Notebooks Integration with Other Services
Notebooks running on EGI can access other existing computing and storage services from EGI or other e-Infrastructures. For data services, check data section of the documentation
EGI services: access tokens
Most services integrated with EGI Check-in can handle valid access tokens for authorising users. These are short-lived (normally less than 1-hour) and need to be renewed for longer usage. EGI Notebooks provides a ready to use access token that can be accessed from your notebooks and is automatically refreshed so you can always have a valid one.
The token is available at /var/run/secrets/egi.eu/access_token
and you can use
it for example to access cloud providers of the EGI cloud. See the following
sample code where a list of VMs is obtained for CESGA:
from keystoneauth1.identity import v3
from keystoneauth1 import session
from novaclient import client
with open("/var/run/secrets/egi.eu/access_token") as f:
access_token = f.read()
auth = v3.OidcAccessToken(auth_url="https://fedcloud-osservices.egi.cesga.es:5000/v3",
identity_provider="egi.eu",
protocol="openid",
project_id="3a8e9d966e644405bf19b536adf7743d",
access_token=access_token)
sess = session.Session(auth=auth)
nova = client.Client(session=sess, version=2)
nova.servers.list()
A valid ID token is also available at /var/run/secrets/egi.eu/id_token
.
fedcloud client
A direct benefit of the integration with access tokens in EGI Notebooks is that you can easily work with the fedcloud client. Once logged into the EGI Notebooks open a terminal and run:
export OIDC_ACCESS_TOKEN=`cat /var/run/secrets/egi.eu/access_token`
fedcloud token check
If the fedcloud
command is not available, please follow the
getting started guide to get it.
EGI Workload Manager (DIRAC)
If you are using a Notebooks instance integrated with EGI Workload Manager, you may access the DIRAC client via CVMFS with the following two command lines:
$ source /cvmfs/dirac.egi.eu/dirac/bashrc_egi_dev
$ dirac-login --issuer=https://dirac.egi.eu/auth
D4Science
If you are using a Notebooks instance integrated with D4Science, you can easily
invoke DataMiner or any other D4Science functionality as the service will
provide the GCUBE_TOKEN
environment variable with a valid token.
This code will print the list of DataMiner methods available within your VRE:
import os
from owslib.wps import WebProcessingService
# init http header parameter and base folders for gCube REST API
gcube_vre_token_header = {'gcube-token': os.environ["GCUBE_TOKEN"]}
# init WPS access for DataMiner algorithms
dataminer_url = 'https://dataminer-prototypes.d4science.org/wps/WebProcessingService'
wps = WebProcessingService(dataminer_url, headers=gcube_vre_token_header)
for process in wps.processes:
print('- Name: ', process.title)
DataMiner algorithms can be invoked also from Notebooks, this code shows a sample:
from owslib.wps import ComplexDataInput, monitorExecution
# define processid and inputs
processid = 'org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.WOFOST_CLOUD_V0_2_1'
inputs = [
('ClassToRun', 'nl.wur.wofostsystem.App'),
('FileInput',
ComplexDataInput(
'https://data.d4science.org/shub/E_eVhZTzBWWktOaVJxQjJkdTUxR3FHaTFFdE9BTDYrZkZxQnFWcGMyaVVJbXptejdDOEFpSVNmam82RllkRUJ6cA==',
mimeType="text/xml")
)
]
# execute the process
execution = wps.execute(processid, inputs)
monitorExecution(execution, sleepSecs=5, download=True)
print(execution.status)
Note that inputs that point to a URL should be specified using the
ComplexDataInput
class as shown above.
Other third-party services
We are open for integration with other services that may be relevant for your
research. Please contact support <at> egi.eu
with your request so we can
investigate the best way to support your needs.