From 32ca7172515ce7f7e889558a8a04199aaac3008b Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 6 Feb 2012 13:16:23 -0500 Subject: [PATCH] Bugfix for the DRMAA job name commit, ensure all characters in the job name string conform to the DRMAA spec. --- lib/galaxy/jobs/runners/drmaa.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py index dc9f9f4c46d..98804cff463 100644 --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -1,4 +1,4 @@ -import os, sys, logging, threading, time +import os, sys, logging, threading, time, string import pprint, pwd from pwd import getpwnam import subprocess @@ -168,9 +168,12 @@ class DRMAAJobRunner( BaseJobRunner ): # 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()) + 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 ) ) + jt = self.ds.createJobTemplate() jt.remoteCommand = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) - jt.jobName = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user.replace( '@', '__at__' ) ) + jt.jobName = job_name jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile native_spec = self.get_native_spec( runner_url )