1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/9576fb8cd71e/ changeset: 9576fb8cd71e user: scot...@gatech.edu date: 2012-06-26 23:31:30 summary: Generalized exit code and regex handling. TaskWrapper now uses the newly-generalized handling, too. affected #: 2 files

diff -r fb67f73df9a24cb9eba278e7c62ba996fa11a6be -r 9576fb8cd71e8ad16e9a6426c0c42dc6aba63716 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -306,78 +306,12 @@ #ERROR at this point means the job was deleted by an administrator. return self.fail( job.info )

- err_msg = "" - # Check exit codes and match regular expressions against stdout and - # stderr if this tool was configured to do so. - if ( len( self.tool.stdio_regexes ) > 0 or - len( self.tool.stdio_exit_codes ) > 0 ): - # We will check the exit code ranges in the order in which - # they were specified. Each exit_code is a ToolStdioExitCode - # that includes an applicable range. If the exit code was in - # that range, then apply the error level and add in a message. - # If we've reached a fatal error rule, then stop. - max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR - for stdio_exit_code in self.tool.stdio_exit_codes: - if ( tool_exit_code >= stdio_exit_code.range_start and - tool_exit_code <= stdio_exit_code.range_end ): - if None != stdio_exit_code.desc: - err_msg += stdio_exit_code.desc - # TODO: Find somewhere to stick the err_msg - possibly to - # the source (stderr/stdout), possibly in a new db column. - max_error_level = max( max_error_level, - stdio_exit_code.error_level ) - if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: - break - # 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 max_error_level < galaxy.tools.StdioErrorLevel.FATAL: - # 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 won't be scanned.) 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 self.tool.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. - # Repeat the stdout stuff for stderr. - # TODO: Collapse this into a single function. - if ( regex.stdout_match ): - regex_match = re.search( regex.match, stdout ) - if ( regex_match ): - err_msg += self.regex_err_msg( regex_match, regex ) - max_error_level = max( max_error_level, regex.error_level ) - if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: - break - if ( regex.stderr_match ): - regex_match = re.search( regex.match, stderr ) - if ( regex_match ): - err_msg += self.regex_err_msg( regex_match, regex ) - max_error_level = max( max_error_level, - regex.error_level ) - if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: - 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 >= galaxy.tools.StdioErrorLevel.FATAL: - job.state = job.states.ERROR - else: - job.state = job.states.OK - # 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. + # Check the + if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): + job.state = job.states.OK else: - if stderr: - job.state = job.states.ERROR - else: - job.state = job.states.OK + job.state = job.states.ERROR + if self.version_string_cmd: version_filename = self.get_version_string_path() if os.path.exists(version_filename): @@ -566,6 +500,107 @@ if self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ): self.cleanup()

+ def check_tool_output( self, stdout, stderr, tool_exit_code ): + """ + Check the output of a tool - given the stdout, stderr, and the tool's + exit code, return True if the tool exited succesfully and False + otherwise. No exceptions should be thrown. If this code encounters + an exception, it returns True 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. + """ + job = self.get_job() + err_msg = "" + # 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. + success = True + + try: + # Check exit codes and match regular expressions against stdout and + # stderr if this tool was configured to do so. + if ( len( self.tool.stdio_regexes ) > 0 or + len( self.tool.stdio_exit_codes ) > 0 ): + # We will check the exit code ranges in the order in which + # they were specified. Each exit_code is a ToolStdioExitCode + # that includes an applicable range. If the exit code was in + # that range, then apply the error level and add in a message. + # If we've reached a fatal error rule, then stop. + max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR + for stdio_exit_code in self.tool.stdio_exit_codes: + if ( tool_exit_code >= stdio_exit_code.range_start and + tool_exit_code <= stdio_exit_code.range_end ): + if None != stdio_exit_code.desc: + err_msg += stdio_exit_code.desc + # TODO: Find somewhere to stick the err_msg - possibly to + # the source (stderr/stdout), possibly in a new db column. + max_error_level = max( max_error_level, + stdio_exit_code.error_level ) + if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: + break + + # 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 max_error_level < galaxy.tools.StdioErrorLevel.FATAL: + # 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 won't be scanned.) 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 self.tool.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. + # Repeat the stdout stuff for stderr. + # TODO: Collapse this into a single function. + if ( regex.stdout_match ): + regex_match = re.search( regex.match, stdout ) + if ( regex_match ): + err_msg += self.regex_err_msg( regex_match, regex ) + max_error_level = max( max_error_level, regex.error_level ) + if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: + break + if ( regex.stderr_match ): + regex_match = re.search( regex.match, stderr ) + if ( regex_match ): + err_msg += self.regex_err_msg( regex_match, regex ) + max_error_level = max( max_error_level, + regex.error_level ) + if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: + 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 >= galaxy.tools.StdioErrorLevel.FATAL: + success = False + else: + success = True + + # 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: + log.debug( "The tool did not define exit code or stdio handling; " + + "checking stderr for success" ) + if stderr: + success = False + else: + success = True + # On any exception, return True. + except: + log.warning( "Tool check encountered unexpected exception; " + + "assuming tool was successful" ) + success = True + return success + def regex_err_msg( self, match, regex ): """ Return a message about the match on tool output using the given @@ -970,7 +1005,7 @@ self.sa_session.add( task ) self.sa_session.flush()

- def finish( self, stdout, stderr ): + def finish( self, stdout, stderr, tool_exit_code=0 ): # DBTODO integrate previous finish logic. # Simple finish for tasks. Just set the flag OK. log.debug( 'task %s for job %d ended' % (self.task_id, self.job_id) ) @@ -991,10 +1026,10 @@ # Job was deleted by an administrator self.fail( task.info ) return - if stderr: + if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): + task.state = task.states.OK + else: task.state = task.states.ERROR - else: - task.state = task.states.OK # Save stdout and stderr if len( stdout ) > 32768: log.error( "stdout for task %d is greater than 32K, only first part will be logged to database" % task.id )

diff -r fb67f73df9a24cb9eba278e7c62ba996fa11a6be -r 9576fb8cd71e8ad16e9a6426c0c42dc6aba63716 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -560,7 +560,7 @@

def fail_job( self, pbs_job_state ): """ - Seperated out so we can use the worker threads for it. + Separated out so we can use the worker threads for it. """ if pbs_job_state.stop_job: self.stop_job( self.sa_session.query( self.app.model.Job ).get( pbs_job_state.job_wrapper.job_id ) )

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