class NewtIntegrationTest(BaseIntegrationTest):
def __init__(self, name, girder_url, girder_user, girder_password, machine, job_timeout=60 * 5):
super(NewtIntegrationTest, self).__init__(name, girder_url, girder_user, girder_password, job_timeout)
self._cluster_id = None
self._machine = machine
def setUp(self):
# First authenticate with NEWT
self._session = Session()
r = self._session.post(
"https://newt.nersc.gov/newt/auth", {"username": self._girder_user, "password": self._girder_password}
)
self.assertEqual(r.status_code, 200)
print r.json()
self._newt_session_id = r.json()["newt_sessionid"]
# Now authenticate with Girder using the session id
url = "%s/api/v1/newt/authenticate/%s" % (self._girder_url, self._newt_session_id)
r = self._session.put(url)
self.assertEqual(r.status_code, 200)
url = "%s/api/v1/newt/authenticate/%s" % (self._girder_url, self._newt_session_id)
r = self._session.put(url)
self.assertEqual(r.status_code, 200)
url = "%s/api/v1" % self._girder_url
self._client = GirderClient(apiUrl=url)
self._client.token = self._session.cookies["girderToken"]
user = self._client.get("user/me")
self._user_id = user["_id"]
r = self._client.listFolder(self._user_id, "user", name="Private")
r = list(r)
self.assertEqual(len(r), 1)
self._private_folder_id = r[0]["_id"]
def tearDown(self):
super(NewtIntegrationTest, self).tearDown()
if self._cluster_id:
try:
url = "clusters/%s" % self._cluster_id
self._client.delete(url)
except Exception:
traceback.print_exc()
def create_cluster(self):
body = {"config": {"host": self._machine}, "name": "NewtIntegrationTest", "type": "newt"}
r = self._client.post("clusters", data=json.dumps(body))
self._cluster_id = r["_id"]
# Now test the connection
r = self._client.put("clusters/%s/start" % self._cluster_id)
sleeps = 0
while True:
time.sleep(1)
r = self._client.get("clusters/%s/status" % self._cluster_id)
if r["status"] == "running":
break
elif r["status"] == "error":
r = self._client.get("clusters/%s/log" % self._cluster_id)
self.fail(str(r))
if sleeps > 9:
self.fail("Cluster never moved into running state")
sleeps += 1
def assert_output(self):
r = self._client.listItem(self._output_folder_id)
self.assertEqual(len(r), 4)
stdout_item = None
for i in r:
if i["name"].startswith("CumulusIntegrationTestJob-%s.o" % self._job_id):
stdout_item = i
break
self.assertIsNotNone(stdout_item)
r = self._client.get("item/%s/files" % i["_id"])
self.assertEqual(len(r), 1)
url = "%s/api/v1/file/%s/download" % (self._girder_url, r[0]["_id"])
r = self._session.get(url)
self.assertEqual(r.content, self._data)
def test(self):
try:
self.create_cluster()
self.create_script()
self.create_input()
self.create_output_folder()
self.create_job()
self.submit_job(timeout=self._job_timeout)
self.assert_output()
except HttpError as error:
self.fail(error.responseText)
def test_upgrade_pipelines(admin_client: GirderClient):
cnf = admin_client.get('dive_configuration/pipelines')
if 'detector' not in cnf:
admin_client.post(
'dive_configuration/upgrade_pipelines',
data=json.dumps(tasks.UPGRADE_JOB_DEFAULT_URLS),
)
wait_for_jobs(admin_client, 1000)
def _update_girder(taskflow, body):
taskflow = to_taskflow(taskflow)
taskflow_id = taskflow['id']
girder_token = taskflow['girder_token']
girder_api_url = taskflow['girder_api_url']
client = GirderClient(apiUrl=girder_api_url)
client.token = girder_token
client = _create_girder_client(girder_api_url, girder_token)
# If this is a retry then we have already create a task get it from
# the current tasks headers.
if body['retries'] > 0:
taskflow_task_id = \
current_task.request.headers[TASKFLOW_TASK_ID_HEADER]
# Celery always fires the postrun handler with a state of SUCCESS
# for retries. So we need to save the retries here so we can
# determine in the postrun handler if the task is really complete.
current_task.request.headers[TASKFLOW_RETRY_HEADER] \
= body['retries']
else:
# This is a new task so create a taskflow task instance
body = {
'celeryTaskId': body['id'],
'name': body['task']
}
url = 'taskflows/%s/tasks' % taskflow_id
r = client.post(url, data=json.dumps(body))
taskflow_task_id = r['_id']
return taskflow, taskflow_task_id
def _update_girder(taskflow, body):
taskflow = to_taskflow(taskflow)
taskflow_id = taskflow['id']
girder_token = taskflow['girder_token']
girder_api_url = taskflow['girder_api_url']
client = GirderClient(apiUrl=girder_api_url)
client.token = girder_token
client = _create_girder_client(girder_api_url, girder_token)
# If this is a retry then we have already create a task get it from
# the current tasks headers.
if body['retries'] > 0:
taskflow_task_id = \
current_task.request.headers[TASKFLOW_TASK_ID_HEADER]
