def get_sal_and_status(host, port):
"""Get Sal or Raise if status isn't successful"""
try:
sal = ServiceAccessLayer(host, port)
sal.get_status()
return sal
except RequestException as e:
log.error("Failed to connect to {h}:{p}".format(h=host, p=port))
raise
def get_sal_and_status(host, port):
"""Get Sal or Raise if status isn't successful"""
try:
sal = ServiceAccessLayer(host, port)
sal.get_status()
return sal
except RequestException as e:
log.error("Failed to connect to {h}:{p}".format(h=host, p=port))
raise
def get_sal_and_status(host, port):
"""Get Sal or Raise if status isn't successful"""
sal = ServiceAccessLayer(host, port)
sal.get_status()
return sal
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
def run_main(path, host, port, job_name, pipeline_id, referenceset_uuid, block=False, custom_options=None):
"""
:param path: Path to SubreadSet XML will be imported (if it's not already been imported)
:param host: SL Host
:param port: SL Port
:param job_name: Job name
:param pipeline_id: Pipeline Id (e.g, pbsmrtpipe.pipelines.my_pipeline
:param referenceset_uuid: UUID of Rset. This *must* already be imported
:param block: To block and poll for the analysis job to complete
:param custom_options: Dictionary of task options for the provided
Pipeline in the form
{"pbalign.task_options.concordant":True}
:type custom_options: dict | None
:rtype: int
"""
# look up the reference set UUID from pbservice CLI util or
# http://smrtlink-beta:8081/secondary-analysis/datasets/references
# TODO. 1. Import SubreadSet if it's not already imported
# TODO. 2. Check and see if the Job with the SubreadSet UUID was already submitted
# TODO. 3. Add option to force a new submission to override (2)
# TODO. 4. Enable custom pipeline options json file at the CLI
# sanity test
sset = SubreadSet(path)
log.info("Loaded SubreadSet {}".format(sset))
sal = ServiceAccessLayer(host, port)
# Sanity Check
_ = sal.get_status()
# Step 1. Import SubreadSet (and block) if it's not imported already
service_sset = sal.get_subreadset_by_id(sset.uuid)
# TODO. Add check to see if Job was successful
if service_sset is None:
log.info("Running Import-DataSet job with {}".format(path))
sset_import_job = sal.run_import_dataset_subread(path)
log.info("Import-DataSet job {}".format(sset_import_job))
else:
log.info("Found already imported SubreadSet {}".format(service_sset))
# Step 2. Check and See if an previous analysis job has already been run
# Immediately exit if an analysis job is found
analysis_job = get_job_by_subreadset_uuid_or_none(sal, sset.uuid)
if analysis_job is not None:
log.info("Found exiting job {} for SubreadSet {}".format(analysis_job, sset))
return 0
# Step 3. Create a new Analysis job with custom task options (if provided)
task_options = {} if custom_options is None else custom_options
# Get the already Successfully imported DataSets
service_sset_d = sal.get_dataset_by_uuid(sset.uuid)
service_rset_d = sal.get_dataset_by_uuid(referenceset_uuid)
f = sal.run_by_pipeline_template_id if block else sal.create_by_pipeline_template_id
# The API takes the Int id of the DataSet
epoints = (ServiceEntryPoint("eid_subread", FileTypes.DS_SUBREADS.file_type_id, service_sset_d['id']),
ServiceEntryPoint("eid_ref_dataset", FileTypes.DS_REF.file_type_id, service_rset_d['id']))
job = f(job_name, pipeline_id, epoints, task_options=task_options)
log.info("Analysis Job {}".format(job))
if block:
exit_code = 0 if job.state == JobStates.SUCCESSFUL else 1
else:
# the job is in the created state
exit_code = 0
return exit_code
