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datanator_rest_api/util/taxon_distance.py

Summary

Maintainability
A
1 hr
Test Coverage
A
100%

Function get_dist_object has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def get_dist_object(self, doc, queried_species, distance_obj,
Severity: Major
Found in datanator_rest_api/util/taxon_distance.py - About 50 mins to fix

Function get_dist_object has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def get_dist_object(self, doc, queried_species, distance_obj,
                    target_species, org_format='tax_id',
                    tax_field='species_name', obj_name='taxon_distance'):
        """Return taxon_distance object for frontend.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py - About 25 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

Method "get_dist_object" has 8 parameters, which is greater than the 7 authorized.
Open

    def get_dist_object(self, doc, queried_species, distance_obj,
                    target_species, org_format='tax_id',
                    tax_field='species_name', obj_name='taxon_distance'):
Severity: Major
Found in datanator_rest_api/util/taxon_distance.py by sonar-python

A long parameter list can indicate that a new structure should be created to wrap the numerous parameters or that the function is doing too many things.

Noncompliant Code Example

With a maximum number of 4 parameters:

def do_something(param1, param2, param3, param4, param5):
    ...

Compliant Solution

def do_something(param1, param2, param3, param4):
    ...

Line too long (97 > 79 characters)
Open

            docs(:obj:`Iter`): Documents that need calculation of taxon_distance and rearranging.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (101 > 79 characters)
Open

            obj_name(:obj:`str`, optional): name of the object containing taxon distance information.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (102 > 79 characters)
Open

            dist = manager.get_canon_common_ancestor_fast(name, target_species, org_format=org_format)
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (96 > 79 characters)
Open

            (:obj:`list` of :obj:`Obj`): List of documents that have the taxon_distance objects.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Continuation line under-indented for visual indent
Open

                    target_species, org_format='tax_id',
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Continuation line under-indented for visual indent
Open

                    tax_field='species_name', obj_name='taxon_distance'):
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Continuation lines indentation.

Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

Line too long (91 > 79 characters)
Open

            distance_obj (:obj:`Obj`): distance objects containing already queried species.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (129 > 79 characters)
Open

                                                                      target_species, tax_field=tax_field, org_format=org_format)
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (93 > 79 characters)
Open

            tax_field(:obj:`str`, optional): Field containing taxon information in documents.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (105 > 79 characters)
Open

            queried_species, distance_obj, doc = self.get_dist_object(doc, queried_species, distance_obj,
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (94 > 79 characters)
Open

            target_species(:obj:`str` or :obj:`int`, optional): User input for target species.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (119 > 79 characters)
Open

            org_format (:obj:`str`, optional): format of species identifier (tax_id or tax_name). Defaults to 'tax_id'.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

No newline at end of file
Open

        return result
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Trailing blank lines are superfluous.

Okay: spam(1)
W391: spam(1)\n

However the last line should end with a new line (warning W292).

Line too long (119 > 79 characters)
Open

            org_format (:obj:`str`, optional): format of species identifier (tax_id or tax_name). Defaults to 'tax_id'.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (93 > 79 characters)
Open

            tax_field(:obj:`str`, optional): field containing taxon information in documents.
Severity: Minor
Found in datanator_rest_api/util/taxon_distance.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

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