def run_audit(docstore, sample_list):
doc = FileDocStore(file_path=docstore)
master_list = []
with open(sample_list) as handle:
for line in handle:
master_list.append(line.rstrip())
results = {}
pending = {}
for id, entry in doc.filter(visible=True, data_type='galaxy.datatypes.tabular.Vcf'):
if 'tags' in entry:
sample = None
for s in entry['tags']:
tmp = s.split(":")
if tmp[0] == 'sample':
sample = tmp[1]
if doc.size(entry) > 0:
results[sample] = results.get(sample, []) + [entry['name']]
for sample, files in results.items():
print "%s (%s) %s" % (sample, len(files), "\t".join(files))
for sample in master_list:
if sample not in results or len(results[sample]) < 3:
print "missing (%s)" % (len(results.get(sample, []))), sample
def run_audit(docstore, sample_list):
doc = FileDocStore(file_path=docstore)
master_list = []
with open(sample_list) as handle:
for line in handle:
master_list.append(line.rstrip())
results = {}
pending = {}
for id, entry in doc.filter(visible=True, data_type='galaxy.datatypes.tabular.Vcf'):
if 'tags' in entry:
sample = None
for s in entry['tags']:
tmp = s.split(":")
if tmp[0] == 'sample':
sample = tmp[1]
if doc.size(entry) > 0:
results[sample] = results.get(sample, []) + [entry['name']]
for sample, files in results.items():
print "%s (%s) %s" % (sample, len(files), "\t".join(files))
for sample in master_list:
if sample not in results or len(results[sample]) < 3:
print "missing (%s)" % (len(results.get(sample, []))), sample
def run_errors(docstore):
doc = FileDocStore(file_path=docstore)
results = {}
pending = {}
for id, entry in doc.filter(visible=True):
if entry.get('state', 'ok') in ['error']:
print entry
def run_ls(docstore, size=False):
doc = FileDocStore(file_path=docstore)
for id, entry in doc.filter():
#if doc.size(entry) > 0:
if size:
print id, entry.get('name', id), doc.size(entry)
else:
print id, entry.get('name', id)
def run_ls(docstore, size=False):
doc = FileDocStore(file_path=docstore)
for id, entry in doc.filter():
#if doc.size(entry) > 0:
if size:
print id, entry.get('name', id), doc.size(entry)
else:
print id, entry.get('name', id)
def run_timing(docstore):
doc = FileDocStore(file_path=docstore)
for id, entry in doc.filter():
if 'job' in entry and 'job_metrics' in entry['job']:
timing = None
for met in entry['job']['job_metrics']:
if met['name'] == 'runtime_seconds':
timing = met['raw_value']
if timing is not None:
print id, entry["name"], timing
def testNebulaLaunch(self):
input = {
"input_file_1" :
Target("c39ded10-6073-11e4-9803-0800200c9a66"),
"input_file_2" :
Target("26fd12a2-9096-4af2-a989-9e2f1cb692fe")
}
parameters = {
"tail_select" : {
"lineNum" : 3
}
}
doc = FileDocStore(
file_path=get_abspath("../test_tmp/docstore")
)
logging.info("Adding files to object store")
sync_doc_dir("examples/simple_galaxy/", doc,
uuid_set=["c39ded10-6073-11e4-9803-0800200c9a66", "26fd12a2-9096-4af2-a989-9e2f1cb692fe"]
)
logging.info("Creating Task")
workflow = GalaxyWorkflow(ga_file=get_abspath("../examples/simple_galaxy/SimpleWorkflow.ga"))
task = nebula.tasks.GalaxyWorkflowTask(
"test_workflow",
workflow,
inputs=input,
parameters=parameters
)
service = GalaxyService(
docstore=doc,
name="nosetest_galaxy",
galaxy="bgruening/galaxy-stable:dev",
port=20022
)
task_path = get_abspath("../test_tmp/test.tasks")
service_path = get_abspath("../test_tmp/test.service")
taskset = TaskGroup()
