def main(config):
client = GirderClient(apiUrl=config.girder_api_url)
client.authenticate(config.girder_user,
config.girder_password)
# Load any parameters
params = {}
if config.taskflow_start_params is not None:
with open(config.taskflow_start_params) as fp:
params = json.load(fp)
print params
try:
print ('Running %s taskflow ...' % config.taskflow_start_params)
taskflow_id = create_taskflow(
client, config.taskflow_class)
# Start the task flow
url = 'taskflows/%s/start' % (taskflow_id)
client.put(url, data=json.dumps(params))
# Wait for it to complete
wait_for_complete(client, taskflow_id)
except HttpError as ex:
print( ex.responseText)
def main():
parser = argparse.ArgumentParser(
description='Import analyses into minerva')
parser.add_argument('--username', required=False, default=None)
parser.add_argument('--password', required=False, default=None)
parser.add_argument('--scheme', required=False, default='http')
parser.add_argument('--host', required=False, default='localhost')
parser.add_argument('--port', required=False, default='8080')
parser.add_argument('--api-root',
required=False,
default='/api/v1',
help='path to the Girder REST API')
parser.add_argument('--path',
required=True,
help='the path to import the analyses from')
config = parser.parse_args()
client = GirderClient(host=config.host,
port=config.port,
apiRoot=config.api_root,
scheme=config.scheme)
client.authenticate(config.username, config.password)
import_analyses(client, config.path)
class GirderClient(object):
def __init__(self):
token_obj = get_oc_token_obj()
url = token_obj.get('apiUrl')
api_key = token_obj.get('apiKey')
url = os.environ.get('OC_API_URL', url)
internal_url = os.environ.get('OC_INTERNAL_API_URL', url)
api_key = os.environ.get('OC_API_KEY', api_key)
token = os.environ.get('GIRDER_TOKEN')
self.client = None
self.url = url
self.internal_url = internal_url
if internal_url is not None:
self.client = GC(apiUrl=internal_url)
if api_key is not None:
self.client.authenticate(apiKey=api_key)
elif token is not None:
self.client.token = token
def __getattr__(self, name):
return getattr(self.client, name)
def get_girder_client() -> GirderClient:
client = GirderClient(apiUrl="https://viame.kitware.com/api/v1")
apikey = os.environ.get('GIRDER_API_KEY', None)
if apikey:
client.authenticate(apiKey=apikey)
else:
client.authenticate(interactive=True)
return client
def import_calc(config):
try:
target_port = None
if config.port:
target_port = config.port
target_scheme = None
if config.scheme:
target_scheme = config.scheme
target_apiroot = None
if config.apiroot:
target_apiroot = config.apiroot
client = GirderClient(host=config.host, port=target_port,
scheme=target_scheme, apiRoot=target_apiroot)
client.authenticate(apiKey=config.apiKey)
me = client.get('/user/me')
if not me:
print('Error: Girder token invalid, please verify')
return
folderParams = {
'parentId': me['_id'],
'parentType': 'user',
'name': 'Private'
}
# Get the private folder id first
folder = next(client.listResource('folder', folderParams))
folder = next(client.listFolder(me['_id'], 'user', 'Private'))
for file_name in config.datafile:
print ('\nUploading ' + file_name)
file_id = {}
with open(file_name, 'r') as fp:
fileNameBase = os.path.basename(file_name)
size = os.path.getsize(file_name)
file_id = client.uploadFile(folder['_id'], fp, fileNameBase,
size, 'folder')
body = {
'fileId': file_id['_id']
}
if config.public:
body['public'] = True
mol = client.sendRestRequest('POST', 'molecules', data=json.dumps(body))
if mol and '_id' in mol:
config.moleculeId = mol['_id']
print('Molecule ID: ' + mol['_id'])
else:
print(mol)
except HttpError as error:
print(error.responseText, file=sys.stderr)
def test_extract_download(data):
fileId, filename = data
filepath = localDataRoot / str(filename)
if not filepath.exists():
gc = GirderClient(apiUrl=source_api_root)
gc.authenticate(apiKey=os.environ.get('GIRDER_API_KEY'))
gc.downloadFile(fileId, str(filepath))
with zipfile.ZipFile(filepath, 'r') as zipref:
zipref.extractall(localDataRoot)
def _importAnalysis(self):
"""Setup and import analyses for bsve tests."""
if self._import_done:
return
path = "/minerva_analysis/folder"
response = self.request(path=path, method="POST", user=self._user)
self.assertStatusOk(response)
analyses_folder = response.json["folder"]
# import the bsve analysis
client = GirderClient("localhost", girder_port)
client.authenticate("minervauser", "password")
bsve_analysis_path = os.path.abspath(
os.path.join(os.path.dirname(os.path.realpath(__file__)), "../analyses/bsve")
)
import_analyses.import_analyses(client, bsve_analysis_path)
path = "/item"
params = {"folderId": analyses_folder["_id"]}
response = self.request(path=path, method="GET", params=params, user=self._user)
self.assertStatusOk(response)
self.assertEquals(len(response.json), 2, "Expecting only one analysis")
for analysis in response.json:
if analysis["name"] == "bsve search":
search_analysis = analysis
elif analysis["name"] == "MMWR data import":
soda_analysis = analysis
else:
self.fail('Unexpected analysis found "%s".' % analysis["name"])
expected_meta = {
u"minerva": {
u"analysis_type": u"bsve_search",
u"analysis_name": u"bsve search",
u"analysis_id": search_analysis["_id"],
}
}
self.assertEquals(search_analysis["meta"], expected_meta, "Unexpected value for search meta data")
expected_meta = {
u"minerva": {
u"analysis_type": u"mmwr_import_data",
u"analysis_name": u"MMWR data import",
u"analysis_id": soda_analysis["_id"],
}
}
self.assertEquals(soda_analysis["meta"], expected_meta, "Unexpected value for soda meta data")
# create the dataset folder
path = "/minerva_dataset/folder"
params = {"userId": self._user["_id"]}
response = self.request(path=path, method="POST", params=params, user=self._user)
self.assertStatusOk(response)
self._importDone = True
def main(ctx, api_key, api_url):
"""Openchemistry Client
The client can be used to fetch molecules, add molecules, etc.
