details: http://www.bx.psu.edu/hg/galaxy/rev/ea0342f2df03 changeset: 2926:ea0342f2df03 user: Nate Coraor <nate@bx.psu.edu> date: Tue Oct 27 15:11:41 2009 -0400 description: Fix a bug whereby PYTHONPATH would grow endlessly in the local runner 1 file(s) affected in this change: lib/galaxy/jobs/runners/local.py diffs (47 lines): diff -r c2bed70a9b58 -r ea0342f2df03 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py Tue Oct 27 14:31:59 2009 -0400 +++ b/lib/galaxy/jobs/runners/local.py Tue Oct 27 15:11:41 2009 -0400 @@ -20,6 +20,12 @@ """Start the job runner with 'nworkers' worker threads""" self.app = app self.sa_session = app.model.context + # put lib into the PYTHONPATH for subprocesses + if 'PYTHONPATH' in os.environ: + os.environ['PYTHONPATH'] = '%s:%s' % ( os.environ['PYTHONPATH'], os.path.abspath( 'lib' ) ) + else: + os.environ['PYTHONPATH'] = os.path.abspath( 'lib' ) + # start workers self.queue = Queue() self.threads = [] nworkers = app.config.local_job_queue_workers @@ -54,12 +60,6 @@ return # If we were able to get a command line, run the job if command_line: - env = os.environ - if job_wrapper.galaxy_lib_dir is not None: - if 'PYTHONPATH' in os.environ: - env['PYTHONPATH'] = "%s:%s" % ( os.environ['PYTHONPATH'], job_wrapper.galaxy_lib_dir ) - else: - env['PYTHONPATH'] = job_wrapper.galaxy_lib_dir try: log.debug( 'executing: %s' % command_line ) proc = subprocess.Popen( args = command_line, @@ -67,7 +67,7 @@ cwd = job_wrapper.working_directory, stdout = subprocess.PIPE, stderr = subprocess.PIPE, - env = env, + env = os.environ, preexec_fn = os.setpgrp ) job_wrapper.set_runner( 'local:///', proc.pid ) job_wrapper.change_state( model.Job.states.RUNNING ) @@ -110,7 +110,7 @@ log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) external_metadata_proc = subprocess.Popen( args = external_metadata_script, shell = True, - env = env, + env = os.environ, preexec_fn = os.setpgrp ) job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) external_metadata_proc.wait()