taskset.append(task)
with open(task_path, "w") as handle:
taskset.store(handle)
with open(service_path, "w") as handle:
service.get_config().set_docstore_config(cache_path=get_abspath("../test_tmp/cache")).store(handle)
env = dict(os.environ)
if 'PYTHONPATH' in env:
env['PYTHONPATH'] += ":" + get_abspath("../")
else:
env['PYTHONPATH'] = get_abspath("../")
subprocess.check_call([get_abspath("../bin/nebula"), "run", service_path, task_path], env=env)
for i in doc.filter():
print json.dumps(i, indent=4)
def run_ls(docstore, size=False, extra=[]):
doc = FileDocStore(file_path=docstore)
for id, entry in doc.filter():
#if doc.size(entry) > 0:
extra = []
for e in args.extra:
extra.append( str(entry.get(e,"")) )
if size:
print id, entry.get('name', id), doc.size(entry), " ".join(extra)
else:
print id, entry.get('name', id), " ".join(extra)
def run_errors(docstore):
doc = FileDocStore(file_path=docstore)
for id, entry in doc.filter():
if entry.get('state', '') == 'error':
print "Dataset", id, entry.get("tags", "")
if 'provenance' in entry:
print "tool:", entry['provenance']['tool_id']
print "-=-=-=-=-=-=-"
print entry['job']['stdout']
print "-------------"
print entry['job']['stderr']
print "-=-=-=-=-=-=-"
def testNebulaLaunch(self):
input = {
"input_file_1": Target("c39ded10-6073-11e4-9803-0800200c9a66"),
"input_file_2": Target("26fd12a2-9096-4af2-a989-9e2f1cb692fe")
}
parameters = {"tail_select": {"lineNum": 3}}
doc = FileDocStore(file_path=get_abspath("../test_tmp/docstore"))
logging.info("Adding files to object store")
sync_doc_dir("examples/simple_galaxy/",
doc,
uuid_set=[
"c39ded10-6073-11e4-9803-0800200c9a66",
"26fd12a2-9096-4af2-a989-9e2f1cb692fe"
])
logging.info("Creating Task")
workflow = GalaxyWorkflow(
ga_file=get_abspath("../examples/simple_galaxy/SimpleWorkflow.ga"))
task = nebula.tasks.GalaxyWorkflowTask("test_workflow",
workflow,
inputs=input,
parameters=parameters)
service = GalaxyService(docstore=doc,
name="nosetest_galaxy",
galaxy="bgruening/galaxy-stable:dev",
port=20022)
task_path = get_abspath("../test_tmp/test.tasks")
service_path = get_abspath("../test_tmp/test.service")
taskset = TaskGroup()
taskset.append(task)
with open(task_path, "w") as handle:
taskset.store(handle)
with open(service_path, "w") as handle:
service.get_config().set_docstore_config(
cache_path=get_abspath("../test_tmp/cache")).store(handle)
env = dict(os.environ)
if 'PYTHONPATH' in env:
env['PYTHONPATH'] += ":" + get_abspath("../")
else:
env['PYTHONPATH'] = get_abspath("../")
subprocess.check_call(
[get_abspath("../bin/nebula"), "run", service_path, task_path],
env=env)
for i in doc.filter():
print json.dumps(i, indent=4)
def testServiceDescription(self):
store = FileDocStore("./test_tmp/docstore")
service = nebula.service.GalaxyService(store)
service_dict = service.to_dict()
self.assertIn('service_type', service_dict)
self.assertEqual('Galaxy', service_dict['service_type'])
print service_dict
def testMesosLaunch(self):
input_file_1 = Target("c39ded10-6073-11e4-9803-0800200c9a66"),
input_file_2 = Target("26fd12a2-9096-4af2-a989-9e2f1cb692fe")
doc = FileDocStore(file_path="./test_tmp/docstore")
logging.info("Adding files to object store")
sync_doc_dir("examples/simple_galaxy/",
doc,
uuid_set=[
"c39ded10-6073-11e4-9803-0800200c9a66",
"26fd12a2-9096-4af2-a989-9e2f1cb692fe"
])
task_1 = MD5Task(input_file_1)
md5_service = nebula.service.md5_service.MD5Service(doc)
