---
proxy:
service:
type: NodePort
ingress:
enabled: true
annotations:
kubernetes.io/ingress.class: "nginx"
kubernetes.io/tls-acme: "true"
hosts:
- fullhub.eosc.zcu.cz
tls:
- hosts:
- fullhub.eosc.zcu.cz
secretName: acme-tls-fullhub
singleuser:
# keep resource limits in sync with:
# - profileList
storage:
type: none
extraVolumes:
- name: cvmfs-host
hostPath:
path: /cvmfs
type: Directory
- name: owncloud-home
empty_dir:
# - name: scratch
# ephemeral:
# volumeClaimTemplate:
# spec:
# accessModes: [ "ReadWriteOnce" ]
# storageClassName: local-path
# resources:
# requests:
# storage: "10Gi"
extraVolumeMounts:
- name: cvmfs-host
mountPath: "/cvmfs:shared"
- name: owncloud-home
mountPath: '/home/jovyan:shared'
# - name: scratch
# mountPath: '/scratch'
memory:
limit: 4G
guarantee: 128M
cpu:
limit: 2
guarantee: .02
defaultUrl: "/lab"
image:
name: eginotebooks/single-user
tag: "sha-b94a3ef"
profileList:
- display_name: Small Environment - 2 vCPU / 4 GB RAM (non-collaboratice)
description: >
The notebook environment includes Python, R, Julia and Octave kernels. Non-collaborative.
default: true
kubespawner_override:
args:
- "--CondaKernelSpecManager.env_filter='/opt/conda$'"
image: "eginotebooks/single-user:sha-b94a3ef"
- display_name: Small Environment - 2 vCPU / 4 GB RAM (collaboratice)
description: >
The notebook environment includes Python, R, Julia and Octave kernels. Collaborative.
kubespawner_override:
args:
- "--CondaKernelSpecManager.env_filter='/opt/conda$'"
image: "valtri/single-user:jupyter-4e-collab"
cmd: jupyterhub-singleuser-webdav-wrapper
extraFiles:
wait-remote-home.sh:
mode: 0755
mountPath: /usr/local/bin/jupyterhub-wait-remote-home
stringData: |-
#! /bin/sh
#
# Dirty hack to make remote mount on home directory working properly:
#
# 1) wait for webdav sidecar image to kick in
# 2) change directory to the mounted version of itself
# 3) launch notebook server
#
i=0
while ! grep '^webdav-fs: /home/jovyan ' /proc/mounts && test $i -lt 30; do
echo 'Waiting for ownClound mount...'
sleep 0.5
i=$((i+1))
done
singleuser-webdav-wrapper.sh:
mode: 0755
mountPath: /usr/local/bin/jupyterhub-singleuser-webdav-wrapper
stringData: |-
#! /bin/sh
/usr/local/bin/jupyterhub-wait-remote-home
cd .
exec jupyterhub-singleuser "$@"
hub:
services:
status:
url: "http://status-web/"
admin: true
jwt:
url: "http://jwt/"
display: false
image:
name: valtri/hub
tag: "eosc9-jwt"
config:
Authenticator:
enable_auth_state: true
admin_users:
# valtri@civ.zcu.cz
- c36b18fe-e03a-4a22-ab14-5965e0171410@eosc-federation.eu
allowed_groups:
- urn:geant:eosc-federation.eu:testing:group:eosc#testing.eosc-federation.eu
auto_login: true
claim_groups_key: "entitlements"
EGICheckinAuthenticator:
checkin_host: "{{ secret['checkin_host'] }}"
authorize_url: "https://{{ secret['checkin_host'] }}/OIDC/authorization"
token_url: "https://{{ secret['checkin_host'] }}/OIDC/token"
userdata_url: "https://{{ secret['checkin_host'] }}/OIDC/userinfo"
client_id: "{{ secret['client_id'] }}"
client_secret: "{{ secret['client_secret'] }}"
oauth_callback_url: "https://fullhub.eosc.zcu.cz/hub/oauth_callback"
openid_configuration_url: "https://proxy.testing.eosc-federation.eu/.well-known/openid-configuration"
scope: ["openid", "profile", "email", "offline_access", "entitlements"]
username_claim: "sub"
extra_authorize_params:
prompt: consent
JupyterHub:
admin_access: true
