def testTaskGenerate(self):
targets = []
for a in glob(get_abspath("../examples/simple_galaxy/*.fasta")):
targets.append(TargetFile(a))
tasks = TaskGroup()
for i, t in enumerate(targets):
workflow = GalaxyWorkflow(ga_file=get_abspath(
"../examples/simple_galaxy/SimpleWorkflow.ga"))
task = GalaxyWorkflowTask("workflow_%s" % (i),
workflow,
inputs={'input_file': t})
tasks.append(task)
#check if elements can be serialized
for a in tasks.to_dict():
task_json = json.dumps(a)
with open(get_abspath("../test_tmp/nebula_tasks"), "w") as handle:
tasks.store(handle)
new_tasks = TaskGroup()
with open(get_abspath("../test_tmp/nebula_tasks")) as handle:
new_tasks.load(handle)
self.assertEqual(len(tasks), len(new_tasks))
for task in new_tasks:
print task
def testTaskGenerate(self):
targets = []
for a in glob(get_abspath("../examples/simple_galaxy/*.fasta")):
targets.append(TargetFile(a))
tasks = TaskGroup()
for i, t in enumerate(targets):
workflow = GalaxyWorkflow(ga_file=get_abspath("../examples/simple_galaxy/SimpleWorkflow.ga"))
task = GalaxyWorkflowTask("workflow_%s" % (i), workflow,
inputs={
'input_file' : t
}
)
tasks.append(task)
#check if elements can be serialized
for a in tasks.to_dict():
task_json = json.dumps(a)
with open(get_abspath("../test_tmp/nebula_tasks"), "w") as handle:
tasks.store(handle)
new_tasks = TaskGroup()
with open(get_abspath("../test_tmp/nebula_tasks")) as handle:
new_tasks.load(handle)
self.assertEqual(len(tasks), len(new_tasks))
for task in new_tasks:
print task
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 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)