sched = nebula.scheduler.Scheduler({})
mesos = nebula.drms.mesos_runner.MesosDRMS(
sched, {"mesos": "%s:%s" % (self.host_ip, CONFIG_PARENT_PORT)})
mesos.start()
mesos_md5_service = mesos.deploy_service(md5_service)
job_1 = mesos_md5_service.submit(task_1)
mesos_md5_service.wait([job_1])
print job_1
logging.info("Sleeping for 15")
time.sleep(15)
mesos.stop()
def testServiceGenerate(self):
doc = FileDocStore(file_path=get_abspath("../test_tmp/docstore"))
service = GalaxyService(docstore=doc,
name="nosetest_galaxy",
galaxy="bgruening/galaxy-stable",
port=20022)
json.dumps(service.to_dict())
def testServiceStart(self):
store = FileDocStore("./test_tmp/docstore")
self.service = nebula.service.GalaxyService(store,
name="nosetest_galaxy",
force=True,
port=20022)
self.service.start()
time.sleep(10)
self.assertFalse(self.service.in_error())
def run_query(docstore, fields, size, filters):
doc = FileDocStore(file_path=docstore)
filter = {}
for k in filters:
tmp=k.split("=")
filter[tmp[0]] = tmp[1]
for id, entry in doc.filter(**filter):
if fields is None or len(fields) == 0:
line = entry
else:
line = dict( (i, entry.get(i, "")) for i in fields )
if size:
size_value = doc.size(Target(uuid=entry['uuid']))
else:
size_value = ""
print size_value, json.dumps(line)
def run_synapse(docstore, parent, workdir):
doc = FileDocStore(file_path=docstore)
syn = synapseclient.Synapse()
syn.login()
for id, entry in doc.filter(visible=True, data_type='galaxy.datatypes.tabular.Vcf'):
if 'tags' in entry:
sample = None
for s in entry['tags']:
tmp = s.split(":")
if tmp[0] == 'sample':
sample = tmp[1]
name = entry['name']
name = re.sub(r'.vcf$', '', name)
file_name = sample + "." + name + ".snv_mnv.vcf"
target = Target(uuid=entry['uuid'])
if doc.size(target) > 0:
src_file = doc.get_filename(target)
dst_file = os.path.join(workdir, file_name)
query = "select * from entity where parentId=='%s' and name=='%s'" % (parent, file_name + ".gz")
r = syn.query(query)['results']
if len(r) == 0:
#print r
print dst_file
shutil.copy(src_file, dst_file)
subprocess.check_call("bgzip %s" % (dst_file), shell=True)
f = synapseclient.File(dst_file + ".gz", parentId = parent, name=file_name + ".gz" )
f.fileType = 'vcf'
f.pipeline = 'UCSC'
f.variant_type = "snv"
f = syn.store(f,
executed="https://github.com/ucsccancer/pcawg_tools"
)
else:
print "Skipping", file_name
def run_synapse(docstore, parent, workdir):
doc = FileDocStore(file_path=docstore)
syn = synapseclient.Synapse()
syn.login()
for id, entry in doc.filter(visible=True, data_type='galaxy.datatypes.tabular.Vcf'):
if 'tags' in entry:
sample = None
for s in entry['tags']:
tmp = s.split(":")
if tmp[0] == 'sample':
sample = tmp[1]
name = entry['name']
name = re.sub(r'.vcf$', '', name)
file_name = sample + "." + name + ".snv_mnv.vcf"
target = Target(uuid=entry['uuid'])
if doc.size(target) > 0:
src_file = doc.get_filename(target)
dst_file = os.path.join(workdir, file_name)
query = "select * from entity where parentId=='%s' and name=='%s'" % (parent, file_name + ".gz")
r = syn.query(query)['results']
if len(r) == 0:
#print r
print dst_file
shutil.copy(src_file, dst_file)
subprocess.check_call("bgzip %s" % (dst_file), shell=True)
f = synapseclient.File(dst_file + ".gz", parentId = parent, name=file_name + ".gz" )
f.fileType = 'vcf'
f.pipeline = 'UCSC'
f.variant_type = "snv"
f = syn.store(f,