authenticate_prometheus: false
authenticator_class: egi_notebooks_hub.egiauthenticator.EGICheckinAuthenticator
# spawner_class: (in egi-notebooks-b2drop)
extraConfig:
egi-notebooks-welcome: |-
from egi_notebooks_hub.welcome import WelcomeHandler
c.JupyterHub.default_url = "/welcome"
c.JupyterHub.extra_handlers = [(r'/welcome', WelcomeHandler)]
egi-notebooks-b2drop: |-
{% raw %}
import base64
import json
from jinja2 import BaseLoader
from jinja2 import Environment
from egi_notebooks_hub.onedata import OnedataSpawner
from kubernetes_asyncio.client.rest import ApiException
from tornado.httpclient import AsyncHTTPClient, HTTPClientError, HTTPRequest
class B2DropSpawner(OnedataSpawner):
async def auth_state_hook(self, spawner, auth_state):
await super().auth_state_hook(spawner, auth_state)
self.b2drop_ready = False
self.b2drop_user = ""
self.b2drop_pwd = ""
try:
secret = await self.api.read_namespaced_secret(self.token_secret_name, self.namespace)
except ApiException:
return
if secret and secret.data:
self.b2drop_user = base64.b64decode(secret.data.get("b2drop-user", "")).decode()
self.b2drop_pwd = base64.b64decode(secret.data.get("b2drop-pwd", "")).decode()
self.b2drop_ready = (self.b2drop_user and self.b2drop_pwd)
def _render_options_form(self, profile_list):
# old:self._profile_list = self._init_profile_list(profile_list)
self._profile_list = self._get_initialized_profile_list(profile_list)
profile_form_template = Environment(loader=BaseLoader).from_string(
self.profile_form_template
)
return profile_form_template.render(profile_list=self._profile_list, b2drop_ready=self.b2drop_ready, b2drop_user=self.b2drop_user, b2drop_pwd=self.b2drop_pwd)
async def pre_spawn_hook(self, spawner):
await super(B2DropSpawner, self).pre_spawn_hook(spawner)
b2drop_user = self.user_options.get("b2drop-user", "")
b2drop_pwd = self.user_options.get("b2drop-pwd", "")
if not (b2drop_user and b2drop_pwd):
secret = await self.api.read_namespaced_secret(self.token_secret_name, self.namespace)
if secret and secret.data:
b2drop_user = base64.b64decode(secret.data.get("b2drop-user", "")).decode()
b2drop_pwd = base64.b64decode(secret.data.get("b2drop-pwd", "")).decode()
if b2drop_user and b2drop_pwd:
volume_mounts = [
{"mountPath": "/owncloud:shared", "name": "owncloud-home"},
]
spawner.extra_containers.append(
{
"name": "b2drop",
"image": "eginotebooks/webdav-rclone-sidecar:sha-0a62679",
"env": [
{"name": "WEBDAV_URL", "value": "https://b2drop.eudat.eu/remote.php/webdav"},
{"name": "WEBDAV_PWD", "value": b2drop_pwd},
{"name": "WEBDAV_USER", "value": b2drop_user},
{"name": "WEBDAV_VENDOR", "value": "other"},
{"name": "MOUNT_PATH", "value": "/owncloud/b2drop"},
{"name": "MOUNT_WAIT_POINT", "value": "webdav-fs: /owncloud fuse.rclone"},
],
"resources": self.sidecar_resources,
"securityContext": {
"runAsUser": 1000,
"fsUser": 1000,
"fsGroup": 100,
"privileged": True,
"capabilities": {"add": ["SYS_ADMIN"]},
},
"volumeMounts": volume_mounts,
}
)
def options_from_form(self, formdata):
data = super(B2DropSpawner, self)._options_from_form(formdata)
data.update({'b2drop-user': formdata.get('b2drop-user', [None])[0],
'b2drop-pwd': formdata.get('b2drop-pwd', [None])[0]})
return data
class WebDavOIDCSpawner(B2DropSpawner):
# ownCloud Infinite Scale parameters
# (https://owncloud.dev/apis/http/graph/spaces/#list-my-spaces-get-medrives)
OCIS_URL = "https://ocis.aaitest.owncloud.works"
