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v2: prettify petablint output #400

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Merged
dweindl merged 1 commit into from
Jul 3, 2025
Merged

v2: prettify petablint output #400

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23 changes: 18 additions & 5 deletions petab/petablint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import logging
import sys

import pydantic
from colorama import Fore
from colorama import init as init_colorama
from jsonschema.exceptions import ValidationError as SchemaValidationError
Expand Down Expand Up @@ -179,12 +180,24 @@ def main():
case 2:
from petab.v2.lint import lint_problem

validation_issues = lint_problem(args.yaml_file_name)
if validation_issues:
validation_issues.log(logger=logger)
try:
validation_issues = lint_problem(args.yaml_file_name)
if validation_issues:
# Handle petab.v2.lint.ValidationTask issues
validation_issues.log(logger=logger)
sys.exit(1)
logger.info("PEtab format check completed successfully.")
sys.exit(0)
except pydantic.ValidationError as e:
# Handle Pydantic validation errors
for err in e.errors():
loc = ", ".join(str(loc) for loc in err["loc"])
msg = err["msg"]
# TODO: include model info here once available
# https://github.com/pydantic/pydantic/issues/7224
logger.error(f"Error in field(s) `{loc}`: {msg}")
sys.exit(1)
logger.info("PEtab format check completed successfully.")
sys.exit(0)

case _:
logger.error(
"The provided PEtab files are of unsupported version "
Expand Down