Unverified Commit 9a08a76a authored by Nicola Soranzo's avatar Nicola Soranzo Committed by GitHub
Browse files

Merge pull request #14284 from mvdbeek/fix_json_encoding_things

parents 881ed5c7 73c73e08

lib/galaxy/tools/__init__.py

+5 −2
Original line number Diff line number Diff line
@@ -120,7 +120,10 @@ from galaxy.util.bunch import Bunch 
from galaxy.util.dictifiable import Dictifiable

from galaxy.util.expressions import ExpressionContext

from galaxy.util.form_builder import SelectField

from galaxy.util.json import safe_loads

from galaxy.util.json import (

    safe_loads,

    swap_inf_nan,

)

from galaxy.util.rules_dsl import RuleSet

from galaxy.util.template import (

    fill_template,
@@ -2459,7 +2462,7 @@ class Tool(Dictifiable): 
                "enctype": self.enctype,

            }

        )

        return tool_model

        return swap_inf_nan(tool_model)



    def populate_model(self, request_context, inputs, state_inputs, group_inputs, other_values=None):

        """

lib/galaxy/util/json.py

+8 −4
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ from collections.abc import ( 
    Mapping,

    Sequence,

)

from decimal import Decimal



from ..util import unicodify
@@ -22,7 +23,8 @@ from_json_string = json.loads 


def swap_inf_nan(val):

    """

    This takes an arbitrary object and preps it for jsonifying safely, templating Inf/NaN.

    This takes an arbitrary object and preps it for jsonifying safely, templating Inf/NaN and

    casting Decimal instances as strings.

    """

    if isinstance(val, str):

        # basestring first, because it's a sequence and would otherwise get caught below.
@@ -40,6 +42,8 @@ def swap_inf_nan(val): 
            return "__-Infinity__"

        else:

            return val

    elif isinstance(val, Decimal):

        return str(val)

    else:

        return val
@@ -63,12 +67,12 @@ def safe_dumps(obj, **kwargs): 
    """

    This is a wrapper around dumps that encodes Infinity and NaN values.  It's a

    fairly rare case (which will be low in request volume).  Basically, we tell

    json.dumps to blow up if it encounters Infinity/NaN, and we 'fix' it before

    re-encoding.

    json.dumps to blow up if it encounters Infinity/NaN, or Decimal values

    and we 'fix' it before re-encoding.

    """

    try:

        dumped = json.dumps(obj, allow_nan=False, **kwargs)

    except ValueError:

    except (ValueError, TypeError):

        obj = swap_inf_nan(obj)

        dumped = json.dumps(obj, allow_nan=False, **kwargs)

    if kwargs.get("escape_closing_tags", True):

test/unit/util/test_json.py

0 → 100644
+25 −0
Original line number Diff line number Diff line 
from decimal import Decimal



import pytest



from galaxy.util.json import (

    safe_dumps,

    swap_inf_nan,

)





@pytest.mark.parametrize(

    "val,expected_val",

    [

        (float("inf"), "__Infinity__"),

        (float("-inf"), "__-Infinity__"),

        (float("NaN"), "__NaN__"),

        (Decimal("1"), "1"),

    ],

)

def test_swap_inf_nan(val, expected_val):

    assert swap_inf_nan(val) == expected_val





def test_safe_dumps():

    assert safe_dumps({"a": Decimal("0.1")}) == """{"a": "0.1"}"""