from grisu.frontend.control.login import LoginManager
from grisu.frontend.model.job import JobObject
from grisu.model import GrisuRegistryManager
si = LoginManager.loginCommandline("LOCAL")
appInfo = GrisuRegistryManager.getDefault(si).getApplicationInformation(
"ImageJ")
print 'app: ' + appInfo.getApplicationName()
for subloc in appInfo.getAvailableAllSubmissionLocations():
print subloc
job = JobObject(si)
job.setTimestampJobname("imageJ")
job.setApplication("java")
job.setApplication("ImageJ")
job.setCommandline("echo Hello")
job.setSubmissionLocation("normal:ng2.ivec.org")
job.createJob("/ARCS/StartUp")
job.submitJob()
job.waitForJobToFinish(3)
print "Stdout: " + job.getStdOutContent()
print "Stderr: " + job.getStdErrContent()
from grisu.frontend.control.login import LoginManager
from grisu.frontend.model.job import JobObject
si = LoginManager.loginCommandline("BeSTGRID-DEV")
print "Logged in."
job = JobObject(si)
job.setUniqueJobname("cat_job", si)
job.setCommandline("cat text0.txt")
job.addInputFileUrl("/home/markus/tmp/text0.txt")
job.createJob("/nz/nesi")
# job.setSubmissionLocation('[email protected]:ng2.auckland.ac.nz')
job.submitJob()
print "Job submitted."
job.waitForJobToFinish(10)
print "Job finished. Status: " + job.getStatusString(False)
print "Stdout: " + job.getStdOutContent()
print "Stderr: " + job.getStdErrContent()
job.kill(True)
print "Job distribution for restarted jobs:"
for subLoc in batch_job.getOptimizationResult().keySet():
resubmitted = True
print subLoc + " : " + batch_job.getOptimizationResult().get(
subLoc)
else:
print "Job not restarted (yet)."
print "Job not finished yet. Waiting..."
time.sleep(3)
print "Multipartjob " + batch_job.getBatchJobname() + " finished."
# finally, everything is ready. We could do a lot more here, but you get the idea...
for job in batch_job.getJobs():
print "Job: " + job.getJobname() + ", Status: " + job.getStatusString(
False)
print
print "Stdout: "
print job.getStdOutContent()
print
print "Stderr: "
print job.getStdErrContent()
print
print
print "Finished."
# don't forget to exit properly. this cleans up possible existing threads/executors
sys.exit()
if not os.path.isdir(output_path):
os.mkdir(output_path)
# This method on the BatchJobObject _should_ download the output files for all the
# jobs into the output_path directory.
# BUT it is currently incomplete and does not work
# See issue at
# batch_jobs.downloadResults(True,output_path,['.txt'],True,False)
for job in batch_jobs.getJobs():
if job.isSuccessful(True):
print "INFO: Downloading stdout for " + job.getJobname()
stdout_file = open(os.path.join(output_path, job.getJobname() + "-stdout.txt"), "w")
stdout_file.write(job.getStdOutContent())
stdout_file.close()
print "INFO: Downloading stderr for " + job.getJobname()
stderr_file = open(os.path.join(output_path, job.getJobname() + "-stderr.txt"), "w")
stderr_file.write(job.getStdErrContent())
stderr_file.close()
else:
print "INFO: " + job.getJobname() + "failed! Nothing to download."
print "INFO: Outputs retrieved"
print ("INFO: Kill and clean " + batch_job_name + " jobs")
del_str = "" # to put in scope
try:
service_interface.kill(batch_job_name, True)
status = service_interface.getActionStatus(batch_job_name)
while not status.isFinished():
print "Submitting jobs..."
batch_job.submit()
# now we wait for all jobs to be finished, checking for updates every 10 seconds. in real life we would set a much higher check intervall since we don't want to overload
# the backend and also it's not really necessary
batch_job.waitForJobToFinish(10)
print "BatchJob "+batch_job.getJobname()+" finished."
# finally, everything is ready. We could do a lot more here, but you get the idea...
for job in batch_job.getJobs():
print "Job: "+job.getJobname()+", Status: "+job.getStatusString(False)
print "Submitted to: "+job.getJobProperty(Constants.SUBMISSION_SITE_KEY)
print
print "Stdout: "
print job.getStdOutContent()
print
print "Stderr: "
print job.getStdErrContent()
print
print
print "Finished."
# don't forget to exit properly. this cleans up possible existing threads/executors
sys.exit()
job_name = sys.argv[4]
working_directory = sys.argv[5]
output_files = list()
# get list of output files for this job
for f in sys.argv[6:]:
output_files.append(f)
print output_files
job = JobObject(si, job_name)
# Save stdout and stderr to files to be read by galaxy
try:
out = open(outfile, "w")
out.write(job.getStdOutContent())
out.close()
except:
print "Cannot open files to write results to"
sys.exit(-2)
try:
err = open(errfile, "w")
err.write(job.getStdErrContent())
except:
# There is no stderr so just write blank file
print "No stderr So just writing blakn file"
err.write("")
err.close()
try:
ec = open(error_codefile, "w")
exit_code = job.getStatus(False) - 1000
try:
os.mkdir(output_dir)
print "INFO: Output directory is " + output_dir
except:
print "HALT: Could not create output directory " + output_dir
sys.exit(1)
# Retrieve job output
print "INFO: Downloading output to " + output_dir
for job in jobs:
if job.isSuccessful(True):
print "INFO: Downloading stdout for " + job.getJobname()
stdout_file = open(
os.path.join(current_dir, output_dir,
job.getJobname() + "-stdout.txt"), 'w')
stdout_file.write(job.getStdOutContent())
stdout_file.close()
print "INFO: Downloading stderr for " + job.getJobname()
stderr_file = open(
os.path.join(current_dir, output_dir,
job.getJobname() + "-stderr.txt"), 'w')
stderr_file.write(job.getStdErrContent())
stderr_file.close()
else:
print "INFO: " + job.getJobname(
) + " was not successful, skipping download"
print "INFO: Kill all jobs to clean up"
for job in jobs:
print "INFO: Killing " + job.getJobname()
job.kill(True)
