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5 changes: 1 addition & 4 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -228,8 +228,6 @@ helm install jupyterhub bioos/jupyterhub \
kubectl -n bioos port-forward --address 0.0.0.0 service/hub 8081:8081
```

打开浏览器访问:http://Server-IP/jupyterhub, 申请新 token.
![jupyterhub token](./img/jupyterhub.png)
## 3.3 安装 Cromwell
```bash
helm repo add https://bio-os.github.io/helm-charts/charts
Expand All @@ -255,8 +253,7 @@ helm install bioos bioos/bioos \
--set mysql.username=root \
--set mysql.password=Bytedance2023 \
--set wes.endpoint=http://cromwell.bioos.svc.cluster.local:8000 \ #配置cromwell在K8S中的访问地址
--set jupyterhub.endpoint=http://{{INGRESS-ADDRESS:PORT}}/jupyterhub/ \
--set jupyterhub.adminToken=${jupyterhub-token} # 这里填写2.2步骤中获取的token
--set jupyterhub.endpoint=http://{{INGRESS-ADDRESS:PORT}}/jupyterhub

# 端口转发:
kubectl -n ingress-nginx port-forward --address 0.0.0.0 service/ingress-nginx-controller 8888:80
Expand Down
6 changes: 3 additions & 3 deletions charts/bioos/values.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -90,9 +90,9 @@ storage:

wes:
# cromwell service address
endpoint: http://180.184.43.61:8000
endpoint: http://10.0.0.0:8000

jupyterhub:
# jupyterhub service address
endpoint: http://180.184.43.61/jupyterhub
adminToken: c876b254956a433aaf02836605565af6
endpoint: http://10.0.0.0/jupyterhub
adminToken: mybioostoken
3 changes: 2 additions & 1 deletion charts/jupyterhub/files/hub/jupyterhub_config.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
from jupyterhub.utils import url_path_join
from kubernetes_asyncio import client
from tornado.httpclient import AsyncHTTPClient
import kubespawner

# Make sure that modules placed in the same directory as the jupyterhub config are added to the pythonpath
configuration_directory = os.path.dirname(os.path.realpath(__file__))
Expand Down Expand Up @@ -36,7 +37,7 @@ def camelCaseify(s):
# at the rate required.
AsyncHTTPClient.configure("tornado.curl_httpclient.CurlAsyncHTTPClient")

c.JupyterHub.spawner_class = "myspawner.KubeSpawner"
c.JupyterHub.spawner_class = kubespawner.KubeSpawner

# Connect to a proxy running in a different pod. Note that *_SERVICE_*
# environment variables are set by Kubernetes for Services
Expand Down
54 changes: 0 additions & 54 deletions charts/jupyterhub/values.example.yaml

This file was deleted.

10 changes: 9 additions & 1 deletion charts/jupyterhub/values.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,14 @@ hub:
headers:
Access-Control-Allow-Origin: "*"
Content-Security-Policy: "frame-ancestors 'self' http://localhost"
service_tokens:
# The token MUST be same with apiserver jupyterhub.adminToken
mybioostoken: bioos
load_roles:
- name: bioos
description: 'bioos apiserver access'
scopes: ['admin:users', 'admin:servers']
services: ['bioos']
Spawner:
args:
- "--NotebookApp.allow_origin=*"
Expand Down Expand Up @@ -670,4 +678,4 @@ debug:
enabled: false

global:
safeToShowValues: false
safeToShowValues: false
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