# Celery always fires the postrun handler with a state of SUCCESS
# for retries. So we need to save the retries here so we can
# determine in the postrun handler if the task is really complete.
current_task.request.headers[TASKFLOW_RETRY_HEADER] \
= body['retries']
else:
# This is a new task so create a taskflow task instance
body = {'celeryTaskId': body['id'], 'name': body['task']}
url = 'taskflows/%s/tasks' % taskflow_id
r = client.post(url, data=json.dumps(body))
taskflow_task_id = r['_id']
return taskflow, taskflow_task_id
def test_upload_zip_data(dataset: dict):
user = zipUser
client = GirderClient(apiUrl='http://localhost:8010/api/v1')
client.authenticate(username=user['login'], password=user['password'])
dsPath = localDataRoot / str(dataset['path'])
privateFolder = getTestFolder(client)
newDatasetFolder = client.createFolder(
privateFolder['_id'],
dataset['name'],
metadata={
'fps': dataset['fps'],
'type': dataset['type'],
},
)
if Path(dsPath).is_file():
client.uploadFileToFolder(newDatasetFolder['_id'], str(dsPath))
client.post(f'dive_rpc/postprocess/{newDatasetFolder["_id"]}')
wait_for_jobs(client,
max_wait_timeout=30,
expected_status=dataset['job_status'])
resultFolder = client.getFolder(newDatasetFolder['_id'])
# verify sub datasets if they exist
if dataset.get('subDatasets', False):
folders = list(client.listFolder(newDatasetFolder['_id']))
for item in dataset["subDatasets"]:
matches = [x for x in folders if x["name"] == item["name"]]
if len(matches) > 0:
meta = matches[0].get("meta", {})
assert meta.get("fps", -1) == item["fps"]
assert meta.get("type", "") == item["type"]
assert meta.get("annotate", False)
elif dataset['job_status'] == JobStatus.SUCCESS:
assert resultFolder['meta'].get("annotate", False)
assert type(resultFolder['meta'].get("fps")) in [int, float]
assert type(resultFolder['meta'].get("type")) == str
else:
assert resultFolder['meta'].get("annotate", None) is None
class NewtIntegrationTest(BaseIntegrationTest):
def __init__(self,
name,
girder_url,
girder_user,
girder_password,
machine,
job_timeout=60 * 5):
super(NewtIntegrationTest,
self).__init__(name, girder_url, girder_user, girder_password,
job_timeout)
self._cluster_id = None
self._machine = machine
def setUp(self):
# First authenticate with NEWT
self._session = Session()
r = self._session.post('https://newt.nersc.gov/newt/auth', {
'username': self._girder_user,
'password': self._girder_password
})
self.assertEqual(r.status_code, 200)
print r.json()
self._newt_session_id = r.json()['newt_sessionid']
# Now authenticate with Girder using the session id
url = '%s/api/v1/newt/authenticate/%s' % (self._girder_url,
self._newt_session_id)
r = self._session.put(url)
self.assertEqual(r.status_code, 200)
url = '%s/api/v1/newt/authenticate/%s' % (self._girder_url,
self._newt_session_id)
r = self._session.put(url)
self.assertEqual(r.status_code, 200)
url = '%s/api/v1' % self._girder_url
self._client = GirderClient(apiUrl=url)
self._client.token = self._session.cookies['girderToken']
user = self._client.get('user/me')
self._user_id = user['_id']
r = self._client.listFolder(self._user_id, 'user', name='Private')
r = list(r)
self.assertEqual(len(r), 1)
self._private_folder_id = r[0]['_id']
def tearDown(self):
super(NewtIntegrationTest, self).tearDown()
if self._cluster_id:
try:
url = 'clusters/%s' % self._cluster_id
self._client.delete(url)
except Exception:
traceback.print_exc()
def create_cluster(self):
body = {
'config': {
'host': self._machine
},
'name': 'NewtIntegrationTest',
'type': 'newt'
}
r = self._client.post('clusters', data=json.dumps(body))
self._cluster_id = r['_id']
# Now test the connection
r = self._client.put('clusters/%s/start' % self._cluster_id)
sleeps = 0
while True:
time.sleep(1)
r = self._client.get('clusters/%s/status' % self._cluster_id)
if r['status'] == 'running':
break
elif r['status'] == 'error':
r = self._client.get('clusters/%s/log' % self._cluster_id)
self.fail(str(r))
if sleeps > 9:
self.fail('Cluster never moved into running state')
sleeps += 1
def assert_output(self):
r = self._client.listItem(self._output_folder_id)
self.assertEqual(len(r), 4)
stdout_item = None
for i in r:
if i['name'].startswith('CumulusIntegrationTestJob-%s.o' %
self._job_id):
stdout_item = i
break
self.assertIsNotNone(stdout_item)
r = self._client.get('item/%s/files' % i['_id'])
self.assertEqual(len(r), 1)
url = '%s/api/v1/file/%s/download' % (self._girder_url, r[0]['_id'])
r = self._session.get(url)
self.assertEqual(r.content, self._data)
def test(self):
try:
self.create_cluster()
self.create_script()
self.create_input()
self.create_output_folder()
self.create_job()
self.submit_job(timeout=self._job_timeout)
self.assert_output()
except HttpError as error:
self.fail(error.responseText)
def upload_exported_zipped_dataset(
gc: GirderClient,
manager: JobManager,
folderId: str,
working_directory: Path,
create_subfolder='',
):
"""Uploads a folder that is generated from the export of a zip file and sets metadata"""
listOfFileNames = os.listdir(working_directory)
potential_meta_files = list(
filter(constants.metaRegex.match, listOfFileNames))
if len(potential_meta_files) == 0:
manager.write(
"Could not find meta.json or config.json file within the subdirectroy\n"
)
return
print(listOfFileNames)
# load meta.json to get datatype and verify list of files
meta = {}
for meta_name in potential_meta_files:
with open(f"{working_directory}/{meta_name}") as f:
meta = json.load(f)
type = meta[constants.TypeMarker]
if type == constants.ImageSequenceType:
imageData = meta['imageData']
for image in imageData:
if image["filename"] not in listOfFileNames:
manager.write(
"Could not find {item['filename']} file within the list of files\n"
)
return
elif type == constants.VideoType:
video = meta["video"]
