Sign upLogin

KarrLab/bpforms

View on GitHub
Star
bpforms/rest.py

Summary

Maintainability
C
1 day
Test Coverage
A
100%

Function post has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

    def post(self):
        """ Optionally, calculate the major protonation and tautomerization form a biopolymer form and calculate its properties """
        """
        Returns:
            :obj:`dict`
Severity: Minor
Found in bpforms/rest.py - About 2 hrs to fix

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 rest.py has 273 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" REST JSON API

:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2019-02-05
:Copyright: 2019, Karr Lab
Severity: Minor
Found in bpforms/rest.py - About 2 hrs to fix

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        try:
        alphabet_obj = bpforms.util.get_alphabet(id)
    except ValueError as error:
        flask_restplus.abort(400, 'Invalid alphabet "{}"'.format(id))
    Severity: Major
    Found in bpforms/rest.py and 1 other location - About 1 hr to fix
    bpforms/rest.py on lines 281..284

    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 38.

    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

    Further Reading

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        try:
        alphabet_obj = bpforms.util.get_alphabet(alphabet)
    except ValueError as error:
        flask_restplus.abort(400, 'Invalid alphabet "{}"'.format(alphabet))
    Severity: Major
    Found in bpforms/rest.py and 1 other location - About 1 hr to fix
    bpforms/rest.py on lines 237..240

    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 38.

    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

    Further Reading

    Identical blocks of code found in 3 locations. Consider refactoring.
    Open

    @bpforms.core.cache.memoize(typed=False, expire=30 * 24 * 60 * 60)
    Severity: Major
    Found in bpforms/rest.py and 2 other locations - About 40 mins to fix
    bpforms/rest.py on lines 227..227
    bpforms/rest.py on lines 269..269

    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 34.

    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

    Further Reading

    Identical blocks of code found in 3 locations. Consider refactoring.
    Open

    @bpforms.core.cache.memoize(typed=False, expire=30 * 24 * 60 * 60)
    Severity: Major
    Found in bpforms/rest.py and 2 other locations - About 40 mins to fix
    bpforms/rest.py on lines 227..227
    bpforms/rest.py on lines 312..312

    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 34.

    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

    Further Reading

    Identical blocks of code found in 3 locations. Consider refactoring.
    Open

    @bpforms.core.cache.memoize(typed=False, expire=30 * 24 * 60 * 60)
    Severity: Major
    Found in bpforms/rest.py and 2 other locations - About 40 mins to fix
    bpforms/rest.py on lines 269..269
    bpforms/rest.py on lines 312..312

    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 34.

    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

    Further Reading

    There are no issues that match your filters.

    Category
    Status