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[24.2] ValueError: invalid literal for int() with base 10: 'inf' #19456

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galaxyproject-sentryintegration bot opened this issue Jan 24, 2025 · 3 comments

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@galaxyproject-sentryintegration

Sentry Issue: GALAXY-MAIN-10TB

ValueError: invalid literal for int() with base 10: 'inf'
(16 additional frame(s) were not displayed)
...
  File "galaxy/tools/parameters/basic.py", line 204, in __init__
    self.validators = validation.to_validators(tool.app if tool else None, input_source.parse_validators())
  File "galaxy/tool_util/parser/xml.py", line 1352, in parse_validators
    return parse_xml_validators(self.input_elem)
  File "galaxy/tool_util/parser/parameter_validators.py", line 489, in parse_xml_validators
    models.append(parse_xml_validator(validator_el))
  File "galaxy/tool_util/parser/parameter_validators.py", line 529, in parse_xml_validator
    max=_parse_number(validator_el, "max"),
  File "galaxy/tool_util/parser/parameter_validators.py", line 701, in _parse_number
    return int(raw_value)

Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/0b9feb0ed628/fastq_trimmer/fastq_trimmer.xml
@mvdbeek
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mvdbeek commented Jan 24, 2025

The validator in question is <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> ... obviously a little nonsensical.

mvdbeek added a commit to mvdbeek/galaxy that referenced this issue Jan 24, 2025
@mvdbeek mvdbeek self-assigned this Jan 24, 2025
@nsoranzo
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This is from fastq_trimmer 1.0.1 when it was still in tools-devteam, and it was fixed in version 1.1.1 galaxyproject/tools-devteam#449 . Do we have other cases of this? Otherwise not sure it's worth workaround it.

@mvdbeek
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mvdbeek commented Jan 24, 2025

It's pretty obviously a bug with a simple fix, I think we should just merge #19459 ?

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