if video["filename"] not in listOfFileNames:
manager.write(
"Could not find {item['filename']} file within the list of files\n"
)
return
# remove the auxilary directory so we don't have to tag them all
if constants.AuxiliaryFolderName in listOfFileNames and os.path.isdir(
f'{working_directory}/{constants.AuxiliaryFolderName}'):
shutil.rmtree(f'{working_directory}/{constants.AuxiliaryFolderName}')
root_folderId = folderId
if create_subfolder != '':
sub_folder = gc.createFolder(
folderId,
create_subfolder,
reuseExisting=True,
)
root_folderId = str(sub_folder['_id'])
manager.updateStatus(JobStatus.PUSHING_OUTPUT)
# create a source folder to place the zipFile inside of
gc.upload(f'{working_directory}/*', root_folderId)
# Now we set all the metadata for the folders and items
all_files = list(gc.listItem(root_folderId))
root_meta = {
"type": type,
"attributes": meta.get("attributes", None),
"customTypeStyling": meta.get("customTypeStyling", None),
"confidenceFilters": meta.get("confidenceFilters", None),
"fps": meta["fps"],
"version": meta["version"],
}
if type == constants.VideoType:
# set transcoded and non-transcoded versions
transcoded_video = list(
gc.listItem(root_folderId, name=video["filename"]))
if len(transcoded_video) == 1:
ffprobe = meta["ffprobe_info"]
avgFpsString = ffprobe["avg_frame_rate"]
dividend, divisor = [int(v) for v in avgFpsString.split('/')]
originalFps = dividend / divisor
transcoded_metadata = {
"codec": "h264",
"originalFps": originalFps,
"originalFpsString": avgFpsString,
"source_video": False,
"transcoder": "ffmpeg",
}
gc.addMetadataToItem(str(transcoded_video[0]['_id']),
transcoded_metadata)
# other video is tagged as the source video
for item in all_files:
if (item["name"].endswith(tuple(constants.validVideoFormats))
and item["name"] != video["filename"]):
source_metadata = {
"codec": ffprobe["codec_name"],
"originalFps": originalFps,
"originalFpsString": avgFpsString,
"source_video": False,
}
gc.addMetadataToItem(str(item['_id']), source_metadata)
root_meta["originalFps"] = originalFps
root_meta["originalFpsString"] = avgFpsString
# Need to tag folder Level data (annotate, and others)
root_meta[constants.DatasetMarker] = True
gc.addMetadataToFolder(root_folderId, root_meta)
gc.post(f'dive_rpc/postprocess/{root_folderId}', data={"skipJobs": True})
offset += limit
return result
client = GirderClient(host='localhost', port=8080)
if find_user('girder'):
client.authenticate('girder', 'girder')
ensure_user(client,
login='******',
password='******',
email='*****@*****.**',
firstName='girder',
lastName='girder')
client.authenticate('girder', 'girder')
if find_assetstore('local') is None:
client.post('assetstore',
parameters=dict(name='local',
type=str(AssetstoreType.GRIDFS),
db='sumoLocalStore',
mongohost='mongodb://localhost:27017',
replicaset=''))
client.put('system/plugins',
parameters=dict(plugins=json.dumps(['jobs', 'worker', 'osumo'])))
class NewtIntegrationTest(BaseIntegrationTest):
def __init__(self, name, girder_url, girder_user, girder_password, machine,
job_timeout=60*5):
super(NewtIntegrationTest, self).__init__(name, girder_url, girder_user,
girder_password, job_timeout)
self._cluster_id = None
self._machine = machine
def setUp(self):
# First authenticate with NEWT
self._session = Session()
r = self._session.post('https://newt.nersc.gov/newt/auth',
{
'username': self._girder_user,
'password': self._girder_password})
self.assertEqual(r.status_code, 200)
print r.json()
self._newt_session_id = r.json()['newt_sessionid']
# Now authenticate with Girder using the session id
url = '%s/api/v1/newt/authenticate/%s' % (self._girder_url, self._newt_session_id)
r = self._session.put(url)
self.assertEqual(r.status_code, 200)
url = '%s/api/v1/newt/authenticate/%s' % (self._girder_url, self._newt_session_id)
r = self._session.put(url)
self.assertEqual(r.status_code, 200)
url = '%s/api/v1' % self._girder_url
self._client = GirderClient(apiUrl=url)
self._client.token = self._session.cookies['girderToken']
user = self._client.get('user/me')
self._user_id = user['_id']
r = self._client.listFolder(self._user_id, 'user', name='Private')
self.assertEqual(len(r), 1)
self._private_folder_id = r[0]['_id']
def tearDown(self):
super(NewtIntegrationTest, self).tearDown()
if self._cluster_id:
try:
url = 'clusters/%s' % self._cluster_id
self._client.delete(url)
except Exception:
traceback.print_exc()
def create_cluster(self):
body = {
'config': {
'host': self._machine
},
'name': 'NewtIntegrationTest',
'type': 'newt'
}
r = self._client.post('clusters', data=json.dumps(body))
self._cluster_id = r['_id']
# Now test the connection
r = self._client.put('clusters/%s/start' % self._cluster_id)
sleeps = 0
while True:
time.sleep(1)
r = self._client.get('clusters/%s/status' % self._cluster_id)
if r['status'] == 'running':
break
elif r['status'] == 'error':
r = self._client.get('clusters/%s/log' % self._cluster_id)
self.fail(str(r))
if sleeps > 9:
self.fail('Cluster never moved into running state')
sleeps += 1
def assert_output(self):
r = self._client.listItem(self._output_folder_id)
self.assertEqual(len(r), 4)
stdout_item = None
for i in r:
if i['name'].startswith('CumulusIntegrationTestJob-%s.o' % self._job_id):
stdout_item = i
break
self.assertIsNotNone(stdout_item)
r = self._client.get('item/%s/files' % i['_id'])
self.assertEqual(len(r), 1)
url = '%s/api/v1/file/%s/download' % (self._girder_url, r[0]['_id'])
r = self._session.get(url)
self.assertEqual(r.content, self._data)
def test(self):
try:
self.create_cluster()
self.create_script()
self.create_input()
self.create_output_folder()
self.create_job()
self.submit_job(timeout=self._job_timeout)
self.assert_output()
except HttpError as error:
self.fail(error.responseText)
ensure_user(client,
login=user,