"""
gc = GirderClient(apiUrl=api_url)
if api_key is not None:
gc.authenticate(apiKey=api_key)
ctx.obj = gc
def _ingest(project, composite, dir, channel_map, api_url, api_key):
if dir[-1] != '/':
dir += '/'
gc = GirderClient(apiUrl=api_url)
gc.authenticate(apiKey=api_key)
channel_map = json.load(channel_map)
channel_map = {channel.upper():element.lower() for (channel,element) in channel_map.items()}
experiments = _ingest_runs(gc, project, composite, dir)
#(run_ids, runs) = _ingest_runs(gc, project, composite, dir)
_ingest_samples(gc, project, composite, dir, experiments, channel_map)
def gc_init(api_url='https://girder.hub.yt/api/v1', api_key=None):
from girder_client import GirderClient
if api_key is None:
try:
api_key = os.environ['GIRDER_API_KEY']
except KeyError as err:
msg = 'please define GIRDER_API_KEY environment variable\n'
msg += ' or pass api_key kwargs.'
raise KeyError(msg)
gc = GirderClient(apiUrl=api_url)
gc.authenticate(apiKey=api_key)
return gc
def main(args=None):
parser = argparse.ArgumentParser(
description='Mount Girder filesystem assetstore.')
parser.add_argument('--api-url',
required=True,
default=None,
help='full URL to the RESTful API of Girder server')
parser.add_argument('--username', required=False, default=None)
parser.add_argument('--password', required=False, default=None)
parser.add_argument('--api-key', required=False, default=None)
parser.add_argument('--token', required=False, default=None)
parser.add_argument('-c',
default='remote',
choices=['remote', 'direct'],
help='command to run')
parser.add_argument('--foreground', dest='foreground', action='store_true')
parser.add_argument('--hostns', dest='hostns', action='store_true')
parser.add_argument('local_folder', help='path to local target folder')
parser.add_argument('remote_folder', help='Girder\'s folder id')
args = parser.parse_args()
gc = GirderClient(apiUrl=args.api_url)
if args.token:
gc.token = args.token
elif args.api_key:
gc.authenticate(apiKey=args.api_key)
elif args.username and args.password:
gc.authenticate(username=args.username, password=args.password)
else:
raise RuntimeError("You need to specify apiKey or user/pass")
if args.hostns:
targetns = os.path.join(os.environ.get('HOSTDIR', '/'),
'proc/1/ns/mnt')
with open(targetns) as fd:
setns(fd, CLONE_NEWNS)
if args.c == 'remote':
FUSE(RESTGirderFS(args.remote_folder, gc),
args.local_folder,
foreground=args.foreground,
ro=True,
allow_other=True)
elif args.c == 'direct':
FUSE(LocalGirderFS(args.remote_folder, gc),
args.local_folder,
foreground=args.foreground,
ro=True,
allow_other=True)
else:
print('No implementation for command %s' % args.c)
def upload_benchmark_results(benchmark_bin, api_key=None):
hostname = socket.gethostname().lower()
results_dir = os.path.join(benchmark_bin, 'BenchmarkResults',
hostname)
if not os.path.exists(results_dir):
sys.stderr.write('Expected results directory does not exist: ' + results_dir)
sys.exit(1)
from girder_client import GirderClient
gc = GirderClient(apiUrl='https://data.kitware.com/api/v1')
gc.authenticate(apiKey=api_key)
# ITK/PerformanceBenchmarkingResults
folder_id = '5af50c818d777f06857985e3'
hostname_folder = gc.loadOrCreateFolder(hostname, folder_id, 'folder')
gc.upload(os.path.join(results_dir, '*.json'), hostname_folder['_id'],
leafFoldersAsItems=False, reuseExisting=True)
def testClientMetadataExtractor(testData, user):
item = Item().load(testData['item']['_id'], user=user)
assert item['name'] == testData['name']
del item['meta']
item = Item().save(item)
assert 'meta' not in item
client = GirderClient('localhost', int(os.environ['GIRDER_PORT']))
client.authenticate(user['login'], 'password')
extractor = ClientMetadataExtractor(client, testData['path'], testData['item']['_id'])
extractor.extractMetadata()
item = Item().load(testData['item']['_id'], user=user)
assert item['name'] == testData['name']
assert 'meta' in item
assert item['meta']['MIME type'] == testData['mimeType']
def upload_benchmark_results(benchmark_bin, api_key=None):
hostname = socket.gethostname().lower()
results_dir = os.path.join(benchmark_bin, 'BenchmarkResults', hostname)
if not os.path.exists(results_dir):
sys.stderr.write('Expected results directory does not exist: ' +
results_dir)
sys.exit(1)
from girder_client import GirderClient
gc = GirderClient(apiUrl='https://data.kitware.com/api/v1')
gc.authenticate(apiKey=api_key)
# ITK/PerformanceBenchmarkingResults
folder_id = '5af50c818d777f06857985e3'
hostname_folder = gc.loadOrCreateFolder(hostname, folder_id, 'folder')
gc.upload(os.path.join(results_dir, '*.json'),
hostname_folder['_id'],
leafFoldersAsItems=False,
reuseExisting=True)
def init_girder(api_key=None, api_url='https://girder.hub.yt/api/v1'):
"""Initialize girder client, rely on environment variable:
GIRDER_API_KEY, connect to yt Hub.
