KarrLab/datanator_rest_api

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Showing 272 of 273 total issues

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.

Trailing whitespace
Open

                    "Homo sapiens": 51775, 
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

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

                    "Escherichia coli": 7875, 
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

Line too long (84 > 79 characters)
Open

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

Trailing blank lines are superfluous.

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

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

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 (93 > 79 characters)
Open

filename = os.path.join(os.path.dirname(__file__), "..", "datanator_rest_api", "_version.py")
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.

Module level import not at top of file
Open

import re
Severity: Minor
Found in docs/conf.py by pep8

Place imports at the top of the file.

Always put imports at the top of the file, just after any module
comments and docstrings, and before module globals and constants.

Okay: import os
Okay: # this is a comment\nimport os
Okay: '''this is a module docstring'''\nimport os
Okay: r'''this is a module docstring'''\nimport os
Okay:
try:\n\timport x\nexcept ImportError:\n\tpass\nelse:\n\tpass\nimport y
Okay:
try:\n\timport x\nexcept ImportError:\n\tpass\nfinally:\n\tpass\nimport y
E402: a=1\nimport os
E402: 'One string'\n"Two string"\nimport os
E402: a=1\nfrom sys import x

Okay: if x:\n    import os

Possible binding to all interfaces.
Open

    create_app().run(host='0.0.0.0', port=8080, debug=True)
Severity: Minor
Found in datanator_rest_api/core.py by bandit

Use of possibly insecure function - consider using safer ast.literal_eval.
Open

        projection = eval(projection)

Library itsdangerous contains unrecogonized licenses: Unknown
Open

itsdangerous==1.1.0
Severity: Minor
Found in requirements.txt by git-legal

No licenses found for py. Either the library reports the licenses in an unsupported format, or the library is unlicensed.
Open

py==1.8.1
Severity: Minor
Found in requirements.txt by git-legal

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

    assert match and tuple(match.group(1).split('.')) >= ('0', '0', '5')
Severity: Info
Found in setup.py by bandit

Consider possible security implications associated with subprocess module.
Open

import subprocess
Severity: Info
Found in setup.py by bandit

No licenses found for pluggy. Either the library reports the licenses in an unsupported format, or the library is unlicensed.
Open

pluggy==0.13.1
Severity: Minor
Found in requirements.txt by git-legal

subprocess call - check for execution of untrusted input.
Open

    result = subprocess.run(
        [sys.executable, "-m", "pip", "show", "pkg_utils"],
        check=True, capture_output=True)
Severity: Info
Found in setup.py by bandit

subprocess call - check for execution of untrusted input.
Open

    subprocess.run(
        [sys.executable, "-m", "pip", "install", "-U", "pkg_utils"],
        check=True)
Severity: Info
Found in setup.py by bandit

Use of possibly insecure function - consider using safer ast.literal_eval.
Open

        projection = eval(projection)

A Flask app appears to be run with debug=True, which exposes the Werkzeug debugger and allows the execution of arbitrary code.
Open

    create_app().run(host='0.0.0.0', port=8080, debug=True)
Severity: Major
Found in datanator_rest_api/core.py by bandit
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