password=password,
email='*****@*****.**',
firstName='Girder',
lastName='Admin')
client.authenticate(user, password)
s3_assetstore_name = 's3'
if find_assetstore(s3_assetstore_name) is None:
client.post('assetstore',
parameters=dict(name=s3_assetstore_name,
type=str(AssetstoreType.S3),
bucket=args.s3,
accessKeyId=args.aws_key_id,
secret=args.aws_secret_key))
client.put('system/plugins',
parameters=dict(plugins=json.dumps(['jobs', 'worker', 'osumo'])))
client.put('system/restart')
sleep(30)
client.put(
'system/setting',
parameters=dict(list=json.dumps([
dict(key='worker.broker', value=args.broker),
dict(key='worker.backend', value=args.broker),
dict(key='core.route_table',
class CumulusClient():
'''Application interface to cumulus-based client for HPC systems
supporting NEWT API.
Note: the methods must be called in a specific order!
create_cluster()
create_omega3p_script()
create_job()
upload_inputs()
submit_job()
Then optionally:
monitor_job()
download_results()
release_resources()
'''
# ---------------------------------------------------------------------
def __init__(self, girder_url, newt_sessionid):
'''
'''
self._client = None
self._cluster_id = None
self._girder_url = girder_url
self._input_folder_id = None
self._job_folder_id = None
self._job_id = None
self._output_folder_id = None
self._private_folder_id = None
self._script_id = None
self._session = requests.Session()
# Authenticate with Girder using the newt session id
url = '%s/api/v1/newt/authenticate/%s' % \
(self._girder_url, newt_sessionid)
r = self._session.put(url)
if r.status_code != 200:
raise HttpError(r.status_code, r.text, r.url, r.request.method)
# Instantiate Girder client
url = '%s/api/v1' % self._girder_url
self._client = GirderClient(apiUrl=url)
self._client.token = self._session.cookies['girderToken']
user = self._client.get('user/me')
#print 'user', user
user_id = user['_id']
r = self._client.listFolder(user_id, 'user', name='Private')
if len(r) != 1:
raise Exception('Wrong number of users; should be 1 got %s' %
len(r))
self._private_folder_id = r[0]['_id']
print 'private_folder_id', self._private_folder_id
# ---------------------------------------------------------------------
def job_id(self):
'''Returns current job id (which may be None)
'''
return self._job_id
# ---------------------------------------------------------------------
def create_cluster(self, machine_name, cluster_name=None):
'''
'''
if cluster_name is None:
user = self._client.get('user/me')
user_name = user.get('firstName', 'user')
cluster_name = '%s.%s' % (machine_name, user_name)
cluster = None
cluster_list = self._client.get('clusters')
for extant_cluster in cluster_list:
if extant_cluster['name'] == cluster_name:
cluster = extant_cluster
self._cluster_id = extant_cluster['_id']
break
if not cluster:
body = {
'config': {
'host': machine_name
},
'name': cluster_name,
'type': 'newt'
}
r = self._client.post('clusters', data=json.dumps(body))
self._cluster_id = r['_id']
print 'cluster_id', self._cluster_id
# Reset the state of the cluster
body = {'status': 'created'}
r = self._client.patch('clusters/%s' % self._cluster_id,
data=json.dumps(body))
# Now test the connection
r = self._client.put('clusters/%s/start' % self._cluster_id)
sleeps = 0
while True:
time.sleep(1)
r = self._client.get('clusters/%s/status' % self._cluster_id)
if r['status'] == 'running':
break
elif r['status'] == 'error':
r = self._client.get('clusters/%s/log' % self._cluster_id)
print r
raise Exception('ERROR creating cluster')
if sleeps > 9:
raise Exception('Cluster never moved into running state')
sleeps += 1
# ---------------------------------------------------------------------
def create_omega3p_script(self,
omega3p_filename,
name=None,
number_of_tasks=1):
'''Creates script to submit omega3p job
'''
command = 'srun -n %s /project/projectdirs/ace3p/{{machine}}/omega3p %s' % \
(number_of_tasks, omega3p_filename)
if name is None:
name = omega3p_filename
body = {'commands': [command], 'name': name}
r = self._client.post('scripts', data=json.dumps(body))
self._script_id = r['_id']
print 'script_id', self._script_id
# ---------------------------------------------------------------------
def create_input(self, input_paths, folder_name='input_files'):
'''DEPRECATED Uploads input files
'''
folder_id = self.get_folder(self._private_folder_id, folder_name)
if folder_id is None:
return
print 'input_folder_id', folder_id
self._input_folder_id = folder_id
def upload_file(path):
name = os.path.basename(path)
size = os.path.getsize(path)
with open(path, 'rb') as fp:
self._client.uploadFile(self._input_folder_id,
fp,
name,
size,
parentType='folder')
for input_path in input_paths:
if not input_path or not os.path.exists(input_path):
raise Exception('Input file not found: %s' % input_path)
upload_file(input_path)
# ---------------------------------------------------------------------
def create_output_folder(self, folder_name='output_files'):
'''DEPRECATED
'''
folder_id = self.get_folder(self._private_folder_id, folder_name)
print 'output_folder_id', folder_id
self._output_folder_id = folder_id
# ---------------------------------------------------------------------
def create_job(self, job_name, tail=None):
'''
'''
# Create job folders
folder_name = uuid.uuid4().hex # unique name
self._job_folder_id = self.get_folder(self._private_folder_id,
folder_name)
print 'Created job folder', folder_name
self._input_folder_id = self.get_folder(self._job_folder_id,
'input_files')
self._output_folder_id = self.get_folder(self._job_folder_id,
'output_files')
# Make sure job_name isn't null
if not job_name:
job_name = 'CumulusJob'
# Create job spec
body = {
'name': job_name,
'scriptId': self._script_id,
'output': [{
'folderId': self._output_folder_id,
'path': '.'
