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