executed="https://github.com/ucsccancer/pcawg_tools"
)
else:
print "Skipping", file_name
def testToolTagging(self):
doc = FileDocStore(file_path=get_abspath("../test_tmp/docstore"))
sync_doc_dir(get_abspath("../examples/simple_galaxy/"),
doc,
uuid_set=[
"c39ded10-6073-11e4-9803-0800200c9a66",
"26fd12a2-9096-4af2-a989-9e2f1cb692fe"
])
input_file_1 = Target(uuid="c39ded10-6073-11e4-9803-0800200c9a66")
input_file_2 = Target(uuid="26fd12a2-9096-4af2-a989-9e2f1cb692fe")
workflow = GalaxyWorkflow(
ga_file=get_abspath("../examples/simple_galaxy/SimpleWorkflow.ga"))
task_tag = nebula.tasks.GalaxyWorkflowTask(
"workflow_ok",
workflow,
inputs={
'input_file_1': input_file_1,
'input_file_2': input_file_2
},
parameters={"tail_select": {
"lineNum": 3
}},
tags=["run:testing"],
tool_tags={
"tail_select": {
"out_file1": ["file:tail"]
},
"concat_out": {
"out_file1": ["file:output"]
}
})
print "Starting Service"
service = GalaxyService(docstore=doc,
name="nosetest_galaxy",
galaxy="bgruening/galaxy-stable:dev",
force=True,
port=20022)
service.start()
self.service = service
job = service.submit(task_tag)
print "JOB", job.get_status()
service.wait([job])
self.assertIn(job.get_status(), ['ok'])
self.assertFalse(service.in_error())
print service.in_error()
def run_workflow(args):
data_map = {}
for meta_path in glob(os.path.join(args['lib_data'], "*.json")):
data_path = re.sub(r'.json$', "", meta_path)
if os.path.exists(data_path):
try:
with open(meta_path) as handle:
meta = json.loads(handle.read())
if 'uuid' in meta:
data_map[meta['uuid']] = data_path
except:
pass
d_url = urlparse(args['doc_store'])
if d_url.scheme == '':
doc = FileDocStore(file_path=d_url.path)
else:
raise Exception("Object Store type not supported: %s" % (o_url.scheme))
#this side happens on the master node
tasks = {}
task_request = {}
input_uuids = {}
for i, input_file in enumerate(args['inputs']):
with open(input_file) as handle:
meta = json.loads(handle.read())
inputs = {}
for k, v in meta.get('ds_map').items():
input_uuids[v['uuid']] = True
t = Target(v['uuid'])
if not doc.exists(t):
if t.uuid not in data_map:
raise Exception("Can't find input data: %s" % (t.uuid))
doc.update_from_file(t, data_map[t.uuid], create=True)
doc.put(t.uuid, t.to_dict())
inputs[k] = t
params = meta.get("parameters", {})
task_name = 'task_%s' % (i)
if args['workflow'] is not None:
task = GalaxyWorkflow(task_name,
args['workflow'],
inputs=inputs,
parameters=params,
tags=meta.get("tags", None),
galaxy=args['galaxy'],
tool_dir=args['tool_dir'],
tool_data=args['tool_data'])
else:
with open(args['yaml_workflow']) as handle:
yaml_text = handle.read()
task = GalaxyWorkflow(task_name,
yaml=yaml_text,
inputs=inputs,
parameters=params,
tags=meta.get("tags", None),
docker=args['galaxy'],
tool_dir=args['tools'],
tool_data=args['tool_data'])
task_request[task_name] = meta
task_data = task.get_task_data()
tasks[task_name] = task_data
#this side happens on the worker node
service = ServiceFactory('galaxy',
objectstore=doc,
lib_data=[doc.file_path],
tool_dir=args['tool_dir'],
tool_data=args['tool_data'],
galaxy=args['galaxy'],
config_dir=args['config_dir'],
sudo=args['sudo'],
force=True,
tool_docker=True,
smp=args['smp'],
cpus=args['cpus'],
work_dir=args['work_dir'])
service.start()
task_job_ids = {}
for task_name, task_data in tasks.items():
task = TaskJob(task_data)
i = service.submit(task)