}],
'input': [{
'folderId': self._input_folder_id,
'path': '.'
}]
}
if tail:
body['output'].append({"path": tail, "tail": True})
job = self._client.post('jobs', data=json.dumps(body))
self._job_id = job['_id']
print 'Created job_id', self._job_id
# ---------------------------------------------------------------------
def upload_inputs(self, input_paths):
'''Uploads input files to input folder
'''
if not self._input_folder_id:
raise Exception('Input folder missing')
def upload_file(path):
name = os.path.basename(path)
size = os.path.getsize(path)
with open(path, 'rb') as fp:
self._client.uploadFile(self._input_folder_id,
fp,
name,
size,
parentType='folder')
for input_path in input_paths:
if not input_path or not os.path.exists(input_path):
raise Exception('Input file not found: %s' % input_path)
upload_file(input_path)
# ---------------------------------------------------------------------
def submit_job(self,
machine,
project_account,
timeout_minutes,
queue='debug',
qos=None,
number_of_nodes=1,
job_output_dir=None):
'''
'''
body = {
'machine': machine,
'account': project_account,
'numberOfNodes': number_of_nodes,
'maxWallTime': {
'hours': 0,
'minutes': timeout_minutes,
'seconds': 0
},
'queue': queue,
}
if qos:
body['qualityOfService'] = qos
#print 'jobOutputDir', job_output_dir
if job_output_dir:
body['jobOutputDir'] = job_output_dir
print 'Setting jobOutputDir', job_output_dir
url = 'clusters/%s/job/%s/submit' % (self._cluster_id, self._job_id)
self._client.put(url, data=json.dumps(body))
print 'Submitted job', self._job_id
# ---------------------------------------------------------------------
def monitor_job(self, tail=None):
'''Periodically monitors job status
'''
log_offset = 0
job_timeout = 60 * timeout_minutes
start = time.time()
while True:
time.sleep(2)
# Provide some feedback at startup
if log_offset == 0:
sys.stdout.write('.')
#print 'Checking status'
r = self._client.get('jobs/%s' % self._job_id)
#print r
if r['status'] in ['error', 'unexpectederror']:
r = self._client.get('jobs/%s/log' % self._job_id)
raise Exception(str(r))
elif r['status'] == 'complete':
break
# Tail log file
if tail:
params = {'offset': log_offset, 'path': tail}
#print 'Checking tail'
r = self._client.get('jobs/%s/output' % self._job_id,
parameters=params)
#print r
output = r['content']
if output and log_offset == 0:
print # end the user feedback dots
log_offset += len(output)
for l in output:
print l
sys.stdout.flush()
if time.time() - start > job_timeout:
raise Exception('Job timeout')
# ---------------------------------------------------------------------
def download_results(self, destination_folder):
'''Downloads all output files to a local directory
'''
if not os.path.exists(destination_folder):
os.makedirs(destination_folder)
self._client.downloadFolderRecursive(self._output_folder_id,
destination_folder)
print 'Downloaded files to %s' % destination_folder
# ---------------------------------------------------------------------
def release_resources(self):
'''Closes/deletes any current resources
'''
resource_info = {
'clusters': [self._cluster_id],
'jobs': [self._job_id],
'scripts': [self._script_id],
'folder': [self._job_folder]
}
for resource_type, id_list in resource_info.items():
for resource_id in id_list:
if resource_id is not None:
url = '%s/%s' % (resource_type, resource_id)
self._client.delete(url)
self._input_folder_id = None
self._job_folder_id = None
self._job_id = None
self._output_folder_id = None
self._script_id = None
# ---------------------------------------------------------------------
def get_folder(self, parent_id, name):
'''Returns folder_id, creating one if needed
'''
# Check if folder already exists
folder_list = self._client.listFolder(parent_id, name=name)
if folder_list:
folder = folder_list[0]
#print 'found folder %s: %s' % (name, str(folder))
return folder['_id']
# (else)
try:
r = self._client.createFolder(parent_id, name)
return r['_id']
except HttpError as e:
print e.responseText
return None
try:
# Now download the dataset
(fd, filepath) = tempfile.mkstemp()
os.close(fd)
client.downloadFile(fileId, filepath)
# Create temp file and convert to GeoJs contour JSON format
output_dir = tempfile.mkdtemp()
output_filepath = os.path.join(output_dir, output_file_name)
with open(output_filepath, 'w') as fp:
fp.write(json_util.dumps(convert(filepath, variable, timestep)))
# Create an item for this file
output_item = client.createItem(dataset_folder_id, output_file_name, output_file_name)
# Now upload the result
client.uploadFileToItem(output_item['_id'], output_filepath)
output_item_id = output_item['_id']
# Finally promote item to dataset
client.post('minerva_dataset/%s/dataset' % output_item_id)
