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 testWorkflowCaching(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 = nebula.docstore.FileDocStore(
get_abspath("../test_tmp/docstore"),
cache_path=get_abspath("../test_tmp/cache"))
logging.info("Adding files to object store")
sync_doc_dir(get_abspath("../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,
tags=["run:testing"],
tool_tags={
"tail_select": {
"out_file1":
["file:tail"]
},
"concat_out": {
"out_file1":
["file:output"]
}
})
service = GalaxyService(docstore=doc,
name="nosetest_galaxy",
galaxy="bgruening/galaxy-stable:dev",
force=True,
port=20022)
self.service = service
logging.info("Starting Service")
print "Starting service"
service.start()
self.assertFalse(service.in_error())
logging.info("Starting Tasks")
job = service.submit(task)
self.assertTrue(isinstance(job, TaskJob))
self.assertFalse(service.in_error())
#logging.info("Waiting")
service.wait([job])
found = False
for id, info in doc.filter(tags="file:output"):
logging.info("Found result object: %s size: %d" %
(id, doc.size(info)))
self.assertTrue(doc.size(info) > 0)
found = True
self.assertTrue(found)
self.assertFalse(service.in_error())
self.assertIn(job.get_status(), ['ok'])
def testWorkflowCaching(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 = nebula.docstore.FileDocStore(
get_abspath("../test_tmp/docstore"),
cache_path=get_abspath("../test_tmp/cache")
)
logging.info("Adding files to object store")
sync_doc_dir(get_abspath("../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,
tags = [
"run:testing"
],
tool_tags= {
"tail_select" : {
"out_file1" : [
"file:tail"
]
},
"concat_out" : {
"out_file1" : ["file:output"]
}
}
)
service = GalaxyService(
docstore=doc,
name="nosetest_galaxy",
galaxy="bgruening/galaxy-stable:dev",
force=True,
port=20022
)
self.service = service
logging.info("Starting Service")
print "Starting service"
service.start()
self.assertFalse( service.in_error() )
logging.info("Starting Tasks")
job = service.submit(task)
self.assertTrue( isinstance(job, TaskJob) )
self.assertFalse( service.in_error() )
#logging.info("Waiting")
service.wait([job])
found = False
for id, info in doc.filter(tags="file:output"):
logging.info("Found result object: %s size: %d" % (id, doc.size(info)))
self.assertTrue( doc.size(info) > 0 )
found = True
self.assertTrue(found)
self.assertFalse( service.in_error() )
self.assertIn(job.get_status(), ['ok'])
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() )