# personal space
OCIS_PERSONAL_SPACE = "/graph/v1.0/me/drives?%24filter=driveType+eq+personal"
# shared space
OCIS_SHARED_WITH_ME = "/graph/v1.0/me/drives?%24filter=driveType+eq+virtual"
# otter spaces
OCIS_SPACES = "/graph/v1.0/me/drives?%24filter=driveType+eq+project"
async def append_owncloud_sidecar(self, spawner, type, query, fallback_url=None, headers={}):
owncloud_url = fallback_url
http_client = AsyncHTTPClient()
req = HTTPRequest(
self.OCIS_URL + query,
headers=headers,
method="GET",
)
try:
resp = await http_client.fetch(req)
body = json.loads(resp.body.decode("utf8", "replace"))
self.log.debug("OCIS response: %s", body)
if "value" in body:
ocis_infos = body["value"]
if len(ocis_infos) >= 1 and "root" in ocis_infos[0]:
owncloud_url = ocis_infos[0]["root"].get("webDavUrl", None)
except HTTPClientError as e:
self.log.error("can't query ownCloud: %s", e)
self.log.info("ownCloud %s URL: %s", type, owncloud_url)
if owncloud_url is None:
return
if type == "home":
subpath = ""
else:
subpath = "/" + type.capitalize()
env = [
{"name": "WEBDAV_URL", "value": owncloud_url},
{"name": "WEBDAV_VENDOR", "value": "owncloud"},
# XXX: strict permissions needed for .local/share/jupyter/runtime/jupyter_cookie_secret
# quicker directory cache and polling
{"name": "MOUNT_OPTS", "value": "--file-perms=0600 --dir-perms=0770 --dir-cache-time=1m0s --poll-interval=0m20s"},
{"name": "MOUNT_PATH", "value": "/owncloud" + subpath},
# default mode is "full"
{"name": "VFS_CACHE_MODE", "value": "full"},
]
if type != "home":
env.append({"name": "MOUNT_WAIT_POINT", "value": "webdav-fs: /owncloud fuse.rclone"})
volume_mounts = [
{"mountPath": "/owncloud:shared", "name": "owncloud-home"},
{"mountPath": self.token_mount_path, "name": self.token_secret_volume_name, "readOnly": True},
]
spawner.extra_containers.append(
{
"name": "owncloud-" + type,
"image": "eginotebooks/webdav-rclone-sidecar:sha-0a62679",
"args": ["bearer_token_command=cat " + self.token_path],
"env": env,
"resources": self.sidecar_resources,
"securityContext": {
"runAsUser": 1000,
"fsUser": 1000,
"fsGroup": 100,
"privileged": True,
"capabilities": {"add": ["SYS_ADMIN"]},
},
"volumeMounts": volume_mounts,
}
)
async def pre_spawn_hook(self, spawner):
await super(WebDavOIDCSpawner, self).pre_spawn_hook(spawner)
auth_state = await self.user.get_auth_state()
# volume name as in EGI spawner
self.token_secret_volume_name = self._expand_user_properties(
self.token_secret_volume_name_template
)
self.token_path = os.path.join(self.token_mount_path, "access_token")
if auth_state:
access_token = auth_state.get("access_token", None)
headers = {
"Accept": "application/json",
"User-Agent": "JupyterHub",
"Authorization": "Bearer %s" % access_token,
}
await self.append_owncloud_sidecar(spawner, "home", self.OCIS_PERSONAL_SPACE, headers=headers)
await self.append_owncloud_sidecar(spawner, "shares", self.OCIS_SHARED_WITH_ME, headers=headers)
await self.append_owncloud_sidecar(spawner, "spaces", self.OCIS_SPACES, headers=headers)
else:
self.log.info("No auth state, skipping ownCloud")
c.JupyterHub.spawner_class = WebDavOIDCSpawner
c.B2DropSpawner.http_timeout = 90
c.B2DropSpawner.args = ["--FileCheckpoints.checkpoint_dir='/home/jovyan/.notebookCheckpoints'"]
c.B2DropSpawner.profile_form_template = """
<style>
/*
.profile divs holds two div tags: one for a radio button, and one
for the profile's content.
