1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/40c02d5cfc7d/ Changeset: 40c02d5cfc7d User: jmchilton Date: 2014-05-19 18:02:59 Summary: More reworking of job logging. Drop now duplicated log message in drmaa, condor, cli, etc.... Have local job runner report which job script it is running - but log it as a job script. For each job runner log the full command-line which includes dependency resolution and not the base version produced directly by the tool and use the old format from the external runners. Affected #: 7 files diff -r f73317a85e5cc38492e0338538ada18484701030 -r 40c02d5cfc7da40d6b844a8120a019d611462e02 lib/galaxy/jobs/command_factory.py --- a/lib/galaxy/jobs/command_factory.py +++ b/lib/galaxy/jobs/command_factory.py @@ -19,8 +19,8 @@ - commands to set metadata (if include_metadata is True) """ base_command_line = job_wrapper.get_command_line() - job_id = job_wrapper.job_id - log.debug( 'Tool evaluation for job (%s) produced command-line: %s' % ( job_id, base_command_line ) ) + # job_id = job_wrapper.job_id + # log.debug( 'Tool evaluation for job (%s) produced command-line: %s' % ( job_id, base_command_line ) ) commands_builder = CommandsBuilder(base_command_line) # All job runners currently handle this case which should never occur diff -r f73317a85e5cc38492e0338538ada18484701030 -r 40c02d5cfc7da40d6b844a8120a019d611462e02 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -268,8 +268,8 @@ ) ## Additional logging to enable if debugging from_work_dir handling, metadata ## commands, etc... (or just peak in the job script.) - # job_id = job_wrapper.job_id - # log.debug( 'Extended command-line for job (%s) is: %s' % ( job_id, command_line ) ) + job_id = job_wrapper.job_id + log.debug( '(%s) command is: %s' % ( job_id, command_line ) ) options.update(**kwds) return job_script(**options) diff -r f73317a85e5cc38492e0338538ada18484701030 -r 40c02d5cfc7da40d6b844a8120a019d611462e02 lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -91,7 +91,6 @@ return log.debug( "(%s) submitting file: %s" % ( galaxy_id_tag, ajs.job_file ) ) - log.debug( "(%s) command is: %s" % ( galaxy_id_tag, command_line ) ) cmd_out = shell.execute(job_interface.submit(ajs.job_file)) if cmd_out.returncode != 0: diff -r f73317a85e5cc38492e0338538ada18484701030 -r 40c02d5cfc7da40d6b844a8120a019d611462e02 lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -120,7 +120,6 @@ return log.debug( "(%s) submitting file %s" % ( galaxy_id_tag, executable ) ) - log.debug( "(%s) command is: %s" % ( galaxy_id_tag, command_line ) ) external_job_id, message = condor_submit(submit_file) if external_job_id is None: diff -r f73317a85e5cc38492e0338538ada18484701030 -r 40c02d5cfc7da40d6b844a8120a019d611462e02 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -114,9 +114,6 @@ if not self.prepare_job( job_wrapper, include_metadata=True ): return - # command line has been added to the wrapper by prepare_job() - command_line = job_wrapper.runner_command_line - # get configured job destination job_destination = job_wrapper.job_destination @@ -164,7 +161,6 @@ return log.debug( "(%s) submitting file %s", galaxy_id_tag, ajs.job_file ) - log.debug( "(%s) command is: %s", galaxy_id_tag, command_line ) if native_spec: log.debug( "(%s) native specification is: %s", galaxy_id_tag, native_spec ) diff -r f73317a85e5cc38492e0338538ada18484701030 -r 40c02d5cfc7da40d6b844a8120a019d611462e02 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -88,6 +88,7 @@ try: stdout_file = tempfile.NamedTemporaryFile( suffix='_stdout', dir=job_wrapper.working_directory ) stderr_file = tempfile.NamedTemporaryFile( suffix='_stderr', dir=job_wrapper.working_directory ) + log.debug( '(%s) executing job script: %s' % ( job_id, command_line ) ) proc = subprocess.Popen( args=command_line, shell=True, cwd=job_wrapper.working_directory, diff -r f73317a85e5cc38492e0338538ada18484701030 -r 40c02d5cfc7da40d6b844a8120a019d611462e02 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -317,7 +317,6 @@ # (if a TaskWrapper was passed in): galaxy_job_id = job_wrapper.get_id_tag() log.debug("(%s) submitting file %s" % ( galaxy_job_id, job_file ) ) - log.debug("(%s) command is: %s" % ( galaxy_job_id, command_line ) ) tries = 0 while tries < 5: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.