of double_thing
by calls to @other.double_thing
:
class Other
def double_thing()
thing + thing
end
end
The approach you take will depend on balancing other factors in your code.
AccessionService#post_files calls 'ENV['http_proxy']' 2 times Open
elsif ENV['http_proxy'].present?
RestClient.proxy = ENV['http_proxy']
- Read upRead up
- Exclude checks
Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.
Reek implements a check for Duplicate Method Call.
Example
Here's a very much simplified and contrived example. The following method will report a warning:
def double_thing()
@other.thing + @other.thing
end
One quick approach to silence Reek would be to refactor the code thus:
def double_thing()
thing = @other.thing
thing + thing
end
A slightly different approach would be to replace all calls of double_thing
by calls to @other.double_thing
:
class Other
def double_thing()
thing + thing
end
end
The approach you take will depend on balancing other factors in your code.
AccessionService#submit calls 'xmldoc.root' 2 times Open
success = xmldoc.root.attributes['success']
accession_numbers = []
# for some reasons, ebi doesn't give us back a accession number for the submission if it's a MODIFY action
# therefore, we should be ready to get one or not
- Read upRead up
- Exclude checks
Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.
Reek implements a check for Duplicate Method Call.
Example
Here's a very much simplified and contrived example. The following method will report a warning:
def double_thing()
@other.thing + @other.thing
end
One quick approach to silence Reek would be to refactor the code thus:
def double_thing()
thing = @other.thing
thing + thing
end
A slightly different approach would be to replace all calls of double_thing
by calls to @other.double_thing
:
class Other
def double_thing()
thing + thing
end
end
The approach you take will depend on balancing other factors in your code.
AccessionService::AccessionServiceError has no descriptive comment Open
AccessionServiceError = Class.new(StandardError)
- Read upRead up
- Exclude checks
Classes and modules are the units of reuse and release. It is therefore considered good practice to annotate every class and module with a brief comment outlining its responsibilities.
Example
Given
class Dummy
# Do things...
end
Reek would emit the following warning:
test.rb -- 1 warning:
[1]:Dummy has no descriptive comment (IrresponsibleModule)
Fixing this is simple - just an explaining comment:
# The Dummy class is responsible for ...
class Dummy
# Do things...
end
AccessionService::NumberNotGenerated has no descriptive comment Open
NumberNotGenerated = Class.new(AccessionServiceError)
- Read upRead up
- Exclude checks
Classes and modules are the units of reuse and release. It is therefore considered good practice to annotate every class and module with a brief comment outlining its responsibilities.
Example
Given
class Dummy
# Do things...
end
Reek would emit the following warning:
test.rb -- 1 warning:
[1]:Dummy has no descriptive comment (IrresponsibleModule)
Fixing this is simple - just an explaining comment:
# The Dummy class is responsible for ...
class Dummy
# Do things...
end
AccessionService::NumberNotRequired has no descriptive comment Open
NumberNotRequired = Class.new(AccessionServiceError)
- Read upRead up
- Exclude checks
Classes and modules are the units of reuse and release. It is therefore considered good practice to annotate every class and module with a brief comment outlining its responsibilities.
Example
Given
class Dummy
# Do things...
end
Reek would emit the following warning:
test.rb -- 1 warning:
[1]:Dummy has no descriptive comment (IrresponsibleModule)
Fixing this is simple - just an explaining comment:
# The Dummy class is responsible for ...
class Dummy
# Do things...
end
AccessionService#submit calls 'acc.schema_type' 2 times Open
file = Tempfile.open("#{acc.schema_type}_file")
files << file
file.puts(acc.xml)
file.open # reopen for read
- Read upRead up
- Exclude checks
Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.
Reek implements a check for Duplicate Method Call.
Example
Here's a very much simplified and contrived example. The following method will report a warning:
def double_thing()
@other.thing + @other.thing
end
One quick approach to silence Reek would be to refactor the code thus:
def double_thing()
thing = @other.thing
thing + thing
end
A slightly different approach would be to replace all calls of double_thing
by calls to @other.double_thing
:
class Other
def double_thing()
thing + thing
end
end
The approach you take will depend on balancing other factors in your code.
AccessionService#accession_submission_xml calls 'xml.ACTION' 2 times Open
xml.ACTION do
if accession_number.blank?
xml.ADD(source: submission[:source], schema: submission[:schema])
else
xml.MODIFY(source: submission[:source], target: '')
- Read upRead up
- Exclude checks
Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.
