Showing 16,957 of 16,957 total issues
Similar blocks of code found in 3 locations. Consider refactoring. Open
def rfam
return nil unless id.match(RFAM_ID_PATTERN) or title.match(RFAM_ID_PATTERN)
rfam_id = Regexp.last_match[1]
rfam_id = encode rfam_id
url = "https://rfam.xfam.org/family/#{rfam_id}"
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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 33.
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
Avoid too many return
statements within this function. Open
return v / conf.ticks.labelDenominator + conf.ticks.labelSuffix;
Similar blocks of code found in 2 locations. Consider refactoring. Open
let lsend =
nsseq +
(lsseq.length - lsseq.split("-").length) *
sframe_unit() *
sframe_sign();
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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 45.
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
Similar blocks of code found in 2 locations. Consider refactoring. Open
let lqend =
nqseq +
(lqseq.length - lqseq.split("-").length) *
qframe_unit() *
qframe_sign();
- Read upRead up
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 45.
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
Method validate_options
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def validate_options(options)
return true if !options || (options.is_a?(String) &&
options.strip.empty?)
fail InputError, 'Invalid characters detected in options.' unless allowed_chars.match(options)
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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 check_num_threads
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def check_num_threads
num_threads = Integer(config[:num_threads])
fail NUM_THREADS_INCORRECT unless num_threads.positive?
logger.debug "Will use #{num_threads} threads to run BLAST."
if num_threads > 256
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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 write_entries
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def write_entries(entries, path, zipfile)
entries.each do |e|
zipfile_path = path == '' ? e : File.join(path, e)
disk_file_path = File.join(@input_dir, zipfile_path)
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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 update_searchdata_from_job
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def update_searchdata_from_job(searchdata)
job = fetch_job(params[:job_id])
return { error: 'Job not found' }.to_json if job.nil?
return if job.imported_xml_file
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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 probably_fastas
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def probably_fastas
return @probably_fastas if defined?(@probably_fastas)
@probably_fastas = []
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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 init_binaries
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def init_binaries
if config[:bin]
config[:bin] = File.expand_path config[:bin]
unless File.exist?(config[:bin]) && File.directory?(config[:bin])
fail ENOENT.new('bin dir', config[:bin])
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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
Function determineBlastMethods
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
determineBlastMethods() {
var database_type = this.databaseType;
var sequence_type = this.sequenceType;
if (this.query.current.isEmpty()) {
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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
Function selectHit
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
selectHit(id) {
var checkbox = $('#' + id);
var num_checked = $('.hit-links :checkbox:checked').length;
if (!checkbox || !checkbox.val()) return;
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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
Incorrect indentation detected (column 7 instead of 4). Open
# 'Run SequenceServer doctor'
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- Exclude checks
This cop checks the indentation of comments.
Example:
# bad
# comment here
def method_name
end
# comment here
a = 'hello'
# yet another comment
if true
true
end
# good
# comment here
def method_name
end
# comment here
a = 'hello'
# yet another comment
if true
true
end
Final newline missing. Open
end
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- Exclude checks
This cop looks for trailing blank lines and a final newline in the source code.
Example: EnforcedStyle: finalblankline
# `final_blank_line` looks for one blank line followed by a new line
# at the end of files.
# bad
class Foo; end
# EOF
# bad
class Foo; end # EOF
# good
class Foo; end
# EOF
Example: EnforcedStyle: final_newline (default)
# `final_newline` looks for one newline at the end of files.
# bad
class Foo; end
# EOF
# bad
class Foo; end # EOF
# good
class Foo; end
# EOF
Prefer single-quoted strings when you don't need string interpolation or special symbols. Open
post_email_cmd = "curl -m 5 https://docs.google.com/forms/u/0/d/e/" \
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- Exclude checks
Checks if uses of quotes match the configured preference.
Example: EnforcedStyle: single_quotes (default)
# bad
"No special symbols"
"No string interpolation"
"Just text"
# good
'No special symbols'
'No string interpolation'
'Just text'
"Wait! What's #{this}!"
Example: EnforcedStyle: double_quotes
# bad
'Just some text'
'No special chars or interpolation'
# good
"Just some text"
"No special chars or interpolation"
"Every string in #{project} uses double_quotes"
Favor modifier unless
usage when having a single-line body. Another good alternative is the usage of control flow &&
/||
. Open
unless environment == 'test'
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- Exclude checks
Checks for if
and unless
statements that would fit on one line if
written as modifier if
/unless
. The cop also checks for modifier
if
/unless
lines that exceed the maximum line length.
The maximum line length is configured in the Layout/LineLength
cop. The tab size is configured in the IndentationWidth
of the
Layout/IndentationStyle
cop.
Example:
# bad
if condition
do_stuff(bar)
end
unless qux.empty?
Foo.do_something
end
do_something_with_a_long_name(arg) if long_condition_that_prevents_code_fit_on_single_line
# good
do_stuff(bar) if condition
Foo.do_something unless qux.empty?
if long_condition_that_prevents_code_fit_on_single_line
do_something_with_a_long_name(arg)
end
if short_condition # a long comment that makes it too long if it were just a single line
do_something
end
Use raise
instead of fail
to rethrow exceptions. Open
fail BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE
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- Exclude checks
This cop checks for uses of fail
and raise
.
Example: EnforcedStyle: only_raise (default)
# The `only_raise` style enforces the sole use of `raise`.
# bad
begin
fail
rescue Exception
# handle it
end
def watch_out
fail
rescue Exception
# handle it
end
Kernel.fail
# good
begin
raise
rescue Exception
# handle it
end
def watch_out
raise
rescue Exception
# handle it
end
Kernel.raise
Example: EnforcedStyle: only_fail
# The `only_fail` style enforces the sole use of `fail`.
# bad
begin
raise
rescue Exception
# handle it
end
def watch_out
raise
rescue Exception
# handle it
end
Kernel.raise
# good
begin
fail
rescue Exception
# handle it
end
def watch_out
fail
rescue Exception
# handle it
end
Kernel.fail
Example: EnforcedStyle: semantic
# The `semantic` style enforces the use of `fail` to signal an
# exception, then will use `raise` to trigger an offense after
# it has been rescued.
# bad
begin
raise
rescue Exception
# handle it
end
def watch_out
# Error thrown
rescue Exception
fail
end
Kernel.fail
Kernel.raise
# good
begin
fail
rescue Exception
# handle it
end
def watch_out
fail
rescue Exception
raise 'Preferably with descriptive message'
end
explicit_receiver.fail
explicit_receiver.raise
Assignment Branch Condition size for initialize is too high. [<12, 24, 2> 26.91/17] Open
def initialize(params)
if params.key?(:xml)
super do
@imported_xml_file = File.basename params[:xml]
# Copy over the XML file to job directory so that a job dir in
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- Exclude checks
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
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- Exclude checks
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 []
)
Add empty line after guard clause. Open
return if alias?
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- Exclude checks
This cop enforces empty line after guard clause
Example:
# bad
def foo
return if need_return?
bar
end
# good
def foo
return if need_return?
bar
end
# good
def foo
return if something?
return if something_different?
bar
end
# also good
def foo
if something?
do_something
return if need_return?
end
end