task_job_ids[task_name] = i
sleep_time = 1
while True:
waiting = False
for i in task_job_ids.values():
status = service.status(i)
logging.info("Status check %s %s" % (status, i))
if status not in ['ok', 'error']:
waiting = True
if not waiting:
break
time.sleep(sleep_time)
if sleep_time < 60:
sleep_time += 1
#move the output data into the datastore
for task_name, i in task_job_ids.items():
job = service.get_job(i)
if job.error is None:
for a in job.get_outputs():
meta = service.get_meta(a)
#if 'tags' in task_request[task_name]:
# meta["tags"] = task_request[task_name]["tags"]
#print "meta!!!", json.dumps(meta, indent=4)
doc.put(meta['uuid'], meta)
if meta.get('visible', True):
if meta['state'] == "ok":
if meta['uuid'] not in input_uuids:
logging.info("Downloading: %s" % (meta['uuid']))
service.store_data(a, doc)
else:
logging.info("Skipping input file %s" % (a))
else:
logging.info("Skipping non-ok file: %s" %
(meta['state']))
else:
logging.info("Skipping Download %s (not visible)" % (a))
logging.info("Done")
if not args['hold']:
service.stop()
def run_get(docstore, uuid, outpath):
doc = FileDocStore(file_path=docstore)
print doc.get_filename(Target(uuid=uuid))
def testRunSimple(self):
input = {
"input_file_1" :
Target("c39ded10-6073-11e4-9803-0800200c9a66"),
"input_file_2" :
Target("26fd12a2-9096-4af2-a989-9e2f1cb692fe")
}
parameters = {
"tail_select" : {
"lineNum" : 3
}
}
bad_parameters = dict(parameters)
del bad_parameters['tail_select']
doc = FileDocStore(file_path="./test_tmp/docstore")
logging.info("Adding files to object store")
sync_doc_dir("examples/simple_galaxy/", doc,
uuid_set=["c39ded10-6073-11e4-9803-0800200c9a66", "26fd12a2-9096-4af2-a989-9e2f1cb692fe"]
)
logging.info("Creating Task")
workflow = GalaxyWorkflow(ga_file="examples/simple_galaxy/SimpleWorkflow.ga")
task = nebula.tasks.GalaxyWorkflowTask(
"test_workflow", workflow,
inputs=input,
parameters=parameters
)
task_data = task.to_dict()
#make sure the task data can be serialized
task_data_str = json.dumps(task_data)
service = GalaxyService(
docstore=doc,
name="nosetest_galaxy",
galaxy="bgruening/galaxy-stable",
force=True,
port=20022
)
self.service = service
#make sure the generated task is serializable
new_task_data = json.loads(task_data_str)
new_task = nebula.tasks.from_dict(new_task_data)
logging.info("Starting Service")
print "Starting service"
service.start()
self.assertFalse( service.in_error() )
logging.info("Starting Tasks")
job = service.submit(new_task)
self.assertTrue( isinstance(job, TaskJob) )
self.assertFalse( service.in_error() )
#logging.info("Waiting")
service.wait([job])
self.assertIn(job.get_status(), ['ok'])
bad_task = nebula.tasks.GalaxyWorkflowTask(
"test_workflow_bad",
workflow,
inputs=input,
parameters=bad_parameters
)
job = service.submit(bad_task)
service.wait([job])
self.assertIn(job.get_status(), ['error'])
self.assertFalse( service.in_error() )
def run_copy(docstore, out_docstore):
doc = FileDocStore(file_path=docstore)
out_doc = FileDocStore(file_path=out_docstore)
for id, entry in doc.filter():
if out_doc.get(id) is None:
print "copy", id
out_doc.put(id, entry)
if doc.exists(entry):
src_path = doc.get_filename(entry)
out_doc.create(entry)
dst_path = out_doc.get_filename(entry)
shutil.copy(src_path, dst_path)
out_doc.update_from_file(entry)
else:
#print "skip", id, doc.size(entry), out_doc.size(entry)
