def run_main(host, port, nprocesses, ntimes, profile_csv):
# logging.basicConfig(level=logging.DEBUG, file=sys.stdout)
profile_d = {}
started_at = time.time()
log.info(FUNCS.keys())
sal = ServiceAccessLayer(host, port)
status = sal.get_status()
log.info("Status {}".format(status))
profile_d['nprocesses'] = nprocesses
profile_d["init_nsubreads"] = len(sal.get_subreadsets())
profile_d['init_nreferences'] = len(sal.get_referencesets())
profile_d['init_njobs'] = len(sal.get_analysis_jobs())
chunksize = 6
info = "{h}:{p} with ntimes:{n} with processors:{x}".format(h=host,
p=port,
n=ntimes,
x=nprocesses)
# FIXME. All paths are relative to smrtflow root
def to_p(rpath):
return os.path.join(os.getcwd(), rpath)
# DataSet
referenceset_path = to_p(
"test-data/smrtserver-testdata/ds-references/mk-01/mk_name_01/referenceset.xml"
)
subreadset_path = to_p(
"test-data/smrtserver-testdata/ds-subreads/PacBioTestData/m54006_160504_020705.tiny.subreadset.xml"
)
# Run Design
run_design_path = to_p(
"smrt-server-link/src/test/resources/runCreate2.xml")
# Dev Diagnostic
analysis_json = to_p(
"smrt-server-link/src/test/resources/analysis-dev-diagnostic-stress-01.json"
)
output_dir_prefix = to_p("test-output")
if not os.path.exists(output_dir_prefix):
os.mkdir(output_dir_prefix)
# import referenceset with original UUID for the dev_diagnostic run
_run_cmd("{pbservice} import-dataset --host={h} --port={p} {x}".format(
pbservice=pbservice, h=host, p=port, x=referenceset_path))
xs = _generate_data(host, port, [referenceset_path, subreadset_path],
analysis_json, run_design_path, output_dir_prefix,
ntimes)
log.info("Starting {i}".format(i=info))
p = multiprocessing.Pool(nprocesses)
results = p.map(runner, xs, chunksize=chunksize)
failed = [r for r in results if r.exit_code != 0]
was_successful = len(failed) == 0
for f in failed:
log.error(f)
log.debug("exiting {i}".format(i=info))
if failed:
log.error("Failed Results {r} of {x}".format(r=len(failed),
x=len(results)))
run_time_sec = time.time() - started_at
profile_d['nresults'] = len(results)
profile_d['nfailed'] = len(failed)
profile_d['was_successful'] = was_successful
profile_d["final_nsubreads"] = len(sal.get_subreadsets())
profile_d['final_nreferences'] = len(sal.get_referencesets())
profile_d['final_njobs'] = len(sal.get_analysis_jobs())
profile_d['run_time_sec'] = run_time_sec
write_profile(profile_d, profile_csv)
return 0 if was_successful else 1
def run_main(host, port, nprocesses, ntimes, profile_csv):
# logging.basicConfig(level=logging.DEBUG, file=sys.stdout)
profile_d = {}
started_at = time.time()
log.info(FUNCS.keys())
sal = ServiceAccessLayer(host, port)
status = sal.get_status()
log.info("Status {}".format(status))
profile_d['nprocesses'] = nprocesses
profile_d["init_nsubreads"] = len(sal.get_subreadsets())
profile_d['init_nreferences'] = len(sal.get_referencesets())
profile_d['init_njobs'] = len(sal.get_analysis_jobs())
chunksize = 6
info = "{h}:{p} with ntimes:{n} with processors:{x}".format(h=host, p=port, n=ntimes, x=nprocesses)
# FIXME. All paths are relative to smrtflow root
def to_p(rpath):
return os.path.join(os.getcwd(), rpath)
# DataSet
referenceset_path = to_p("test-data/smrtserver-testdata/ds-references/mk-01/mk_name_01/referenceset.xml")
subreadset_path = to_p("test-data/smrtserver-testdata/ds-subreads/PacBioTestData/m54006_160504_020705.tiny.subreadset.xml")
# Run Design
run_design_path = to_p("smrt-server-link/src/test/resources/runCreate2.xml")
# Dev Diagnostic
analysis_json = to_p("smrt-server-analysis/src/test/resources/analysis-dev-diagnostic-stress-01.json")
output_dir_prefix = to_p("test-output")
if not os.path.exists(output_dir_prefix):
os.mkdir(output_dir_prefix)
# import referenceset with original UUID for the dev_diagnostic run
_run_cmd("pbservice import-dataset --host={h} --port={p} {x}".format(h=host, p=port, x=referenceset_path))
xs = _generate_data(host, port, [referenceset_path, subreadset_path],
analysis_json, run_design_path, output_dir_prefix, ntimes)
log.info("Starting {i}".format(i=info))
p = multiprocessing.Pool(nprocesses)
results = p.map(runner, xs, chunksize=chunksize)
failed = [r for r in results if r.exit_code != 0]
was_successful = len(failed) == 0
for f in failed:
log.error(f)
log.debug("exiting {i}".format(i=info))
if failed:
log.error("Failed Results {r} of {x}".format(r=len(failed), x=len(results)))
run_time_sec = time.time() - started_at
profile_d['nresults'] = len(results)
profile_d['nfailed'] = len(failed)
profile_d['was_successful'] = was_successful
profile_d["final_nsubreads"] = len(sal.get_subreadsets())
profile_d['final_nreferences'] = len(sal.get_referencesets())
profile_d['final_njobs'] = len(sal.get_analysis_jobs())
profile_d['run_time_sec'] = run_time_sec
write_profile(profile_d, profile_csv)
return 0 if was_successful else 1
