KarrLab/datanator_rest_api

View on GitHub

Showing 272 of 273 total issues

Blank line contains whitespace
Open

            
Severity: Minor
Found in datanator_rest_api/routes/reactions.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Continuation line over-indented for visual indent
Open

                                                   projection={"_id": 0})
Severity: Minor
Found in datanator_rest_api/routes/rna.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 (89 > 79 characters)
Open

            pipeline = pipelines.Pipeline().aggregate_total_array_length("modifications")
Severity: Minor
Found in datanator_rest_api/routes/rna.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 (85 > 79 characters)
Open

            pipeline = pipelines.Pipeline().aggregate_total_array_length("halflives")
Severity: Minor
Found in datanator_rest_api/routes/rna.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

                                    skip=skip)
Severity: Minor
Found in datanator_rest_api/routes/v2/entity.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 (81 > 79 characters)
Open

            # pipeline = pipelines.Pipeline().aggregate_total_array_length("poi")
Severity: Minor
Found in datanator_rest_api/routes/reactions.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.

Trailing whitespace
Open

            return result                
Severity: Minor
Found in datanator_rest_api/routes/rna.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Blank line contains whitespace
Open

    
Severity: Minor
Found in datanator_rest_api/routes/rna.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Continuation line under-indented for visual indent
Open

                                    limit=limit,
Severity: Minor
Found in datanator_rest_api/routes/v2/entity.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)

Trailing whitespace
Open

def create_app(apiName="DatanatorAPI.yaml", entryModule="datanator_rest_api.routes", 
Severity: Minor
Found in datanator_rest_api/core.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Line too long (101 > 79 characters)
Open

        return "https://github.com/KarrLab/datanator_rest_api/blob/master/{}.py".format(rel_filename)
Severity: Minor
Found in docs/conf.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 (110 > 79 characters)
Open

        return "https://github.com/KarrLab/datanator_rest_api/blob/master/{}/__init__.py".format(rel_filename)
Severity: Minor
Found in docs/conf.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

            #                 "if": {"$eq": [ {"$ifNull": ["$namespace", "pubmed"]}, "pubmed"]},
Severity: Minor
Found in datanator_rest_api/routes/reactions.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.

Trailing whitespace
Open

                        "count": 1, 
Severity: Minor
Found in datanator_rest_api/routes/reactions.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Closing bracket does not match visual indentation
Open

                    ]
Severity: Minor
Found in datanator_rest_api/routes/reactions.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)

Blank line contains whitespace
Open

    
Severity: Minor
Found in datanator_rest_api/routes/rna.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Trailing whitespace
Open

    class get_distinct:        
Severity: Minor
Found in datanator_rest_api/routes/rna.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

Trailing whitespace
Open

                    "Escherichia coli K-12": 8317, 
Severity: Minor
Found in datanator_rest_api/routes/taxon.py by pep8

Trailing whitespace is superfluous.

The warning returned varies on whether the line itself is blank,
for easier filtering for those who want to indent their blank lines.

Okay: spam(1)\n#
W291: spam(1) \n#
W293: class Foo(object):\n    \n    bang = 12

No newline at end of file
Open

application = create_app().app
Severity: Minor
Found in datanator_rest_api/core.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).

Too many blank lines (2)
Open

    class num_refs:
Severity: Minor
Found in datanator_rest_api/routes/reactions.py by pep8

Separate top-level function and class definitions with two blank lines.

Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass
Severity
Category
Status
Source
Language