Function parse has a Cognitive Complexity of 111 (exceeds 5 allowed). Consider refactoring. Open
def parse(self):
print('Parsing Entrez...')
symbol_to_info = dict()
hgnc_id_to_info = dict()
entrez_to_info = dict()- 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 write has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring. Open
def write(self):
print('Writing to .tsv...')
i = 0
no_ensembl = no_entrez = total = 0
header = ('count', 'drug_id', 'drug_name', 'drug_synonyms', 'drug_cas_number', 'drug_brands',- 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 get_drugbank.py has 257 lines of code (exceeds 250 allowed). Consider refactoring. Open
__author__ = 'Kelsy C Cotto'
import zipfile
import os
import sysAvoid deeply nested control flow statements. Open
if isinstance(datum, tuple):
datum = ';'.join(str(x) for x in datum)
datum = str(datum).replace("\t", '')Avoid deeply nested control flow statements. Open
if identifier.find('entry:resource',ns).text == 'HUGO Gene Nomenclature Committee (HGNC)':
hgnc_gene_acc = identifier.find('entry:identifier', ns).text
# Some identifiers are incorrectly labeled by DrugBank
r = re.compile(r'^\d+$')
if hgnc_gene_acc.startswith('GNC:'):Avoid deeply nested control flow statements. Open
if not datum or datum == 'None':
datum = 'N/A'
out.append(datum)Identical blocks of code found in 2 locations. Consider refactoring. Open
def download_file(self, url, local_filename):
# NOTE the stream=True parameter
r = requests.get(url, stream=True, allow_redirects=True, auth=HTTPBasicAuth(self.username, self.password))
with open(local_filename, 'wb') as f:
for chunk in r.iter_content(chunk_size=1024):- 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 76.
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
Identical blocks of code found in 2 locations. Consider refactoring. Open
def update(self):
if not self.is_current():
self.download_files()
self.parse()
self.write()- 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 39.
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