11 import arvados.commands.put as put
18 t = arvados.current_task().tmpdir
20 api = arvados.api('v1')
22 os.chdir(arvados.current_task().tmpdir)
29 jobp = arvados.current_job()['script_parameters']
30 if len(arvados.current_task()['parameters']) > 0:
31 p = arvados.current_task()['parameters']
36 r = os.path.basename(v)
37 os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
42 return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
45 return os.environ['CRUNCH_NODE_SLOTS']
48 return os.environ['JOB_UUID']
51 return os.environ['TASK_UUID']
53 subst.default_subs["link "] = sub_link
54 subst.default_subs["task.tmpdir"] = sub_tmpdir
55 subst.default_subs["node.cores"] = sub_cores
56 subst.default_subs["job.id"] = sub_jobid
57 subst.default_subs["task.id"] = sub_taskid
61 def machine_progress(bytes_written, bytes_expected):
62 return "run-command: wrote {} total {}\n".format(
63 bytes_written, -1 if (bytes_expected is None) else bytes_expected)
65 class SigHandler(object):
69 def send_signal(self, sp, signum):
70 sp.send_signal(signum)
73 def expand_item(p, c):
74 if isinstance(c, dict):
75 if "foreach" in c and "command" in c:
77 items = get_items(p, p[var])
82 r.extend(expand_list(params, c["command"]))
84 elif isinstance(c, list):
85 return expand_list(p, c)
86 elif isinstance(c, str):
87 return [subst.do_substitution(p, c)]
91 def expand_list(p, l):
92 return [exp for arg in l for exp in expand_item(p, arg)]
94 def get_items(p, value):
95 if isinstance(value, list):
96 return expand_list(p, value)
98 fn = subst.do_substitution(p, value)
99 mode = os.stat(fn).st_mode
100 prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:]
102 if stat.S_ISDIR(mode):
103 items = ["$(dir %s/%s)" % (prefix, l) for l in os.listdir(fn)]
104 elif stat.S_ISREG(mode):
106 items = [line for line in f]
111 if "task.foreach" in jobp:
112 if arvados.current_task()['sequence'] == 0:
113 var = jobp["task.foreach"]
114 items = get_items(jobp, jobp[var])
116 print("run-command: parallelizing on %s with items %s" % (var, items))
119 params = copy.copy(jobp)
121 arvados.api().job_tasks().create(body={
122 'job_uuid': arvados.current_job()['uuid'],
123 'created_by_job_task_uuid': arvados.current_task()['uuid'],
135 cmd = expand_list(p, p["command"])
139 if "save.stdout" in p:
140 stdoutname = subst.do_substitution(p, p["save.stdout"])
141 stdoutfile = open(stdoutname, "wb")
143 print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
145 sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
148 # forward signals to the process.
149 signal.signal(signal.SIGINT, lambda signum, frame: sig.send_signal(sp, signum))
150 signal.signal(signal.SIGTERM, lambda signum, frame: sig.send_signal(sp, signum))
151 signal.signal(signal.SIGQUIT, lambda signum, frame: sig.send_signal(sp, signum))
153 # wait for process to complete.
157 print("run-command: terminating on signal %s" % sig.sig)
160 print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
162 except Exception as e:
163 print("run-command: caught exception: {}".format(e))
165 # restore default signal handlers.
166 signal.signal(signal.SIGINT, signal.SIG_DFL)
167 signal.signal(signal.SIGTERM, signal.SIG_DFL)
168 signal.signal(signal.SIGQUIT, signal.SIG_DFL)
173 print("run-command: the following output files will be saved to keep:")
175 subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
177 print("run-command: start writing output to keep")
180 resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint"))
181 reporter = put.progress_writer(machine_progress)
182 bytes_expected = put.expected_bytes_for(".")
185 out = put.ArvPutCollectionWriter.from_cache(resume_cache, reporter, bytes_expected)
187 out.write_directory_tree(".", max_manifest_depth=0)
188 outuuid = out.finish()
189 api.job_tasks().update(uuid=arvados.current_task()['uuid'],
192 'success': (rcode == 0),
196 except KeyboardInterrupt:
197 print("run-command: terminating on signal 2")
199 except Exception as e:
200 print("run-command: caught exception: {}".format(e))