Args:
api_key (str, optional): use GIRDER_API_KEY env. var. by default
api_url (str, optional): use yt Hub v1 by default
Return:
GirderClient: initialized girder client
"""
from girder_client import GirderClient
if api_key is None:
import os
api_key = os.environ['GIRDER_API_KEY']
gc = GirderClient(apiUrl=api_url)
gc.authenticate(apiKey=api_key)
return gc
def testClientMetadataExtractor(self):
item = self.model('item').load(self.item['_id'], user=self.user)
self.assertEqual(item['name'], self.name)
self.assertNotHasKeys(item, ['meta'])
clientPath = os.path.join(ROOT_DIR, 'clients', 'python')
sys.path.insert(0, clientPath)
from girder_client import GirderClient
client = GirderClient('localhost', int(os.environ['GIRDER_PORT']))
client.authenticate(self.user['login'], self.password)
extractor = ClientMetadataExtractor(client, self.path, self.item['_id'])
extractor.extractMetadata()
sys.path.remove(clientPath)
item = self.model('item').load(self.item['_id'], user=self.user)
self.assertEqual(item['name'], self.name)
self.assertHasKeys(item, ['meta'])
self.assertEqual(item['meta']['MIME type'], self.mimeType)
def main():
parser = argparse.ArgumentParser(description='Import analyses into minerva')
parser.add_argument('--username', required=False, default=None)
parser.add_argument('--password', required=False, default=None)
parser.add_argument('--scheme', required=False, default='http')
parser.add_argument('--host', required=False, default='localhost')
parser.add_argument('--port', required=False, default='8080')
parser.add_argument('--api-root', required=False, default='/api/v1',
help='path to the Girder REST API')
parser.add_argument('--path', required=True, help='the path to import the analyses from')
config = parser.parse_args()
client = GirderClient(host=config.host, port=config.port,
apiRoot=config.api_root, scheme=config.scheme)
client.authenticate(config.username, config.password)
import_analyses(client, config.path)
def testClientMetadataExtractor(self):
item = Item().load(self.item['_id'], user=self.user)
self.assertEqual(item['name'], self.name)
self.assertNotHasKeys(item, ['meta'])
clientPath = os.path.join(ROOT_DIR, 'clients', 'python')
sys.path.insert(0, clientPath)
from girder_client import GirderClient
client = GirderClient('localhost', int(os.environ['GIRDER_PORT']))
client.authenticate(self.user['login'], self.password)
extractor = ClientMetadataExtractor(client, self.path,
self.item['_id'])
extractor.extractMetadata()
sys.path.remove(clientPath)
item = Item().load(self.item['_id'], user=self.user)
self.assertEqual(item['name'], self.name)
self.assertHasKeys(item, ['meta'])
self.assertEqual(item['meta']['MIME type'], self.mimeType)
def main(args=None):
parser = argparse.ArgumentParser(
description='Mount Girder filesystem assetstore.')
parser.add_argument('--api-url', required=True, default=None,
help='full URL to the RESTful API of Girder server')
parser.add_argument('--username', required=False, default=None)
parser.add_argument('--password', required=False, default=None)
parser.add_argument('--api-key', required=False, default=None)
parser.add_argument('--token', required=False, default=None)
parser.add_argument('-c', default='remote', choices=['remote', 'direct'],
help='command to run')
parser.add_argument('--foreground', dest='foreground',
action='store_true')
parser.add_argument('--hostns', dest='hostns', action='store_true')
parser.add_argument('local_folder', help='path to local target folder')
parser.add_argument('remote_folder', help='Girder\'s folder id')
args = parser.parse_args()
gc = GirderClient(apiUrl=args.api_url)
if args.token:
gc.token = args.token
elif args.api_key:
gc.authenticate(apiKey=args.api_key)
elif args.username and args.password:
gc.authenticate(username=args.username, password=args.password)
else:
raise RuntimeError("You need to specify apiKey or user/pass")
if args.hostns:
targetns = os.path.join(os.environ.get('HOSTDIR', '/'),
'proc/1/ns/mnt')
with open(targetns) as fd:
setns(fd, CLONE_NEWNS)
if args.c == 'remote':
FUSE(RESTGirderFS(args.remote_folder, gc), args.local_folder,
foreground=args.foreground, ro=True, allow_other=True)
elif args.c == 'direct':
FUSE(LocalGirderFS(args.remote_folder, gc), args.local_folder,
foreground=args.foreground, ro=True, allow_other=True)
else:
print('No implementation for command %s' % args.c)
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
def main():
"""Create the folder hierarchy with metadata in a Girder instance."""
