Similar blocks of code found in 2 locations. Consider refactoring. Open
@@RESULT_DIRS = {
# Preprocessing
raw_reads: '01.raw_reads',
trimmed_reads: '02.trimmed_reads',
read_quality: '03.read_quality',
- Read upRead up
- Create a ticketCreate a ticket
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 28.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Use snake_case for method names. Open
def KNOWN_TYPES
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Use snake_case for method names. Open
def ONLY_NONMULTI_TASKS
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Use snake_case for method names. Open
def RESULT_DIRS
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Use snake_case for method names. Open
def EXCLUDE_NOREF_TASKS
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Use snake_case for method names. Open
def EXCLUDE_NOMARKER_TASKS
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Use snake_case for method names. Open
def PREPROCESSING_TASKS
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Use snake_case for variable names. Open
@@_ONLY_MULTI_TASKS_H = Hash[@@ONLY_MULTI_TASKS.map { |i| [i, true] }]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Replace class var @@KNOWN_TYPES with a class instance var. Open
@@KNOWN_TYPES = {
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Replace class var @@EXCLUDE_NOREF_TASKS with a class instance var. Open
@@EXCLUDE_NOREF_TASKS = %i[mytaxa_scan taxonomy]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Replace class var @@_ONLY_MULTI_TASKS_H with a class instance var. Open
@@_ONLY_MULTI_TASKS_H = Hash[@@ONLY_MULTI_TASKS.map { |i| [i, true] }]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Use snake_case for method names. Open
def ONLY_MULTI_TASKS
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Use snake_case for variable names. Open
@@RESULT_DIRS = {
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Replace class var @@EXCLUDE_NOMARKER_TASKS with a class instance var. Open
@@EXCLUDE_NOMARKER_TASKS = %i[essential_genes ssu]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Use snake_case for variable names. Open
@@ONLY_NONMULTI_TASKS = %i[mytaxa_scan taxonomy distances]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Replace class var @@RESULT_DIRS with a class instance var. Open
@@RESULT_DIRS = {
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Missing top-level class documentation comment. Open
class MiGA::Dataset < MiGA::MiGA
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for missing top-level documentation of classes and modules. Classes with no body are exempt from the check and so are namespace modules - modules that have nothing in their bodies except classes, other modules, or constant definitions.
The documentation requirement is annulled if the class or module has a "#:nodoc:" comment next to it. Likewise, "#:nodoc: all" does the same for all its children.
Example:
# bad
class Person
# ...
end
# good
# Description/Explanation of Person class
class Person
# ...
end
Missing top-level module documentation comment. Open
module MiGA::Dataset::Base
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for missing top-level documentation of classes and modules. Classes with no body are exempt from the check and so are namespace modules - modules that have nothing in their bodies except classes, other modules, or constant definitions.
The documentation requirement is annulled if the class or module has a "#:nodoc:" comment next to it. Likewise, "#:nodoc: all" does the same for all its children.
Example:
# bad
class Person
# ...
end
# good
# Description/Explanation of Person class
class Person
# ...
end
Use snake_case for variable names. Open
@@EXCLUDE_NOMARKER_TASKS = %i[essential_genes ssu]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Wontfix
@@OPTIONS = {
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Replace class var @@_EXCLUDE_NOMARKER_TASKS_H with a class instance var. Open
@@_EXCLUDE_NOMARKER_TASKS_H =
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Replace class var @@OPTIONS with a class instance var. Wontfix
@@OPTIONS = {
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Replace class var @@ONLY_NONMULTI_TASKS with a class instance var. Open
@@ONLY_NONMULTI_TASKS = %i[mytaxa_scan taxonomy distances]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Use snake_case for variable names. Open
@@_EXCLUDE_NOREF_TASKS_H = Hash[@@EXCLUDE_NOREF_TASKS.map { |i| [i, true] }]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Open
@@ONLY_MULTI_TASKS = %i[mytaxa]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Open
@@EXCLUDE_NOREF_TASKS = %i[mytaxa_scan taxonomy]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Open
@@_EXCLUDE_NOMARKER_TASKS_H =
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Open
@@PREPROCESSING_TASKS = %i[
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Open
@@_ONLY_NONMULTI_TASKS_H = Hash[@@ONLY_NONMULTI_TASKS.map { |i| [i, true] }]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Open
@@KNOWN_TYPES = {
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Replace class var @@PREPROCESSING_TASKS with a class instance var. Open
@@PREPROCESSING_TASKS = %i[
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Replace class var @@_EXCLUDE_NOREF_TASKS_H with a class instance var. Open
@@_EXCLUDE_NOREF_TASKS_H = Hash[@@EXCLUDE_NOREF_TASKS.map { |i| [i, true] }]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Use snake_case for method names. Wontfix
def OPTIONS
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Replace class var @@_ONLY_NONMULTI_TASKS_H with a class instance var. Open
@@_ONLY_NONMULTI_TASKS_H = Hash[@@ONLY_NONMULTI_TASKS.map { |i| [i, true] }]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.
Replace class var @@ONLY_MULTI_TASKS with a class instance var. Open
@@ONLY_MULTI_TASKS = %i[mytaxa]
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.