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Fix to local job runner so jobs run in the working directory rather than the galaxy root..

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This commit is contained in:
Ross Lazarus
2007-09-21 20:01:39 +00:00
parent 031a1f91fe
commit 57750f52cc
1 changed files with 18 additions and 3 deletions
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lib/galaxy/jobs/runners/local.py
+18 -3
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@@ -1,4 +1,4 @@
import logging
import logging,os
import subprocess
from Queue import Queue
import threading
@@ -43,10 +43,24 @@ class LocalJobRunner( object ):
continue
# If we were able to get a command line, run the job
if command_line:
# patched by ross lazarus to really move to job_wrapper.working_directory for execution
# required patches to use abspath for command line and for all datasets
job_working_dir = job_wrapper.working_directory
if not os.path.isabs(job_working_dir):
job_working_dir = os.path.abspath(job_working_dir)
cl = command_line.split()
if len(cl) >= 2: # assume we have a command?
for n,clp in enumerate(cl): # check for relative path in each cl parameter
if (n > 0) and os.access(clp, os.R_OK) :
# ? is a path we might need to make absolute
cl[n] = os.path.abspath(clp) # convert to absolute path
# this is dumb and there will be nasty edge cases but I'm not sure what else to do
command_line = ' '.join(cl) # munged to absolute paths
try:
log.debug( 'executing: %s' % command_line )
log.debug( '## local.py job runner executing: %s in cwd = %s' % (command_line,job_working_dir ))
proc = subprocess.Popen( args = command_line,
shell = True,
cwd = job_working_dir,
stdout = subprocess.PIPE,
stderr = subprocess.PIPE )
stdout = proc.stdout.read()
@@ -56,11 +70,12 @@ class LocalJobRunner( object ):
log.debug('execution finished: %s' % command_line)
except Exception, e:
job_wrapper.fail( "failure running job", exception=True )
log.exception( "failure running job id: %d" % job_wrapper.job_id )
log.exception( "failure running job id: %d, command_line=%s" % (job_wrapper.job_id,command_line) )
continue
# Finish the job
job_wrapper.finish( stdout, stderr )
def put( self, job_wrapper ):
"""Add a job to the queue (by job identifier)"""
self.queue.put( job_wrapper )