Reek implements a check for Duplicate Method Call.
Example
Here's a very much simplified and contrived example. The following method will report a warning:
def double_thing()
@other.thing + @other.thing
end
One quick approach to silence Reek would be to refactor the code thus:
def double_thing()
thing = @other.thing
thing + thing
end
A slightly different approach would be to replace all calls of double_thing
by calls to @other.double_thing
:
class Other
def double_thing()
thing + thing
end
end
The approach you take will depend on balancing other factors in your code.
AccessionService::AccessionedFile has no descriptive comment Open
class AccessionedFile < File
- Read upRead up
- Exclude checks
Classes and modules are the units of reuse and release. It is therefore considered good practice to annotate every class and module with a brief comment outlining its responsibilities.
Example
Given
class Dummy
# Do things...
end
Reek would emit the following warning:
test.rb -- 1 warning:
[1]:Dummy has no descriptive comment (IrresponsibleModule)
Fixing this is simple - just an explaining comment:
# The Dummy class is responsible for ...
class Dummy
# Do things...
end
AccessionService#accession_dac_xml doesn't depend on instance state (maybe move it to another class?) Open
def accession_dac_xml(study)
- Read upRead up
- Exclude checks
A Utility Function is any instance method that has no dependency on the state of the instance.
AccessionService::AccessionedFile#original_filename is a writable attribute Open
attr_accessor :original_filename
- Read upRead up
- Exclude checks
A class that publishes a setter for an instance variable invites client classes to become too intimate with its inner workings, and in particular with its representation of state.
The same holds to a lesser extent for getters, but Reek doesn't flag those.
Example
Given:
class Klass
attr_accessor :dummy
end
Reek would emit the following warning:
reek test.rb
test.rb -- 1 warning:
[2]:Klass declares the writable attribute dummy (Attribute)
AccessionService#accession_policy_xml doesn't depend on instance state (maybe move it to another class?) Open
def accession_policy_xml(study)
- Read upRead up
- Exclude checks
A Utility Function is any instance method that has no dependency on the state of the instance.
AccessionService#accession_sample_xml doesn't depend on instance state (maybe move it to another class?) Open
def accession_sample_xml(sample)
- Read upRead up
- Exclude checks
A Utility Function is any instance method that has no dependency on the state of the instance.
AccessionService#accession_submission_xml doesn't depend on instance state (maybe move it to another class?) Open
def accession_submission_xml(submission, accession_number) # rubocop:todo Metrics/AbcSize
- Read upRead up
- Exclude checks
A Utility Function is any instance method that has no dependency on the state of the instance.
AccessionService#accession_study_xml doesn't depend on instance state (maybe move it to another class?) Open
def accession_study_xml(study)
- Read upRead up
- Exclude checks
A Utility Function is any instance method that has no dependency on the state of the instance.
AccessionService#submit has the variable name 'e' Open
"Could not get accession number. Error in submitted data: #{$!} #{errors.map { |e| "\n - #{e}" }}"
- Read upRead up
- Exclude checks
An Uncommunicative Variable Name
is a variable name that doesn't communicate its intent well enough.
Poor names make it hard for the reader to build a mental picture of what's going on in the code. They can also be mis-interpreted; and they hurt the flow of reading, because the reader must slow down to interpret the names.
AccessionService#post_files has the variable name 'f' Open
AccessionedFile.open(param[:local_name]).tap { |f| f.original_filename = param[:remote_name] }
- Read upRead up
- Exclude checks
An Uncommunicative Variable Name
is a variable name that doesn't communicate its intent well enough.
Poor names make it hard for the reader to build a mental picture of what's going on in the code. They can also be mis-interpreted; and they hurt the flow of reading, because the reader must slow down to interpret the names.
AccessionService#post_files has the variable name 'e' Open
rescue StandardError => e
- Read upRead up
- Exclude checks
An Uncommunicative Variable Name
is a variable name that doesn't communicate its intent well enough.
Poor names make it hard for the reader to build a mental picture of what's going on in the code. They can also be mis-interpreted; and they hurt the flow of reading, because the reader must slow down to interpret the names.
TODO found Open
CenterName = 'SC' # TODO: [xxx] use confing file
- Exclude checks
TODO found Open
# TODO: check error
- Exclude checks