args = parser.parse_args()
g = GirderClient(host=args.host, port=args.port, scheme=args.scheme)
g.authenticate(args.username, args.password)
def create_folder_on_demand(parent_folder_id, folder_name):
existing_folders = list(
g.listFolder(parent_folder_id, name=folder_name))
if not len(existing_folders):
sought_folder = g.createFolder(parent_folder_id, name=folder_name)
else:
sought_folder = existing_folders[0]
return sought_folder
metadata_file = 'metadata.json'
with open(metadata_file) as json_file:
metadata = json.load(json_file)
parent_folder_id = args.parent_folder_id
for subject_id, subject_metadata in metadata.items():
subject_folder = create_folder_on_demand(parent_folder_id, subject_id)
for (scan_time, scan_date, scan_weight) in subject_metadata['scans']:
create_folder_on_demand(subject_folder['_id'], scan_time)
from girder_client import GirderClient
c = GirderClient(host="localhost", port=9000)
# Create an admin user if there isn't one
try:
c.authenticate("girder", "girder")
except:
c.sendRestRequest(
"POST",
"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",
def __init__(self, session_id, api_url, api_key):
super().__init__()
self.session_id = session_id
gc = GirderClient(apiUrl=api_url)
gc.authenticate(apiKey=api_key)
self._fs = WtDmsGirderFS(session_id, gc)
def testBsveSearchAnalysis(self):
# create the analysis folder
path = '/minerva_analysis/folder'
response = self.request(path=path, method='POST', user=self._user)
self.assertStatusOk(response)
analyses_folder = response.json['folder']
# import the bsve analysis
client = GirderClient('localhost', girder_port)
client.authenticate('minervauser', 'password')
bsve_analysis_path = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '../analyses/bsve'))
import_analyses.import_analyses(client, bsve_analysis_path)
path = '/item'
params = {
'folderId': analyses_folder['_id']
}
response = self.request(path=path, method='GET', params=params, user=self._user)
self.assertStatusOk(response)
self.assertEquals(len(response.json), 1, 'Expecting only one analysis')
analysis = response.json[0]
self.assertEquals(analysis['name'], 'bsve search', 'Expecting analysis name to be "bsve search"')
expected_meta = {
u'minerva': {
u'analysis_type': u'bsve_search',
u'analysis_name': u'bsve search',
u'analysis_id': analysis['_id']
}
}
self.assertEquals(analysis['meta'], expected_meta, 'Unexpected value for meta data')
# create the dataset folder
path = '/minerva_dataset/folder'
params = {
'userId': self._user['_id'],
}
response = self.request(path=path, method='POST', params=params, user=self._user)
self.assertStatusOk(response)
# mock the calls to bsve search
@urlmatch(netloc=r'(.*\.)?beta-search.bsvecosystem.net(.*)$')
def bsve_mock(url, request):
if url.path.split('/')[-1] == 'request':
return httmock.response(200, '12345')
else:
pluginTestDir = os.path.dirname(os.path.realpath(__file__))
filepath = os.path.join(pluginTestDir, 'data', 'bsve_search.json')
with open(filepath) as bsve_search_file:
content = {
'status': 1,
'results': json.load(bsve_search_file)
}
headers = {
'content-length': len(content),
'content-type': 'application/json'
}
return httmock.response(200, content, headers, request=request)
with HTTMock(bsve_mock):
response = self.request(
path='/minerva_analysis/bsve_search',
method='POST',
params={
'datasetName': 'test dataset',
'bsveSearchParams': '{}'
},
user=self._user
)
# wait for the async job to complete
searchResultsFinished = False
count = 0
while not searchResultsFinished and count < 5:
# get the dataset and check if it has been updated
path = '/minerva_dataset/%s/dataset' % str(response.json['dataset_id'])
response = self.request(
path=path,
method='GET',
user=self._user
)
dataset = response.json
if 'json_row' in dataset:
searchResultsFinished = True
else:
time.sleep(2)
count += 1
# ensure the first row of results was added to the dataset
self.assertTrue('json_row' in dataset, 'json_row expected in dataset')
self.assertTrue('data' in dataset['json_row'], 'data should be in json_row')
self.assertTrue('Longitude' in dataset['json_row']['data'], 'data.Longitude should be in json_row')
# ensure that we can map the Lat/Long to geojson, as this json has
# unicode values for Lat/Long
# update the minerva metadata with coordinate mapping
metadata = {'minerva': dataset}
metadata['minerva']['mapper'] = {
"latitudeKeypath": "data.Latitude",
"longitudeKeypath": "data.Longitude"
}
path = '/item/{}/metadata'.format(dataset['dataset_id'])
response = self.request(
path=path,
method='PUT',
user=self._user,
body=json.dumps(metadata),
type='application/json'
)
metadata = response.json
# create geojson in the dataset
path = '/minerva_dataset/{}/geojson'.format(dataset['dataset_id'])
response = self.request(
path=path,
method='POST',
user=self._user,
)
self.assertHasKeys(response.json, ['geojson_file'])
def getClient(name: str) -> GirderClient:
gc = GirderClient(apiUrl='http://localhost:8010/api/v1')
gc.authenticate(username=name, password=users[name]['password'])
return gc
