1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/fdccf979fd8f/ changeset: fdccf979fd8f user: Scott McManus date: 2012-06-25 22:43:18 summary: Added exit code/regex parsing PBS runner and fixed DRMAA/SGE runner affected #: 3681 files

diff -r 319b2b0e832c8ea5ef520c76722f7ad6270507c3 -r fdccf979fd8f2a7dcd3de0a8266af1c7c68f0542 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -291,8 +291,6 @@ the output datasets based on stderr and stdout from the command, and the contents of the output files. """ - # TODO: Eliminate debugging code after testing all runners - log.debug( "JobWrapper.finish: exit code:" + str(tool_exit_code) ) # default post job setup self.sa_session.expunge_all() job = self.get_job() @@ -319,6 +317,7 @@ # 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 + tool_exit_code = int( tool_exit_code ) 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 ):

diff -r 319b2b0e832c8ea5ef520c76722f7ad6270507c3 -r fdccf979fd8f2a7dcd3de0a8266af1c7c68f0542 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -39,6 +39,11 @@ drmaa.JobState.FAILED: 'job finished, but failed', }

+# The last four lines (following the last fi) will: +# - setup the env +# - move to the job wrapper's working directory +# - execute the command +# - take the command's exit code ($?) and write it to a file. drm_template = """#!/bin/sh GALAXY_LIB="%s" if [ "$GALAXY_LIB" != "None" ]; then @@ -52,6 +57,7 @@ %s cd %s %s +echo $? > %s """ def __lineno__(): """Returns the current line number in our program.""" @@ -77,7 +83,7 @@ self.job_file = None self.ofile = None self.efile = None - self.rcfile = None + self.ecfile = None self.runner_url = None

class DRMAAJobRunner( BaseJobRunner ): @@ -169,7 +175,7 @@ # define job attributes ofile = "%s.drmout" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) - rcfile = "%s.drmrc" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) + ecfile = "%s.drmec" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) job_name = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) )

@@ -178,7 +184,7 @@ jt.jobName = job_name jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile - jt.returnCodePath = ":%s" % rcfile + # Avoid a jt.exitCodePath for now - it's only used when finishing. native_spec = self.get_native_spec( runner_url ) if native_spec is not None: jt.nativeSpecification = native_spec @@ -187,7 +193,8 @@ script = drm_template % ( job_wrapper.galaxy_lib_dir, job_wrapper.get_env_setup_clause(), os.path.abspath( job_wrapper.working_directory ), - command_line ) + command_line, + ecfile )

try: fh = file( jt.remoteCommand, "w" ) @@ -231,7 +238,7 @@ drm_job_state.job_id = job_id drm_job_state.ofile = ofile drm_job_state.efile = efile - drm_job_state.rcfile = rcfile + drm_job_state.ecfile = ecfile drm_job_state.job_file = jt.remoteCommand drm_job_state.old_state = 'new' drm_job_state.running = False @@ -316,17 +323,22 @@ """ ofile = drm_job_state.ofile efile = drm_job_state.efile - rcfile = drm_job_state.rcfile + ecfile = drm_job_state.ecfile job_file = drm_job_state.job_file # collect the output # wait for the files to appear which_try = 0 + # By default, the exit code is 0, which typically indicates success. + exit_code = 0 while which_try < (self.app.config.retry_job_output_collection + 1): try: ofh = file(ofile, "r") efh = file(efile, "r") + ecfh = file(ecfile, "r") stdout = ofh.read( 32768 ) stderr = efh.read( 32768 ) + # The exit code should only be 8 bits, but read more anyway + exit_code_str = ecfh.read(32) which_try = (self.app.config.retry_job_output_collection + 1) except: if which_try == self.app.config.retry_job_output_collection: @@ -337,8 +349,15 @@ time.sleep(1) which_try += 1

+ # Decode the exit code. If it's bogus, then just use 0. try: - drm_job_state.job_wrapper.finish( stdout, stderr ) + exit_code = int(exit_code_str) + except: + log.warning( "Exit code " + exit_code_str + " invalid. Using 0." ) + exit_code = 0 + + try: + drm_job_state.job_wrapper.finish( stdout, stderr, int(exit_code) ) except: log.exception("Job wrapper finish method failed")

@@ -382,7 +401,7 @@ drm_job_state = DRMAAJobState() drm_job_state.ofile = "%s.drmout" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) drm_job_state.efile = "%s.drmerr" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) - drm_job_state.rcfile = "%s.drmrc" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) + drm_job_state.ecfile = "%s.drmec" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) drm_job_state.job_file = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job.id) drm_job_state.job_id = str( job.job_runner_external_id ) drm_job_state.runner_url = job_wrapper.get_job_runner()

diff -r 319b2b0e832c8ea5ef520c76722f7ad6270507c3 -r fdccf979fd8f2a7dcd3de0a8266af1c7c68f0542 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -532,16 +532,22 @@ stdout = ofh.read( 32768 ) stderr = efh.read( 32768 ) # This should be an 8-bit exit code, but read ahead anyway: - exit_code = ecfh.read(32) + exit_code_str = ecfh.read(32) except: stdout = '' stderr = 'Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error.' # By default, the exit code is 0, which usually indicates success # (although clearly some error happened). + exit_code_str = "" + + # Translate the exit code string to an integer; use 0 on failure. + try: + exit_code = int( exit_code_str ) + except: + log.warning( "Exit code " + exit_code_str + " was invalid. Using 0." ) exit_code = 0 - log.debug(stderr) - log.debug( "Job exit code: " + exit_code )

+ # Call on the job wrapper to complete the call: try: pbs_job_state.job_wrapper.finish( stdout, stderr, exit_code ) except:

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