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KarrLab/datanator_rest_api

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Showing 272 of 273 total issues

Trailing whitespace
Open

        def get(protein_name='Protein translocase subunit SecD', _from=0, size=10,
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

Too many blank lines (2)
Open

    class get_total_docs:
Severity: Minor
Found in datanator_rest_api/routes/rna.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

Too many blank lines (2)
Open

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

Trailing whitespace
Open

                    "Rattus norvegicus": 12124,
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

                                             skip=skip)
Severity: Minor
Found in datanator_rest_api/routes/v2/observation.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).

Continuation line over-indented for visual indent
Open

                                                         collation=r_manager.collation)
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/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

Trailing whitespace
Open

                    "Escherichia coli str. K-12 substr. MG1655": 11788,
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

Trailing whitespace
Open

                    "Lactococcus lactis subsp. lactis Il1403": 10983,
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

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

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

        projection = eval(projection)
Severity: Minor
Found in datanator_rest_api/routes/reactions.py by bandit

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

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

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

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

Consider possible security implications associated with subprocess module.
Open

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

Library itsdangerous contains unrecogonized licenses: Unknown
Open

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

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

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

        projection = eval(projection)
Severity: Minor
Found in datanator_rest_api/routes/reactions.py by bandit
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