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.output_checker

import re
from logging import getLogger

from galaxy.tool_util.parser.stdio import StdioErrorLevel
from galaxy.util import unicodify
from galaxy.util.bunch import Bunch

log = getLogger(__name__)



[docs]def check_output_regex(job_id_tag, regex, stream, stream_name, job_messages, max_error_level): """ check a single regex against a stream regex the regex to check stream the stream to search in job_messages a list where the descriptions of the detected regexes can be appended max_error_level the maximum error level that has been detected so far returns the max of the error_level of the regex and the given max_error_level """ regex_match = re.search(regex.match, stream, re.IGNORECASE) if regex_match: reason = __regex_err_msg(regex_match, stream_name, regex) job_messages.append(reason) return max(max_error_level, regex.error_level) return max_error_level
[docs]def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code, job_id_tag): """ Check the output of a tool - given the stdout, stderr, and the tool's exit code, return DETECTED_JOB_STATE.OK if the tool exited succesfully or error type otherwise. No exceptions should be thrown. If this code encounters an exception, it returns OK so that the workflow can continue; otherwise, a bug in this code could halt workflow progress. Note that, if the tool did not define any exit code handling or any stdio/stderr handling, then it reverts back to previous behavior: if stderr contains anything, then False is returned. """ # By default, the tool succeeded. This covers the case where the code # has a bug but the tool was ok, and it lets a workflow continue. state = DETECTED_JOB_STATE.OK stdout = unicodify(stdout, strip_null=True) stderr = unicodify(stderr, strip_null=True) # messages (descriptions of the detected exit_code and regexes) # to be prepended to the stdout/stderr after all exit code and regex tests # are done (otherwise added messages are searched again). # messages are added it the order of detection # If job is failed, track why. job_messages = [] try: # Check exit codes and match regular expressions against stdout and # stderr if this tool was configured to do so. # If there is a regular expression for scanning stdout/stderr, # then we assume that the tool writer overwrote the default # behavior of just setting an error if there is *anything* on # stderr. if len(stdio_regexes) > 0 or len(stdio_exit_codes) > 0: # Check the exit code ranges in the order in which # they were specified. Each exit_code is a StdioExitCode # that includes an applicable range. If the exit code was in # that range, then apply the error level and add a message. # If we've reached a fatal error rule, then stop. max_error_level = StdioErrorLevel.NO_ERROR if tool_exit_code is not None: for stdio_exit_code in stdio_exit_codes: if (tool_exit_code >= stdio_exit_code.range_start and tool_exit_code <= stdio_exit_code.range_end): # Tack on a generic description of the code # plus a specific code description. For example, # this might prepend "Job 42: Warning (Out of Memory)\n". code_desc = stdio_exit_code.desc if None is code_desc: code_desc = "" desc = "%s: Exit code %d (%s)" % ( StdioErrorLevel.desc(stdio_exit_code.error_level), tool_exit_code, code_desc) reason = { 'type': 'exit_code', 'desc': desc, 'exit_code': tool_exit_code, 'code_desc': code_desc, 'error_level': stdio_exit_code.error_level, } log.info("Job %s: %s" % (job_id_tag, reason)) job_messages.append(reason) max_error_level = max(max_error_level, stdio_exit_code.error_level) if max_error_level >= StdioErrorLevel.MAX: break if max_error_level < StdioErrorLevel.FATAL_OOM: # We'll examine every regex. Each regex specifies whether # it is to be run on stdout, stderr, or both. (It is # possible for neither stdout nor stderr to be scanned, # but those regexes won't be used.) We record the highest # error level, which are currently "warning" and "fatal". # If fatal, then we set the job's state to ERROR. # If warning, then we still set the job's state to OK # but include a message. We'll do this if we haven't seen # a fatal error yet for regex in stdio_regexes: # If ( this regex should be matched against stdout ) # - Run the regex's match pattern against stdout # - If it matched, then determine the error level. # o If it was fatal, then we're done - break. if regex.stderr_match: max_error_level = check_output_regex(job_id_tag, regex, stderr, 'stderr', job_messages, max_error_level) if max_error_level >= StdioErrorLevel.MAX: break if regex.stdout_match: max_error_level = check_output_regex(job_id_tag, regex, stdout, 'stdout', job_messages, max_error_level) if max_error_level >= StdioErrorLevel.MAX: break # If we encountered a fatal error, then we'll need to set the # job state accordingly. Otherwise the job is ok: if max_error_level == StdioErrorLevel.FATAL_OOM: state = DETECTED_JOB_STATE.OUT_OF_MEMORY_ERROR elif max_error_level >= StdioErrorLevel.FATAL: log.debug("Tool exit code indicates an error, failing job.") state = DETECTED_JOB_STATE.GENERIC_ERROR # When there are no regular expressions and no exit codes to check, # default to the previous behavior: when there's anything on stderr # the job has an error, and the job is ok otherwise. else: # TODO: Add in the tool and job id: # log.debug( "Tool did not define exit code or stdio handling; " # + "checking stderr for success" ) if stderr: state = DETECTED_JOB_STATE.GENERIC_ERROR if state != DETECTED_JOB_STATE.OK: peak = stderr[0:ERROR_PEAK] if stderr else "" log.debug("job failed, detected state %s, standard error is - [%s]" % (state, peak)) except Exception: log.exception("Job state check encountered unexpected exception; assuming execution successful") return state, stdout, stderr, job_messages
def __regex_err_msg(match, stream, regex): """ Return a message about the match on tool output using the given ToolStdioRegex regex object. The regex_match is a MatchObject that will contain the string matched on. """ # Get the description for the error level: desc = StdioErrorLevel.desc(regex.error_level) + ": " mstart = match.start() mend = match.end() if mend - mstart > 256: match_str = match.string[mstart : mstart + 256] + "..." else: match_str = match.string[mstart: mend] # If there's a description for the regular expression, then use it. # Otherwise, we'll take the first 256 characters of the match. if regex.desc is not None: desc += regex.desc else: desc += "Matched on %s" % match_str return { "type": "regex", "stream": stream, "desc": desc, "code_desc": regex.desc, "match": match_str, "error_level": regex.error_level, }