finally:
if filepath and os.path.exists(filepath):
os.remove(filepath)
if output_dir and os.path.exists(output_dir):
shutil.rmtree(output_dir)
def create_task_job(job_defaults,
sender=None,
body=None,
exchange=None,
routing_key=None,
headers=None,
properties=None,
declare=None,
retry_policy=None,
**kwargs):
parent_task = current_app.current_task
try:
if parent_task is None:
raise MissingJobArguments('Parent task is None')
if parent_task.request is None:
raise MissingJobArguments("Parent task's request is None")
if not hasattr(parent_task.request, 'girder_api_url'):
raise MissingJobArguments(
"Parent task's request does not contain girder_api_url")
if not hasattr(parent_task.request, 'girder_client_token'):
raise MissingJobArguments(
"Parent task's request does not contain girder_client_token")
if not hasattr(parent_task.request, 'id'):
raise MissingJobArguments(
"Parent task's request does not contain id")
if 'id' not in headers:
raise MissingJobArguments('id is not in headers')
gc = GirderClient(apiUrl=parent_task.request.girder_api_url)
gc.token = parent_task.request.girder_client_token
task_args = tuple(_walk_obj(body[0], _maybe_model_repr))
task_kwargs = _walk_obj(body[1], _maybe_model_repr)
parameters = {
'title':
headers.pop('girder_job_title',
job_defaults.get('girder_job_title', '')),
'type':
headers.pop('girder_job_type',
job_defaults.get('girder_job_type', '')),
'handler':
headers.pop('girder_job_handler',
job_defaults.get('girder_job_handler', '')),
'public':
headers.pop('girder_job_public',
job_defaults.get('girder_job_public', '')),
'args':
json.dumps(task_args),
'kwargs':
task_kwargs,
'otherFields':
json.dumps(
dict(celeryTaskId=headers['id'],
celeryParentTaskId=parent_task.request.id,
**headers.pop(
'girder_job_other_fields',
job_defaults.get('girder_job_other_fields', ''))))
}
try:
response = gc.post('job', parameters=parameters, jsonResp=False)
if response.ok:
headers['jobInfoSpec'] = response.json().get('jobInfoSpec')
except requests.exceptions.RequestException as e:
logger.warn('Failed to post job: {}'.format(e))
except MissingJobArguments as e:
logger.warn('Girder job not created: {}'.format(str(e)))
"email": "*****@*****.**",
"firstName": "Girder",
"lastName": "Admin"
})
c.authenticate('girder', 'girder')
# Create a tangelo hub collection if there isn't one
coll_search = c.get('resource/search',
parameters={
'q': 'Default',
'types': '["collection"]'
})
if len(coll_search["collection"]) == 0:
collection = c.post('collection',
parameters={
'name': 'Default',
'description': 'Default workspace',
'public': 'true'
})
c.post('folder',
parameters={
'parentType': 'collection',
'parentId': collection['_id'],
'name': 'Data',
'description': 'Data Folder',
'public': 'true'
})
c.post('folder',
parameters={
'parentType': 'collection',
'parentId': collection['_id'],
'name': 'Analyses',
"user",
{
"login": "******",
"password": "******",
"email": "*****@*****.**",
"firstName": "Girder",
"lastName": "Admin",
},
)
c.authenticate("girder", "girder")
# Create a tangelo hub collection if there isn't one
coll_search = c.get("resource/search", parameters={"q": "Default", "types": '["collection"]'})
if len(coll_search["collection"]) == 0:
collection = c.post(
"collection", parameters={"name": "Default", "description": "Default workspace", "public": "true"}
)
c.post(
"folder",
parameters={
"parentType": "collection",
"parentId": collection["_id"],
"name": "Data",
"description": "Data Folder",
"public": "true",
},
)
c.post(
"folder",
parameters={
"parentType": "collection",
# We use the directory name as the collection name in Girder.
fullpath = os.path.join(root, file)
analysis_filename = os.path.basename(fullpath)
analysis_name = os.path.splitext(analysis_filename)[0]
analysis_dir = os.path.dirname(fullpath)
collection_name = os.path.basename(analysis_dir)
# Create this collection if it doesn't already exist.
collection_search = c.get('resource/search', parameters={
'q': collection_name,
'types': '["collection"]'
})
if len(collection_search["collection"]) == 0:
collection = c.post('collection', parameters={
'name': collection_name,
'description': collection_name,
'public': 'true'
})
c.post('folder', parameters={
'parentType': 'collection',
'parentId': collection['_id'],
'name': 'Data',
'description': 'Data Folder',
'public': 'true'
})
c.post('folder', parameters={
'parentType': 'collection',
'parentId': collection['_id'],
'name': 'Analyses',
'description': 'Analysis folder',
'public': 'true'
| | / // // /| | / /|_/ / __/ | | /| / / __ \/ ___/ //_/ _ \/ ___/
| |/ // // ___ |/ / / / /___ | |/ |/ / /_/ / / / ,< / __/ /
|___/___/_/ |_/_/ /_/_____/ |__/|__/\____/_/ /_/|_|\___/_/
You are running in private standalone mode.
