Function parse_content has a Cognitive Complexity of 49 (exceeds 5 allowed). Consider refactoring. Open
def parse_content(self, ec_code, ec_data, type, val):
if type == 'PR':
match = re.match((
r'^#(\d+)#'
r'[ \n](.*?)'- 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
Function run has a Cognitive Complexity of 48 (exceeds 5 allowed). Consider refactoring. Open
def run(self, raw_filename=None, processed_filename=None, max_entries=None):
raw_filename = raw_filename or self.RAW_FILENAME
processed_filename = str(Path(processed_filename).expanduser()) or self.PROCESSED_FILENAME
max_entries = max_entries or self.MAX_ENTRIES
- 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
File core.py has 365 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Machinery for parsing k_cats and K_ms from `BRENDA <https://www.brenda-enzymes.org/>`_.
#. Download BRENDA text file from https://www.brenda-enzymes.org/download_brenda_without_registration.php.
#. Extract brenda_download.txt from zip archive and save to `./brenda_download.txt`
#. Run the parser in this module::Function parse_comments has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring. Open
def parse_comments(self, comment_strs):
if not comment_strs:
return []
comment_strs = re.split(r';[ \n]', comment_strs.strip())- 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
Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring. Open
def __init__(self, MongoDB=None, db=None, username=None, password=None,Avoid deeply nested control flow statements. Open
if val_type == 'ID':
ec_data = self.parse_ec_code(data, val_content)
else:
self.parse_content(ec_code, ec_data, val_type, val_content)
Function filter_comments has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def filter_comments(self, comments, enz_id):
filtered_comments = []
for comment in comments:
has_comment = False
for enz_ref_id in comment['enz_ref_ids']:- 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
Similar blocks of code found in 2 locations. Consider refactoring. Open
for k_cat in ec_data['k_cats']:
k_cat['refs'] = [ec_data['refs'][ref_id] for ref_id in k_cat['ref_ids']]- 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 49.
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
for k_m in ec_data['k_ms']:
k_m['refs'] = [ec_data['refs'][ref_id] for ref_id in k_m['ref_ids']]- 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 49.
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