Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tool_util.parser.stdio

import math


[docs]class StdioErrorLevel: """ These determine stdio-based error levels from matching on regular expressions and exit codes. They are meant to be used comparatively, such as showing that warning < fatal. This is really meant to just be an enum. """ NO_ERROR = 0 LOG = 1 QC = 1.1 WARNING = 2 FATAL = 3 FATAL_OOM = 4 MAX = 4 descs = { NO_ERROR: "No error", LOG: "Log", QC: "QC", WARNING: "Warning", FATAL: "Fatal error", FATAL_OOM: "Out of memory error", }
[docs] @staticmethod def desc(error_level): err_msg = "Unknown error" if error_level > 0 and error_level <= StdioErrorLevel.MAX: err_msg = StdioErrorLevel.descs[error_level] return err_msg
[docs]class ToolStdioExitCode: """ This is a container for the <stdio> element's <exit_code> subelement. The exit_code element has a range of exit codes and the error level. """
[docs] def __init__(self, as_dict=None): as_dict = as_dict or {} self.range_start = as_dict.get("range_start", -math.inf) self.range_end = as_dict.get("range_end", math.inf) self.error_level = as_dict.get("error_level", StdioErrorLevel.FATAL) self.desc = as_dict.get("desc", "")
[docs] def to_dict(self): return { "class": "ToolStdioExitCode", "range_start": self.range_start, "range_end": self.range_end, "error_level": self.error_level, "desc": self.desc, }
[docs]class ToolStdioRegex: """ This is a container for the <stdio> element's regex subelement. The regex subelement has a "match" attribute, a "sources" attribute that contains "output" and/or "error", and a "level" attribute that contains "warning" or "fatal". """
[docs] def __init__(self, as_dict=None): as_dict = as_dict or {} self.match = as_dict.get("match", "") self.stdout_match = as_dict.get("stdout_match", False) self.stderr_match = as_dict.get("stderr_match", False) self.error_level = as_dict.get("error_level", StdioErrorLevel.FATAL) self.desc = as_dict.get("desc", "")
[docs] def to_dict(self): return { "class": "ToolStdioRegex", "match": self.match, "stdout_match": self.stdout_match, "stderr_match": self.stderr_match, "error_level": self.error_level, "desc": self.desc, }
[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 = -math.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 = math.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