Troubleshooting: Try running `docker pull kitware/viame-worker` to get the latest image
Documentation: https://kitware.github.io/dive/Deployment-Docker-Compose/
Issues: https://github.com/Kitware/dive/issues
Support: please email [email protected]
""")
# Fetch Celery broker credentials from server
diveclient = GirderClient(apiUrl=dive_api_url)
diveclient.authenticate(username=dive_username, password=dive_password)
me = diveclient.get('user/me')
creds = diveclient.post(f'rabbit_user_queues/user/{me["_id"]}')
broker_url = creds['broker_url']
queue_name = f"{me['login']}@private"
if not me.get(UserPrivateQueueEnabledMarker, False):
warn(" Private queues not enabled for this user.")
warn(
" You can visit https://viame.kitware/com/#jobs to change these settings"
)
info("========================")
task_default_queue = queue_name
if broker_url is None:
raise RuntimeError('CELERY_BROKER_URL must be set')
worker_send_task_events = False
# https://docs.celeryproject.org/en/stable/userguide/configuration.html#std-setting-worker_prefetch_multiplier
client = GirderClient(host=args.host, port=args.port)
register_and_authenticate(client,
login=args.user,
password=args.password,
email='{}@localhost.com'.format(args.user),
firstName='Girder',
lastName='Admin')
local_assetstore_name = 'local'
if find_assetstore(local_assetstore_name) is None:
client.post('assetstore',
parameters=dict(name=local_assetstore_name,
type=str(AssetstoreType.FILESYSTEM),
root=os.path.join(args.data_root,
'assetstores',
'local'),
readOnly="false"))
client.put('system/plugins',
parameters=dict(plugins=json.dumps(['celery_jobs',
'climos_test',
'user_quota',
'hdfs_assetstore',
'jobs',
'romanesco',
'sparktest'])))
client.put('system/restart')
ensure_user(client,
login=user,
password=password,
email='*****@*****.**',
firstName='Girder',
lastName='Admin')
client.authenticate(user, password)
s3_assetstore_name = 's3'
if find_assetstore(s3_assetstore_name) is None:
client.post('assetstore',
parameters=dict(name=s3_assetstore_name,
type=str(AssetstoreType.S3),
bucket=args.s3,
accessKeyId=args.aws_key_id,
secret=args.aws_secret_key))
client.put(
'system/plugins',
parameters=dict(plugins=json.dumps(['jobs', 'worker', 'osumo']))
)
client.put('system/restart')
sleep(30)
client.put('system/setting',
parameters=dict(list=json.dumps([
dict(key='worker.broker', value=args.broker),
dict(key='worker.backend', value=args.broker),
class BaseIntegrationTest(unittest.TestCase):
def __init__(self, name, girder_url, girder_user, girder_password, job_timeout=60, cleanup=True):
super(BaseIntegrationTest, self).__init__(name)
self._job_id = None
self._script_id = None
self._output_folder_id = None
self._input_folder_id = None
self._girder_url = girder_url
self._girder_user = girder_user
self._girder_password = girder_password
self._job_timeout = job_timeout
self._data = 'Need more input!'
self._cleanup = cleanup
def setUp(self):
url = '%s/api/v1' % self._girder_url
self._client = GirderClient(apiUrl=url)
self._client.authenticate(self._girder_user,
self._girder_password)
user = self._client.get('user/me')
self._user_id = user['_id']
r = list(self._client.listFolder(self._user_id, 'user', name='Private'))
self.assertEqual(len(r), 1)
self._private_folder_id = r[0]['_id']
def tearDown(self):
if not self._cleanup:
return
if self._job_id:
try:
url = 'jobs/%s' % self._job_id
self._client.delete(url)
except Exception as e:
traceback.print_exc()
if self._script_id:
try:
url = 'scripts/%s' % self._script_id
self._client.delete(url)
except Exception:
traceback.print_exc()
if self._output_folder_id:
try:
url = 'folder/%s' % self._output_folder_id
self._client.delete(url)
except Exception:
traceback.print_exc()
if self._input_folder_id:
try:
url = 'folder/%s' % self._input_folder_id
self._client.delete(url)
except Exception:
traceback.print_exc()
def create_script(self, commands=[
'sleep 10', 'cat CumulusIntegrationTestInput'
]):
body = {
'commands': commands,
'name': 'CumulusIntegrationTestLob'
}
r = self._client.post('scripts', data=json.dumps(body))
self._script_id = r['_id']
def create_input(self, folder_name='CumulusInput'):
r = self._client.createFolder(self._private_folder_id, folder_name)
self._input_folder_id = r['_id']
size = len(self._data)
item = self._client.uploadFile(self._input_folder_id,
StringIO(self._data), 'CumulusIntegrationTestInput', size,
parentType='folder')
self._item_id = item['itemId']
def create_output_folder(self, folder_name='CumulusOutput'):
r = self._client.createFolder(self._private_folder_id, folder_name)
self._output_folder_id = r['_id']
def create_job(self, job_name='CumulusIntegrationTestJob', tail=None):
body = {
'name': job_name,
'scriptId': self._script_id,
'output': [{
'folderId': self._output_folder_id,
'path': '.'
}],
'input': [
{
'folderId': self._input_folder_id,
'path': '.'
