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Workflow definition document - has the file extension
.wf.xmlJob’s context file aka
_context.jsonDirectory to write outputs of the job i.e.
output
The command to run sciflo is $HOME/verdi/bin/sflExec.py -s -f -o output --args ”_context.json” pge.wf.xml
This command is constructed and run by the python script.
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# build paths to executables
sflexec_path = os.path.join(
os.environ['HOME'], 'verdi', 'bin', 'sflExec.py')
# execute sciflo
cmd = [sflexec_path, "-s", "-f", "-o", output_dir,
"--args", '"%s"' % ','.join(sfl_args), sfl_file]
print("Running sflExec.py command:\n%s" % ' '.join(cmd))
status = os.system(' '.join(cmd)) |
Based on status of the Sciflo run it logs out the error and copies the files generated by the sciflo run into the specified output directory.
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if status != 0:
extract_error('%s/sciflo.json' % output_dir)
status = 1
# copy smap_sciflo work and exec dir
try:
copy_sciflo_work(output_dir)
except Exception:
pass |