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.

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 = 'http://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 ComplextDataInput 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.