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fix sub R1 R2
[arvados.git]
/
crunch_scripts
/
run-command
diff --git
a/crunch_scripts/run-command
b/crunch_scripts/run-command
index 528baab4c18c8f0ea23360719c36b6a1605c9f2e..6335523a74a01b8e22a4b3021a971d9732f640d1 100755
(executable)
--- a/
crunch_scripts/run-command
+++ b/
crunch_scripts/run-command
@@
-50,24
+50,41
@@
try:
stdoutname = subst.do_substitution(p, p["stdout"])
stdoutfile = open(stdoutname, "wb")
stdoutname = subst.do_substitution(p, p["stdout"])
stdoutfile = open(stdoutname, "wb")
- print("
Running
command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
+ print("
run-
command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
rcode = subprocess.call(cmd, stdout=stdoutfile)
rcode = subprocess.call(cmd, stdout=stdoutfile)
+ print("run-command: completed with exit code %i" % rcode)
+
except Exception as e:
except Exception as e:
- print("
Caught exception
{}".format(e))
+ print("
run-command: caught exception:
{}".format(e))
finally:
for l in links:
os.unlink(l)
finally:
for l in links:
os.unlink(l)
+ print("run-command: the follow output files will be saved to keep:")
+
+ subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
+
+ print("run-command: start writing output to keep")
+
out = arvados.CollectionWriter()
out.write_directory_tree(".", max_manifest_depth=0)
out = arvados.CollectionWriter()
out.write_directory_tree(".", max_manifest_depth=0)
- arvados.current_task().set_output(out.finish())
+ outuuid = out.finish()
+ arvados.api('v1').job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={
+ 'output':outuuid,
+ 'success': (rcode == 0),
+ 'progress':1.0
+ }).execute()
if rcode == 0:
os.chdir("..")
shutil.rmtree("tmpdir")
shutil.rmtree("output")
if rcode == 0:
os.chdir("..")
shutil.rmtree("tmpdir")
shutil.rmtree("output")
+ print("run-command: success")
+else:
+ print("run-command: failed")
sys.exit(rcode)
sys.exit(rcode)