def admin_client() -> GirderClient:
gc = GirderClient(apiUrl='http://localhost:8010/api/v1')
gc.authenticate(username='******', password='******')
return gc
girder_scheme = os.environ.get('GIRDER_SCHEME', 'http')
girder_api_root = os.environ.get('GIRDER_API_ROOT', '/api/v1')
girder_api_key = os.environ.get('GIRDER_API_KEY')
girder_token = os.environ.get('GIRDER_TOKEN')
app_base_url = os.environ.get('APP_BASE_URL')
cluster_id = os.environ.get('CLUSTER_ID')
jupyterhub_base_url = os.environ.get('JUPYTERHUB_BASE_URL')
if girder_host:
girder_client = GirderClient(host=girder_host,
port=girder_port,
scheme=girder_scheme,
apiRoot=girder_api_root)
if girder_api_key is not None:
girder_client.authenticate(apiKey=girder_api_key)
elif girder_token is not None:
girder_client.token = girder_token
girder_file = lookup_file(girder_client, jupyterhub_base_url)
# TODO Need to use basis and theory
def _fetch_calculation(molecule_id,
type_=None,
basis=None,
theory=None,
functional=None):
parameters = {'moleculeId': molecule_id, 'sortByTheory': True}
if type_ is not None:
parser.add_argument('--admin', help='name:pass for the admin user')
parser.add_argument('--host', help='host to connect to')
parser.add_argument('--port', type=int, help='port to connect to')
parser.add_argument('--broker', help='girder worker broker URI')
parser.add_argument('--s3', help='name of S3 bucket')
parser.add_argument('--aws-key-id', help='aws key id')
parser.add_argument('--aws-secret-key', help='aws secret key')
args = parser.parse_args()
client = GirderClient(host=args.host, port=args.port)
user, password = args.admin.split(":", 1)
if find_user('girder'):
client.authenticate('girder', 'girder')
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,
def main(args=None):
parser = argparse.ArgumentParser(description="Mount Girder filesystem assetstore.")
parser.add_argument(
"--api-url",
required=True,
default=None,
help="full URL to the RESTful API of Girder server",
)
parser.add_argument("--username", required=False, default=None)
parser.add_argument("--password", required=False, default=None)
parser.add_argument("--api-key", required=False, default=None)
parser.add_argument("--token", required=False, default=None)
parser.add_argument("--foreground", dest="foreground", action="store_true")
parser.add_argument("--hostns", dest="hostns", action="store_true")
parser.add_argument(
"--versions-mountpoint",
dest="versions_mountpoint",
required=False,
help="Mountpoint for the versions FS. If relative, then it should be "
"relative to the runs mountpoint",
default="Versions",
)
parser.add_argument(
"-c",
default="remote",
help="type of filesystem to mount",
choices=[
"remote",
"direct",
"wt_dms",
"wt_home",
"wt_work",
"wt_run",
"wt_versions",
"wt_runs",
],
)
parser.add_argument("local_folder", help="path to local target folder")
parser.add_argument(
"remote_folder",
help="Girder's folder id, a DM session id (for wt_dms), or a tale instance"
"ID (for wt_versions)",
)
args = parser.parse_args()
gc = GirderClient(apiUrl=args.api_url)
if args.token:
gc.token = args.token
elif args.api_key:
gc.authenticate(apiKey=args.api_key)
elif args.username and args.password:
gc.authenticate(username=args.username, password=args.password)
else:
raise RuntimeError("You need to specify apiKey or user/pass")
if args.hostns:
targetns = os.path.join(os.environ.get("HOSTDIR", "/"), "proc/1/ns/mnt")
with open(targetns) as fd:
setns(fd, CLONE_NEWNS)
if args.c == "remote":
FUSE(
RESTGirderFS(args.remote_folder, gc),
args.local_folder,
foreground=args.foreground,
ro=True,
allow_other=True,
)
elif args.c == "direct":
FUSE(
LocalGirderFS(args.remote_folder, gc),
args.local_folder,
foreground=args.foreground,
ro=True,
allow_other=True,
)
elif args.c == "wt_dms":
FUSE(
WtDmsGirderFS(args.remote_folder, gc),
args.local_folder,
foreground=args.foreground,
ro=True,
allow_other=True,
)
elif args.c == "wt_run":
user = gc.get("/user/me")
args = {
"user": user["login"],
"pass": "******".format(gc.token),
"dest": args.local_folder,
"runId": args.remote_folder,
"opts": "-o uid=1000,gid=100,file_mode=0600,dir_mode=2700", # FIXME
"url": gc.urlBase.replace("api/v1", "runs").rstrip("/"), # FIXME
}
cmd = 'echo "{user}\n{pass}" | mount.davfs {opts} {url}/{runId} {dest}'
cmd = cmd.format(**args)
subprocess.check_output(cmd, shell=True) # FIXME
elif args.c == "wt_work":
user = gc.get("/user/me")
args = {
"user": user["login"],
"pass": "******".format(gc.token),
"dest": args.local_folder,
"tale": args.remote_folder,
"opts": "-o uid=1000,gid=100,file_mode=0600,dir_mode=2700", # FIXME
"url": gc.urlBase.replace("api/v1", "tales").rstrip("/"), # FIXME
}
cmd = 'echo "{user}\n{pass}" | mount.davfs {opts} {url}/{tale} {dest}'
cmd = cmd.format(**args)
subprocess.check_output(cmd, shell=True) # FIXME
elif args.c == "wt_home":
user = gc.get("/user/me")
args = {
"user": user["login"],
"pass": "******".format(gc.token),
"dest": args.local_folder,
"opts": "-o uid=1000,gid=100,file_mode=0600,dir_mode=2700", # FIXME
