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Source code for galaxy.tools.parser.util

from galaxy.util.odict import odict
from .error_level import StdioErrorLevel
from .interface import ToolStdioExitCode
from .interface import ToolStdioRegex


[docs]def is_dict(item): return isinstance(item, dict) or isinstance(item, odict)
[docs]def error_on_exit_code(out_of_memory_exit_code=None): exit_codes = [] if out_of_memory_exit_code: exit_code_oom = ToolStdioExitCode() exit_code_oom.range_start = int(out_of_memory_exit_code) exit_code_oom.range_end = int(out_of_memory_exit_code) _set_oom(exit_code_oom) exit_codes.append(exit_code_oom) exit_code_lower = ToolStdioExitCode() exit_code_lower.range_start = float("-inf") exit_code_lower.range_end = -1 _set_fatal(exit_code_lower) exit_codes.append(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) exit_codes.append(exit_code_high) return exit_codes, []
[docs]def aggressive_error_checks(): exit_codes, _ = error_on_exit_code() # these regexes are processed as case insensitive by default regexes = [ _oom_regex("MemoryError"), _oom_regex("std::bad_alloc"), _oom_regex("java.lang.OutOfMemoryError"), _oom_regex("Out of memory"), _error_regex("exception:"), _error_regex("error:") ] return exit_codes, regexes
def _oom_regex(match): regex = ToolStdioRegex() _set_oom(regex) regex.match = match regex.stdout_match = True regex.stderr_match = True return regex def _error_regex(match): regex = ToolStdioRegex() _set_fatal(regex) regex.match = match regex.stdout_match = True regex.stderr_match = True return regex def _set_oom(obj): obj.error_level = StdioErrorLevel.FATAL_OOM def _set_fatal(obj): obj.error_level = StdioErrorLevel.FATAL