Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2024/10/02 18:14
From version 2.1
edited by Susan Evans
on 2023/07/11 14:10
Change comment: There is no comment for this version
To version 13.1
edited by Dennis Segebarth
on 2024/08/16 08:55
Change comment: Deleted image "Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png"

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1 +XWiki.dsegebarth
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5 5  
6 6  JupyterHub is an open-source, multi-user version of Jupyter Notebook for performing analysis of Project files in the Core. More information can be found in the application documentation [[https:~~/~~/jupyter.org/>>https://jupyter.org/]].
7 7  
8 +[[image:1723798240534-407.png||height="189" width="291"]]
9 +
10 +
8 8  = How it Works =
9 9  
10 10  JupyterHub allows Project members to create or import Jupyter Notebooks into the Project Workspace environment, retrieve Project files from the Core, perform computational workflows on the data, and write the outputs back to the Core where they can be accessed by other Project members. JupyterHub spins up a new JupyterLab instance for each Project member.
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24 24  
25 25  = Launching JupyterHub =
26 26  
27 -[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="10%" width="30%"]]
30 +[[image:1723798257792-201.png||height="121" width="349"]]
28 28  
29 29  1. Launch your Project and click the **JupyterHub icon** in the left menu bar.
30 30  1. Click **Sign in with Keycloak** to initiate your session. JupyterHub automatically authenticates with your existing username and password and launches your session - no additional sign-in is required.
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39 39  1. In the Launcher, click the **Python 3 Notebook **icon, or click **File > New > Notebook**.
40 40  1. Create your Notebook.
41 41  
42 -[[image:Project Workspace Jupyter Create Python Notebook v2.1.6 2023-02-07.png||height="22%" width="50%"]]
45 +[[image:1723798278604-114.png||height="376" width="865"]]
43 43  
44 44  = Launching the Terminal =
45 45  
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48 48  1. In the Launcher, click the **Terminal **icon, or click **File > New > Terminal**.
49 49  1. The terminal window opens.
50 50  
51 -[[image:Project Workspace Jupyter Launch Terminal v2.1.6 2023-02-07.png||height="9%" width="50%"]]
54 +[[image:1723798293872-992.png||height="162" width="863"]]
52 52  
53 53  Ubuntu is used to host Jupyter Notebook. Use the command cat /etc/os-release to determine to current version of Ubuntu:
54 54  
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185 185  
186 186  Afterwards, the environment will be listed when you open the Launcher to open a new Jupyter Notebook:
187 187  
188 -[[image:Project Workspace Jupyter view new Kernel 2023-07-11.png||height="25%" width="50%"]]
191 +[[image:1723798325144-485.png||height="436" width="867"]]
189 189  
190 190  
191 191  and also from each opened Notebook, e.g., via **Kernel > Change Kernel…** :
192 192  
193 -[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="64%" width="50%"]]
196 +[[image:1723798338447-469.png||height="317" width="247"]]
194 194  
195 195  = Installing New Python Packages =
196 196  
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280 280  * Open the login window and enter your HDC username and password (i.e. your EBRAINS account credentials).
281 281  * Grant access by clicking **Yes**.
282 282  
283 -[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="46%" width="50%"]]
286 +[[image:1723798355215-434.png||height="352" width="379"]]
284 284  
285 -[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="16%" width="50%"]]
288 +[[image:1723798365454-527.png||height="123" width="376"]]
286 286  
287 287  * After successful confirmation, return to the terminal in your JupyterHub browser tab.
288 288  
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365 365  
366 366  The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface:
367 367  
368 -[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]
371 +[[image:1723798383409-873.png||height="267" width="874"]]
369 369  
370 370  
371 371  == Uploading Project Data from JupyterHub using the Pilot Command Line Interface ==
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406 406  Chemical Tracking Data rev.csv Chemical Tracking Data.csv
407 407  {{/code}}
408 408  
409 -[[image:Jupyterhub file upload back to core v2.4.11 2023-05-25 1926.png||height="13%" width="50%"]]
412 +[[image:1723798397694-530.png||height="217" width="863"]]
410 410  
411 411  ----
412 412  
413 -Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
416 +Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
414 414  
415 -HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].
416 -
418 +HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
419 +
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