*/
#kubespawner-profiles-list .profile {
display: flex;
flex-direction: row;
font-weight: normal;
border-bottom: 1px solid #ccc;
padding-bottom: 12px;
}
#kubespawner-profiles-list .profile .radio {
padding: 12px;
}
/* .option divs holds a label and a select tag */
#kubespawner-profiles-list .profile .option {
display: flex;
flex-direction: row;
align-items: center;
padding-bottom: 12px;
}
#kubespawner-profiles-list .profile .option label {
font-weight: normal;
margin-right: 8px;
min-width: 96px;
}
</style>
<div class='form-group' id='kubespawner-profiles-list'>
{%- for profile in profile_list %}
{#- Wrap everything in a <label> so clicking anywhere selects the option #}
<label for='profile-item-{{ profile.slug }}' class='profile'>
<div class='radio'>
<input type='radio' name='profile' id='profile-item-{{ profile.slug }}' value='{{ profile.slug }}' {% if profile.default %}checked{% endif %} />
</div>
<div>
<h3>{{ profile.display_name }}</h3>
{%- if profile.description %}
<p>{{ profile.description }}</p>
{%- endif %}
{%- if profile.profile_options %}
<div>
{%- for k, option in profile.profile_options.items() %}
<div class='option'>
<label for='profile-option-{{profile.slug}}-{{k}}'>{{option.display_name}}</label>
<select name="profile-option-{{profile.slug}}-{{k}}" class="form-control">
{%- for k, choice in option['choices'].items() %}
<option value="{{ k }}" {% if choice.default %}selected{%endif %}>{{ choice.display_name }}</option>
{%- endfor %}
</select>
</div>
{%- endfor %}
</div>
{%- endif %}
</div>
</label>
{%- endfor %}
<div class="panel-group" id="accordion" role="tablist" aria-multiselectable="true">
<div class="panel panel-default">
<div class="panel-heading" role="tab" id="headingOne">
<h4 class="panel-title">
<a class="collabpsed" role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseOne" aria-expanded="false" aria-controls="collapseOne">
B2DROP connection
</a>
{%if b2drop_ready %}<span class="label label-success">Already configured!</span>{% endif %}
</h4>
</div>
<div id="collapseOne" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingOne">
<div class="panel-body">
<div class='form-group'>
<label for="b2drop-user" class="form-label">B2DROP app Username</label>
<input type="text" class="form-control" name="b2drop-user" id="b2drop-user" aria-describedby="b2drop-user-help" value="{{ b2drop_user }}">
<div id="b2drop-user-help" class="form-text">Create new app password at <a href="https://b2drop.eudat.eu/settings/user/security">B2DROP security configuration</a></div>
</div>
<div class='form-group'>
<label for="b2drop-pwd" class="form-label">B2DROP app Password</label>
<input type="password" class="form-control" name="b2drop-pwd" id="b2drop-pwd" value="{{ b2drop_pwd }}">
</div>
</div>
</div>
</div>
</div>
"""
{% endraw %}
templatePaths:
- /egi-notebooks-hub/templates
extraFiles:
login.html:
mountPath: /egi-notebooks-hub/templates/login.html
stringData: |-
{% raw %}
{% extends "egi-login.html" %}
{% block main_intro %}
<h1><img alt="Notebooks Logo" src="{{ static_url('images/egi-icon-notebooks.svg') }}"
height="100">Notebooks</h1>
<p>
Notebooks is an environment based on <a href="http://jupyter.org/">Jupyter</a> and
the <a href="https://www.egi.eu/services/cloud-compute/">EGI cloud service</a> that
offers a browser-based, scalable tool for interactive data analysis. The Notebooks
environment provides users with notebooks where they can combine text, mathematics,
computations and rich media output.
</p>
<p>
Access requires a valid <a href="https://docs.egi.eu/users/check-in/signup">EGI account</a>
and <a href="https://docs.egi.eu/users/dev-env/notebooks/#notebooks-for-researchers">
enrolling to one of the supported VOs</a>.
</p>
{% endblock main_intro %}
{% endraw %}