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[21.09] Skip non JSON-encodable values in params_to_strings() #13826

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[21.09] Skip non JSON-encodable values in params_to_strings() #13826

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2498912
Skip non JSON-encodable values in ``params_to_strings()``
nsoranzo Apr 28, 2022
cb2ead5
Fix mypy error
davelopez Apr 12, 2022
97a9001
Add type hint suggestion
davelopez Apr 12, 2022
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15 changes: 12 additions & 3 deletions lib/galaxy/tools/parameters/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
"""
Classes encapsulating Galaxy tool parameters.
"""

import logging
from json import dumps

from boltons.iterutils import remap
Expand All @@ -19,6 +19,8 @@
)
from .grouping import Conditional, Repeat, Section, UploadDataset

log = logging.getLogger(__name__)

REPLACE_ON_TRUTHY = object()

# Some tools use the code tag and access the code base, expecting certain tool parameters to be available here.
Expand Down Expand Up @@ -205,14 +207,21 @@ def params_to_strings(params, param_values, app, nested=False, use_security=Fals
Convert a dictionary of parameter values to a dictionary of strings
suitable for persisting. The `value_to_basic` method of each parameter
is called to convert its value to basic types, the result of which
is then json encoded (this allowing complex nested parameters and
is then JSON encoded (this allowing complex nested parameters and
such).
If the value is not JSON-encodable, the key/value pair is skipped.
"""
rval = dict()
for key, value in param_values.items():
if key in params:
value = params[key].value_to_basic(value, app, use_security=use_security)
rval[key] = value if nested or value is None else str(dumps(value, sort_keys=True))
if not nested and value is not None:
try:
value = dumps(value, sort_keys=True)
except Exception as e:
log.warning(f"Error while serializing value {value} for key {key}: {e}")
continue
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Seems risky, don't you want to raise here ?

rval[key] = value
return rval


Expand Down
3 changes: 1 addition & 2 deletions lib/galaxy/util/bool_expressions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,6 @@
from pyparsing import (
alphanums,
CaselessKeyword,
Forward,
infixNotation,
Keyword,
opAssoc,
Expand Down Expand Up @@ -132,7 +131,7 @@ def __init__(self, evaluator: TokenEvaluator, token_format: Optional[str] = None
action.evaluator = evaluator
boolOperand = TRUE | FALSE | Word(token_format or DEFAULT_TOKEN_FORMAT)
boolOperand.setParseAction(action)
self.boolExpr: Forward = infixNotation(
self.boolExpr: ParserElement = infixNotation(
boolOperand,
[
(NOT_OP, 1, opAssoc.RIGHT, BoolNot),
Expand Down