if doc.size(entry) != out_doc.size(entry):
print "mismatch", id
def run_scan(docstore, workdir, keyfile, upload_url, manifest):
doc = FileDocStore(file_path=docstore)
file_map = {
'broad' : {},
'muse' : {}
}
wl_map = {}
with open(manifest) as handle:
reader = csv.DictReader(handle, delimiter="\t")
for row in reader:
wl_map[row['Donor_ID']] = row
for id, entry in doc.filter(visible=True):
if entry.get('extension', None) in ["vcf", "vcf_bgzip"]:
if 'tags' in entry:
sample = None
for s in entry['tags']:
tmp = s.split(":")
if tmp[0] == 'sample':
sample = tmp[1]
pipeline = None
method = None
call_type = None
variant_type = None
if entry['name'] in ['MUSE_1.0rc', 'MUSE_0.9.9.5']:
pipeline = "muse"
method = entry['name'].replace(".", "-")
variant_type = 'somatic'
call_type = 'snv_mnv'
elif entry['name'].split(".")[0] in ['broad-dRanger', 'broad-dRanger_snowman', 'broad-snowman', 'broad-mutect' ]:
pipeline = "broad"
method = entry['name'].split(".")[0]
if 'somatic' in entry['name']:
variant_type = 'somatic'
elif 'germline' in entry['name']:
variant_type = 'germline'
else:
raise Exception("Unknown variant type")
if 'snv_mnv.vcf' in entry['name']:
call_type = 'snv_mnv'
elif 'sv.vcf' in entry['name']:
call_type = 'sv'
elif 'indel.vcf' in entry['name']:
call_type = 'indel'
else:
raise Exception("Unknown call type: %s" % (entry['name']))
else:
raise Exeception("Unknown pipeline %s" % (entry['name']))
datestr = datetime.datetime.now().strftime("%Y%m%d")
name = "%s.%s.%s.%s.%s" % (sample, method, datestr, variant_type, call_type )
name = re.sub(r'.vcf$', '', name)
if entry['extension'] == 'vcf':
file_name = name + ".vcf"
elif entry['extension'] == 'vcf_bgzip':
file_name = name + ".vcf.gz"
print file_name
target = Target(uuid=entry['uuid'])
if doc.size(target) > 0:
src_file = doc.get_filename(target)
dst_file = os.path.join(workdir, file_name)
shutil.copy(src_file, dst_file)
if entry['extension'] == 'vcf':
subprocess.check_call( "bgzip %s" % dst_file, shell=True )
dst_file = dst_file + ".gz"
subprocess.check_call("tabix -p vcf %s" % (dst_file), shell=True)
shutil.move("%s.tbi" % (dst_file), "%s.idx" % (dst_file))
subprocess.check_call("md5sum %s | awk '{print$1}' > %s.md5" % (dst_file, dst_file), shell=True)
subprocess.check_call("md5sum %s.idx | awk '{print$1}' > %s.idx.md5" % (dst_file, dst_file), shell=True)
if sample not in file_map[pipeline]:
file_map[pipeline][sample] = []
input_file = os.path.basename(dst_file)
file_map[pipeline][sample].append(input_file)
for pipeline, samples in file_map.items():
for sample, files in samples.items():
with open( os.path.join(workdir, "%s.%s.sh" %(pipeline, sample)), "w" ) as handle:
input_file = os.path.basename(dst_file)
urls = [
"%scghub/metadata/analysisFull/%s" % (wl_map[sample]['Normal_GNOS_endpoint'], wl_map[sample]['Normal_Analysis_ID']),
"%scghub/metadata/analysisFull/%s" % (wl_map[sample]['Tumour_GNOS_endpoint'], wl_map[sample]['Tumour_Analysis_ID'])
]
cmd_str = "perl /opt/vcf-uploader/gnos_upload_vcf.pl"
cmd_str += " --metadata-urls %s" % (",".join(urls))
cmd_str += " --vcfs %s " % (",".join(files))
cmd_str += " --vcf-md5sum-files %s " % ((",".join( ("%s.md5" % i for i in files) )))
cmd_str += " --vcf-idxs %s" % ((",".join( ("%s.idx" % i for i in files) )))
cmd_str += " --vcf-idx-md5sum-files %s" % ((",".join( ("%s.idx.md5" % i for i in files) )))
cmd_str += " --outdir %s.%s.dir" % (pipeline, sample)
