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Bugfix for the DRMAA job name commit, ensure all characters in the job name string conform to the DRMAA spec.

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Nate Coraor
2012-02-06 13:16:23 -05:00
parent 9a959c14ea
commit 32ca717251
1 changed files with 5 additions and 2 deletions
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lib/galaxy/jobs/runners/drmaa.py
+5 -2
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@@ -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 )