}
]
}
if tail:
body['output'].append({
"path": tail,
"tail": True
})
job = self._client.post('jobs', data=json.dumps(body))
self._job_id = job['_id']
def submit_job(self, job_params={}, timeout=None):
url = 'clusters/%s/job/%s/submit' % (self._cluster_id, self._job_id)
self._client.put(url, data=json.dumps(job_params))
start = time.time()
while True:
time.sleep(1)
r = self._client.get('jobs/%s' % self._job_id)
if r['status'] in ['error', 'unexpectederror']:
r = self._client.get('jobs/%s/log' % self._job_id)
self.fail(str(r))
elif r['status'] == 'complete':
break
if time.time() - start > timeout:
self.fail('Job didn\'t complete in timeout')
def assert_output(self):
r = self._client.listItem(self._output_folder_id)
self.assertEqual(len(r), 4)
stdout_item = None
for i in r:
if i['name'].startswith('CumulusIntegrationTestJob-%s.o' % self._job_id):
stdout_item = i
break
self.assertIsNotNone(stdout_item)
r = self._client.get('item/%s/files' % i['_id'])
self.assertEqual(len(r), 1)
path = os.path.join(tempfile.gettempdir(), self._job_id)
try:
self._client.downloadFile(r[0]['_id'], path)
with open(path, 'rb') as fp:
self.assertEqual(fp.read(), self._data)
finally:
if os.path.exists(path):
os.remove(path)
if __name__ == "__main__":
login = '******'
password = '******'
gc = GirderClient(apiUrl='http://*****:*****@admin.com',
firstName='admin',
lastName='admin',
password=password,
admin=True)
gc.authenticate(username=login, password=password)
# Create an assetstore
gc.post('assetstore',
parameters={
'name': 'TestAssetstore',
'type': 0,
'root': '/home/circleci/project/assetstore'
})
# Enable the 'slicer_extension_manager' plugin
gc.put('system/plugins',
parameters={"plugins": '["slicer_extension_manager"]'})
# Restart the server
gc.put('system/restart')
class BaseIntegrationTest(unittest.TestCase):
def __init__(self,
name,
girder_url,
girder_user,
girder_password,
job_timeout=60,
cleanup=True):
super(BaseIntegrationTest, self).__init__(name)
self._job_id = None
self._script_id = None
self._output_folder_id = None
self._input_folder_id = None
self._girder_url = girder_url
self._girder_user = girder_user
self._girder_password = girder_password
self._job_timeout = job_timeout
self._data = 'Need more input!'
self._cleanup = cleanup
def setUp(self):
url = '%s/api/v1' % self._girder_url
self._client = GirderClient(apiUrl=url)
self._client.authenticate(self._girder_user, self._girder_password)
user = self._client.get('user/me')
self._user_id = user['_id']
r = list(self._client.listFolder(self._user_id, 'user',
name='Private'))
self.assertEqual(len(r), 1)
self._private_folder_id = r[0]['_id']
def tearDown(self):
if not self._cleanup:
return
if self._job_id:
try:
url = 'jobs/%s' % self._job_id
self._client.delete(url)
except Exception as e:
traceback.print_exc()
if self._script_id:
try:
url = 'scripts/%s' % self._script_id
self._client.delete(url)
except Exception:
traceback.print_exc()
if self._output_folder_id:
try:
url = 'folder/%s' % self._output_folder_id
self._client.delete(url)
except Exception:
traceback.print_exc()
if self._input_folder_id:
try:
url = 'folder/%s' % self._input_folder_id
self._client.delete(url)
except Exception:
traceback.print_exc()
def create_script(self,
commands=['sleep 10',
'cat CumulusIntegrationTestInput']):
body = {'commands': commands, 'name': 'CumulusIntegrationTestLob'}
r = self._client.post('scripts', data=json.dumps(body))
self._script_id = r['_id']
def create_input(self, folder_name='CumulusInput'):
r = self._client.createFolder(self._private_folder_id, folder_name)
self._input_folder_id = r['_id']
size = len(self._data)
item = self._client.uploadFile(self._input_folder_id,
StringIO(self._data),
'CumulusIntegrationTestInput',
size,
parentType='folder')
self._item_id = item['itemId']
def create_output_folder(self, folder_name='CumulusOutput'):
r = self._client.createFolder(self._private_folder_id, folder_name)
self._output_folder_id = r['_id']
def create_job(self, job_name='CumulusIntegrationTestJob', tail=None):
body = {
'name': job_name,
'scriptId': self._script_id,
'output': [{
'folderId': self._output_folder_id,
'path': '.'
}],
'input': [{
'folderId': self._input_folder_id,
'path': '.'
}]
}
if tail:
body['output'].append({"path": tail, "tail": True})
job = self._client.post('jobs', data=json.dumps(body))
self._job_id = job['_id']
def submit_job(self, job_params={}, timeout=None):
url = 'clusters/%s/job/%s/submit' % (self._cluster_id, self._job_id)
self._client.put(url, data=json.dumps(job_params))
start = time.time()
while True:
time.sleep(1)
r = self._client.get('jobs/%s' % self._job_id)
if r['status'] in ['error', 'unexpectederror']:
r = self._client.get('jobs/%s/log' % self._job_id)
self.fail(str(r))
elif r['status'] == 'complete':
break
if time.time() - start > timeout:
self.fail('Job didn\'t complete in timeout')
def assert_output(self):
r = self._client.listItem(self._output_folder_id)
self.assertEqual(len(r), 4)
stdout_item = None
for i in r:
if i['name'].startswith('CumulusIntegrationTestJob-%s.o' %
self._job_id):
stdout_item = i
break
self.assertIsNotNone(stdout_item)
r = self._client.get('item/%s/files' % i['_id'])
self.assertEqual(len(r), 1)
path = os.path.join(tempfile.gettempdir(), self._job_id)
try:
self._client.downloadFile(r[0]['_id'], path)
with open(path, 'rb') as fp:
self.assertEqual(fp.read(), self._data)
finally:
if os.path.exists(path):
os.remove(path)