cmd_str += " --key %s " % (keyfile)
cmd_str += " --upload-url %s" % (upload_url)
cmd_str += " --study-refname-override tcga_pancancer_vcf_test"
handle.write("""#!/bin/bash
%s
""" % (cmd_str) )
def run_workflow(args):
data_map = {}
for meta_path in glob(os.path.join(args['lib_data'], "*.json")):
data_path = re.sub(r'.json$', "", meta_path)
if os.path.exists(data_path):
try:
with open(meta_path) as handle:
meta = json.loads(handle.read())
if 'uuid' in meta:
data_map[meta['uuid']] = data_path
except:
pass
d_url = urlparse(args['doc_store'])
if d_url.scheme == '':
doc = FileDocStore(file_path=d_url.path)
else:
raise Exception("Object Store type not supported: %s" % (o_url.scheme))
#this side happens on the master node
tasks = {}
task_request = {}
input_uuids = {}
for i, input_file in enumerate(args['inputs']):
with open(input_file) as handle:
meta = json.loads(handle.read())
inputs = {}
for k, v in meta.get('ds_map').items():
input_uuids[v['uuid']] = True
t = Target(v['uuid'])
if not doc.exists(t):
if t.uuid not in data_map:
raise Exception("Can't find input data: %s" % (t.uuid))
doc.update_from_file(t, data_map[t.uuid], create=True)
doc.put(t.uuid, t.to_dict())
inputs[k] = t
params = meta.get("parameters", {})
task_name = 'task_%s' % (i)
if args['workflow'] is not None:
task = GalaxyWorkflow(task_name, args['workflow'],
inputs=inputs, parameters=params, tags=meta.get("tags", None),
galaxy=args['galaxy'], tool_dir=args['tool_dir'], tool_data=args['tool_data'])
else:
with open(args['yaml_workflow']) as handle:
yaml_text = handle.read()
task = GalaxyWorkflow(task_name, yaml=yaml_text, inputs=inputs, parameters=params, tags=meta.get("tags", None), docker=args['galaxy'], tool_dir=args['tools'], tool_data=args['tool_data'])
task_request[task_name] = meta
task_data = task.get_task_data()
tasks[task_name] = task_data
#this side happens on the worker node
service = ServiceFactory('galaxy', objectstore=doc,
lib_data=[doc.file_path], tool_dir=args['tool_dir'], tool_data=args['tool_data'],
galaxy=args['galaxy'], config_dir=args['config_dir'], sudo=args['sudo'], force=True,
tool_docker=True, smp=args['smp'], cpus=args['cpus'], work_dir=args['work_dir'])
service.start()
task_job_ids = {}
for task_name, task_data in tasks.items():
task = TaskJob(task_data)
i = service.submit(task)
task_job_ids[task_name] = i
sleep_time = 1
while True:
waiting = False
for i in task_job_ids.values():
status = service.status(i)
logging.info("Status check %s %s" % (status, i))
if status not in ['ok', 'error']:
waiting = True
if not waiting:
break
time.sleep(sleep_time)
if sleep_time < 60:
sleep_time += 1
#move the output data into the datastore
for task_name, i in task_job_ids.items():
job = service.get_job(i)
if job.error is None:
for a in job.get_outputs():
meta = service.get_meta(a)
#if 'tags' in task_request[task_name]:
# meta["tags"] = task_request[task_name]["tags"]
#print "meta!!!", json.dumps(meta, indent=4)
doc.put(meta['uuid'], meta)
if meta.get('visible', True):
if meta['state'] == "ok":
if meta['uuid'] not in input_uuids:
logging.info("Downloading: %s" % (meta['uuid']))
service.store_data(a, doc)
else:
logging.info("Skipping input file %s" % (a))
else:
logging.info("Skipping non-ok file: %s" % (meta['state']))
else:
logging.info("Skipping Download %s (not visible)" % (a))
logging.info("Done")
if not args['hold']:
service.stop()