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reimandlab/Visualistion-Framework-for-Genome-Mutations

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website/helpers/filters/manager.py

Summary

Maintainability
C
1 day
Test Coverage

File manager.py has 322 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import re
from collections import namedtuple, defaultdict

from sqlalchemy import and_
Severity: Minor
Found in website/helpers/filters/manager.py - About 3 hrs to fix

    Function joined_query has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
    Open

    def joined_query(query, required_joins, limit_to=None):
    already_joined = set()
    for joins in required_joins:
        for join in joins:
            if limit_to and join not in limit_to:
    Severity: Minor
    Found in website/helpers/filters/manager.py - About 1 hr 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

    Function prepare_filters has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    Open

        def prepare_filters(self, target=None):

        to_apply_manually = []
        query_filters = []
        all_required_joins = []
    Severity: Minor
    Found in website/helpers/filters/manager.py - About 1 hr 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

    Function reformat_request_url has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

        def reformat_request_url(self, request, endpoint, *args, **kwargs):
        from flask import url_for
        from flask import redirect
        from flask import current_app
    Severity: Minor
    Found in website/helpers/filters/manager.py - About 55 mins 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

    Function _parse_request has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def _parse_request(self, request):
        """Extract and normalize filters' data from Flask's request object.

        Arguments will be extracted from request.args or request.form.
    Severity: Minor
    Found in website/helpers/filters/manager.py - About 35 mins 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

    Avoid too many return statements within this function.
    Open

                return [self._parse_value(v, True) for v in splitted]
    Severity: Major
    Found in website/helpers/filters/manager.py - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

              return value
      Severity: Major
      Found in website/helpers/filters/manager.py - About 30 mins to fix

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

                        key: value[0] if isinstance(value, list) and len(value) == 1 else value
        Severity: Minor
        Found in website/helpers/filters/manager.py and 1 other location - About 35 mins to fix
        website/helpers/filters/manager.py on lines 426..428

        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

        Further Reading

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

                            arg + '=' + (
                        value[0]
                        if (isinstance(value, list) and len(value) == 1) else
        Severity: Minor
        Found in website/helpers/filters/manager.py and 1 other location - About 35 mins to fix
        website/helpers/filters/manager.py on lines 301..301

        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

        Further Reading

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

                    if match:
                name = match.group(1)
                filters[name]['value'] = value
        Severity: Minor
        Found in website/helpers/filters/manager.py and 1 other location - About 30 mins to fix
        website/helpers/filters/manager.py on lines 258..260

        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 32.

        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

                    if match:
                name = match.group(1)
                filters[name]['cmp'] = value
        Severity: Minor
        Found in website/helpers/filters/manager.py and 1 other location - About 30 mins to fix
        website/helpers/filters/manager.py on lines 253..255

        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 32.

        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

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