"url": gc.urlBase.replace("api/v1", "homes").rstrip("/"), # FIXME
}
cmd = 'echo "{user}\n{pass}" | mount.davfs {opts} {url}/{user} {dest}'
cmd = cmd.format(**args)
subprocess.check_output(cmd, shell=True) # FIXME
elif args.c == "wt_versions":
FUSE(
WtVersionsFS(args.remote_folder, gc),
args.local_folder,
foreground=args.foreground,
ro=False,
allow_other=True,
)
elif args.c == "wt_runs":
FUSE(
WtRunsFS(args.remote_folder, gc, args.versions_mountpoint),
args.local_folder,
foreground=args.foreground,
ro=False,
allow_other=True,
)
else:
print("No implementation for command %s" % args.c)
def test_reset_integration_env(user: dict):
client = GirderClient(apiUrl='http://localhost:8010/api/v1')
client.authenticate(username=user['login'], password=user['password'])
privateFolder = getTestFolder(client)
client.delete(f"folder/{privateFolder['_id']}")
parser.add_argument('--admin', help='name:pass for the admin user')
parser.add_argument('--host', help='host to connect to')
parser.add_argument('--port', type=int, help='port to connect to')
parser.add_argument('--broker', help='girder worker broker URI')
parser.add_argument('--s3', help='name of S3 bucket')
parser.add_argument('--aws-key-id', help='aws key id')
parser.add_argument('--aws-secret-key', help='aws secret key')
args = parser.parse_args()
client = GirderClient(host=args.host, port=args.port)
user, password = args.admin.split(":", 1)
if find_user('girder'):
client.authenticate('girder', 'girder')
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,
from girder_client import GirderClient
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')
'table8': table8,
'table9': table9
})
def create_items_from_csv(path, data_dir, gc):
with open(path) as csvfile:
reader = csv.reader(csvfile, delimiter=',')
next(reader)
for row in reader:
create_item_from_row(row, data_dir, gc)
if __name__ == '__main__':
if len(sys.argv) < 5:
sys.exit(
'Sample call: python ingest.py ./data localhost 8080 admin letmein'
)
data_dir = sys.argv[1]
host = sys.argv[2]
port = sys.argv[3]
user = sys.argv[4]
password = sys.argv[5]
gc = GirderClient(apiUrl='http://{}:{}/api/v1'.format(host, port))
gc.authenticate(user, password)
create_items_from_csv(
'./jgi_data/NMDC_metadata_datasets - NMDC_datasets_metadata.csv',
data_dir, gc)
# with open("envo_lookup.json", "w") as f:
# f.write(json.dumps(lookup_table))
break
for assetstore in assetstore_list:
if assetstore['name'] == name:
result = assetstore['_id']
break
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',
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)
def main(args=None):
parser = argparse.ArgumentParser(
description='Mount Girder filesystem assetstore.')
parser.add_argument('--api-url',
required=True,
default=None,
help='full URL to the RESTful API of Girder server')
parser.add_argument('--username', required=False, default=None)
parser.add_argument('--password', required=False, default=None)
parser.add_argument('--api-key', required=False, default=None)
parser.add_argument('--token', required=False, default=None)
parser.add_argument('--foreground', dest='foreground', action='store_true')
parser.add_argument('--hostns', dest='hostns', action='store_true')
parser.add_argument('-c',
default='remote',
help='command to run',
choices=['remote', 'direct', 'wt_dms', 'wt_home'])
parser.add_argument('local_folder', help='path to local target folder')
parser.add_argument('remote_folder',
help='Girder\'s folder id or a DM session id')
args = parser.parse_args()
gc = GirderClient(apiUrl=args.api_url)
if args.token:
gc.token = args.token
elif args.api_key:
gc.authenticate(apiKey=args.api_key)
elif args.username and args.password:
gc.authenticate(username=args.username, password=args.password)
else:
raise RuntimeError("You need to specify apiKey or user/pass")
if args.hostns:
targetns = os.path.join(os.environ.get('HOSTDIR', '/'),
'proc/1/ns/mnt')
with open(targetns) as fd:
setns(fd, CLONE_NEWNS)
if args.c == 'remote':
FUSE(RESTGirderFS(args.remote_folder, gc),
args.local_folder,
foreground=args.foreground,
ro=True,
allow_other=True)
elif args.c == 'direct':
FUSE(LocalGirderFS(args.remote_folder, gc),
args.local_folder,
foreground=args.foreground,
ro=True,
allow_other=True)
elif args.c == 'wt_dms':
FUSE(WtDmsGirderFS(args.remote_folder, gc),
args.local_folder,
foreground=args.foreground,
ro=True,
allow_other=True)
elif args.c == 'wt_home':
user = gc.get('/user/me')
args = {
'user': user['login'],
'pass': '******'.format(gc.token),
'dest': args.local_folder,
'opts': '-o uid=1000,gid=100', # FIXME
'url': gc.urlBase.replace('api/v1', 'homes').rstrip('/') # FIXME
}
cmd = 'echo "{user}\n{pass}" | mount.davfs {opts} {url}/{user} {dest}'
cmd = cmd.format(**args)
subprocess.check_output(cmd, shell=True) # FIXME
else:
print('No implementation for command %s' % args.c)
def main(config):
client = GirderClient(apiUrl=config.girder_api_url)
client.authenticate(config.girder_user,
config.girder_password)
try:
# First run the simple flow
print ('Running simple taskflow ...')
