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Source code for galaxy.tools.parser.util

from .interface import ToolStdioExitCode
from .interface import ToolStdioRegex

[docs]def error_on_exit_code(): exit_code_lower = ToolStdioExitCode() exit_code_lower.range_start = float("-inf") exit_code_lower.range_end = -1 _set_fatal(exit_code_lower) exit_code_high = ToolStdioExitCode() exit_code_high.range_start = 1 exit_code_high.range_end = float("inf") _set_fatal(exit_code_high) return [exit_code_lower, exit_code_high], []
[docs]def aggressive_error_checks(): exit_codes, _ = error_on_exit_code() # these regexes are processed as case insensitive by default regexes = [ _error_regex("exception:"), _error_regex("error:") ] return exit_codes, regexes
def _error_regex(match): regex = ToolStdioRegex() _set_fatal(regex) regex.match = match regex.stdout_match = True regex.stderr_match = True return regex def _set_fatal(obj): from galaxy.jobs.error_level import StdioErrorLevel obj.error_level = StdioErrorLevel.FATAL