taskflow_id = create_taskflow(
client, 'cumulus.taskflow.core.test.mytaskflows.SimpleTaskFlow')
# Start the task flow
url = 'taskflows/%s/start' % (taskflow_id)
client.put(url)
# Wait for it to complete
wait_for_complete(client, taskflow_id)
# First run the simple flow
print ('Running linked taskflow ...')
taskflow_id = create_taskflow(
client, 'cumulus.taskflow.core.test.mytaskflows.LinkTaskFlow')
# Start the task flow
url = 'taskflows/%s/start' % (taskflow_id)
client.put(url)
# Wait for it to complete
wait_for_complete(client, taskflow_id)
# Test terminating a simple flow
print ('Running simple taskflow ...')
taskflow_id = create_taskflow(
client, 'cumulus.taskflow.core.test.mytaskflows.SimpleTaskFlow')
# Start the task flow
url = 'taskflows/%s/start' % (taskflow_id)
client.put(url)
time.sleep(4)
print ('Terminate the taskflow')
url = 'taskflows/%s/terminate' % (taskflow_id)
client.put(url)
# Wait for it to terminate
wait_for_terminated(client, taskflow_id)
# Now delete it
print ('Delete the taskflow')
url = 'taskflows/%s' % (taskflow_id)
try:
client.delete(url)
except HttpError as ex:
if ex.status != 202:
raise
# Wait for it to terminate
wait_for_deletion(client, taskflow_id)
# Now try something with a chord
print ('Running taskflow containing a chord ...')
taskflow_id = create_taskflow(
client, 'cumulus.taskflow.core.test.mytaskflows.ChordTaskFlow')
# Start the task flow
url = 'taskflows/%s/start' % (taskflow_id)
client.put(url)
# Wait for it to complete
wait_for_complete(client, taskflow_id)
# Now try a workflow that is the two connected together
print ('Running taskflow that connects to parts together ...')
taskflow_id = create_taskflow(
client, 'cumulus.taskflow.core.test.mytaskflows.ConnectTwoTaskFlow')
# Start the task flow
url = 'taskflows/%s/start' % (taskflow_id)
client.put(url)
# Wait for it to complete
wait_for_complete(client, taskflow_id)
# # Now try a composite workflow approach ...
# print ('Running taskflow that is a composite ...')
# taskflow_id = create_taskflow(
# client, 'cumulus.taskflow.core.test.mytaskflows.MyCompositeTaskFlow')
#
# # Start the task flow
# url = 'taskflows/%s/start' % (taskflow_id)
# client.put(url)
#
# # Wait for it to complete
# wait_for_complete(client, taskflow_id)
except HttpError as ex:
print( ex.responseText)
def girder_client(request, api_url):
username, password = request.param
client = GirderClient(apiUrl=api_url)
client.authenticate(username, password)
yield client
def testImportAnalyses(self):
"""
Test importing a romanesco analysis
"""
client = GirderClient('localhost', girder_port)
client.authenticate(self._username, self._password)
path = os.path.dirname(os.path.realpath(__file__))
analyses_path = os.path.join(path, 'analyses')
import_analyses.import_analyses(client, analyses_path)
# Get the analysis folder
path = '/minerva_analysis/folder'
response = self.request(path=path, method='GET', params={}, user=self._user)
self.assertStatusOk(response)
analyses_folder = response.json['folder']
path = '/item'
params = {
'folderId': analyses_folder['_id']
}
response = self.request(path=path, method='GET', params=params, user=self._user)
self.assertStatusOk(response)
self.assertEquals(len(response.json), 2, 'Expecting two analyses')
analysis = response.json[0]
self.assertEquals(analysis['name'], 'add', 'Expecting analysis one name to be "add"')
expected_meta = {
u'minerva': {
u'analysis_type': u'add',
u'analysis_name': u'add',
u'analysis_id': analysis['_id']
},
u'analysis': {
u'inputs': [{
u'default': {
u'data': u'0',
u'format': u'json'
},
u'type': u'number',
u'name': u'a',
u'format': u'number'
},
{
u'type': u'number',
u'name': u'b',
u'format':
u'number'
}],
u'script': u'c = a + b',
u'mode': u'python',
u'outputs': [{
u'type': u'number',
u'name': u'c',
u'format': u'number'
}],
u'name': u'add'
}
}
self.assertEquals(analysis['meta'], expected_meta, 'Unexpected value for meta data')
analysis = response.json[1]
self.assertEquals(analysis['name'], 'local', 'Expecting analysis two name to be "local"')
expected_meta = {
u'minerva': {
u'analysis_type': u'local type',
u'analysis_name': u'local',
u'analysis_id': analysis['_id']
}
}
self.assertEquals(analysis['meta'], expected_meta, 'Unexpected value for meta data')
_ _________ __ _________ _ __ __
| | / / _/ | / |/ / ____/ | | / /___ _____/ /_____ _____
| | / // // /| | / /|_/ / __/ | | /| / / __ \/ ___/ //_/ _ \/ ___/
| |/ // // ___ |/ / / / /___ | |/ |/ / /_/ / / / ,< / __/ /
|___/___/_/ |_/_/ /_/_____/ |__/|__/\____/_/ /_/|_|\___/_/
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')
parser = argparse.ArgumentParser()
parser.add_argument("path", type=str,
help="path to Arbor web apps")
parser.add_argument("-g", "--girder-host", type=str, default='localhost',
help="host to Girder instance")
parser.add_argument("-p", "--girder-port", type=int, default=9000,
help="port to Girder instance")
args = parser.parse_args()
# Get the ID for our Analyses folder.
c = GirderClient(host=args.girder_host, port=args.girder_port)
c.authenticate('girder', 'girder')
folderSearch = c.get('resource/search', parameters={
'q': 'Analyses',
'types': '["folder"]'
})
folderId = folderSearch['folder'][0]['_id']
# Disable authorization requirements for running romanesco tasks
c.put('system/setting', parameters={
'key': 'flow.require_auth',
'value': 'false'
})
# Check if these analyses already exist. If so, we won't re-upload them.
uploadACR = False
uploadPGS = False
from girder_client import GirderClient
import json
import pymongo
import sys
if len(sys.argv) < 2:
print "%s /path/to/ArborWebApps" % sys.argv[0]
sys.exit(1)
arborWebAppsPath = sys.argv[1]
# Get the ID for our Analyses folder.
c = GirderClient(host='localhost', port=9000)
c.authenticate('girder', 'girder')
folderSearch = c.get('resource/search',
parameters={
'q': 'Analyses',
'types': '["folder"]'
})
folderId = folderSearch['folder'][0]['_id']
# Disable authorization requirements for running romanesco tasks
c.put('system/setting',
parameters={
'key': 'romanesco.require_auth',
'value': 'false'
})
# Check if these analyses already exist. If so, we won't re-upload them.
uploadACR = False
uploadPGS = False
class ContourAnalysesTestCase(base.TestCase):
"""
Tests of the minerva S3 dataset API endpoints.
"""
def setUp(self):
"""
Set up the test case with a user
"""
super(ContourAnalysesTestCase, self).setUp()
self._username = '******'
self._password = '******'
self._user = self.model('user').createUser(
self._username, self._password, 'minerva', 'user',
'*****@*****.**')
# Import the analyses
self._client = GirderClient('localhost', girder_port)
self._client.authenticate(self._username, self._password)
path = os.path.dirname(os.path.realpath(__file__))
analyses_path = os.path.join(path, '../analyses/NEX/')
import_analyses.import_analyses(self._client, analyses_path)
# Get the analysis folder
path = '/minerva_analysis/folder'
response = self.request(path=path, method='GET', params={}, user=self._user)
self.assertStatusOk(response)
analyses_folder = response.json['folder']
path = '/item'
params = {
'folderId': analyses_folder['_id']
}
response = self.request(path=path, method='GET', params=params, user=self._user)
self.assertStatusOk(response)
# Find the contour analysis
for analysis in response.json:
if analysis['name'] == 'contour':
self._analysis = analysis
# Now import an S3 prefix
path = '/minerva_dataset/folder'
params = {
'userId': self._user['_id']
}
response = self.request(path=path, method='POST', params=params, user=self._user)
self.assertStatusOk(response)
folder = response.json['folder']
# create the item
params = {
'name': 'bobby',
'folderId': folder['_id']
}
response = self.request(path='/item', method='POST', params=params, user=self._user)
self.assertStatusOk(response)
itemId = response.json['_id']
# create a s3 dataset from the item
prefix = '/CMIP5/CommonGrid/hadcm3/rcp45/mon/r1i1p1/pr/'
bucket = 'nasanex'
params = {
'name': 'nasanex',
'bucket': bucket,
'prefix': prefix,
'accessKeyId': '',
'secret': '',
'service': '',
'readOnly': True
}
path = '/minerva_dataset_s3/%s/dataset' % str(itemId)
response = self.request(
path=path,
method='POST',
user=self._user,
params=params
)
self.assertStatusOk(response)
import_folder_id = response.json['folderId']
# Wait for import to occur
time.sleep(1)
path = '/item'
params = {
'folderId': import_folder_id
}
response = self.request(path=path, method='GET', user=self._user,
params=params)
self.assertStatusOk(response)
self.assertEqual(len(response.json), 1, 'Excepting only a single item')
item_id = str(response.json[0]['_id'])
# Now list the files
path = '/item/%s/files' % item_id
response = self.request(path=path, method='GET', user=self._user)
self.assertStatusOk(response)
self.assertEqual(len(response.json), 1, 'Excepting only a single file')
self._dataset_file_id = response.json[0]['_id']
def testContourAnalysis(self):
"""
Test contour analysis
"""
inputs = {
'host': {
'format': 'json',
'data': 'localhost'
},
'port': {
'format': 'json',
'data': girder_port
},
'token': {
'format': 'json',
'data': self._client.token
},
'fileId': {
'format': 'json',
'data': self._dataset_file_id
},
'variable': {
'format': 'json',
'data': 'pr'
},
'timestep': {
'format': 'number',
'data': 0
}
}
outputs = {
'result': {
'format': 'json'
}
}
analysis = self._analysis['meta']['analysis']
result = romanesco.run(analysis, inputs=inputs, outputs=outputs)
output_item_id = str(result['output_item_id']['data'])
# Download the item and check it what we expect
path = '/item/%s/download' % output_item_id
response = self.request(path=path, method='GET', user=self._user)
self.assertStatusOk(response)
data_path = os.path.join(os.path.dirname(__file__), 'data', 'expected_contour.json' )
with open(data_path, 'r') as fp:
expected_result = json.load(fp)
self.assertEquals(response.json, expected_result, 'Unexpected result')