Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2024/10/02 18:14
From version 5.1
edited by Susan Evans
on 2023/07/14 17:11
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.sgevans
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:Jupyterhub-Logo-300x100px cropped.png||height="13%" width="20%"]]
8 +[[image:1723798240534-407.png||height="189" width="291"]]
9 9  
10 10  
11 11  = How it Works =
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27 27  
28 28  = Launching JupyterHub =
29 29  
30 -[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="9%" width="25%"]]
30 +[[image:1723798257792-201.png||height="121" width="349"]]
31 31  
32 32  1. Launch your Project and click the **JupyterHub icon** in the left menu bar.
33 33  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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42 42  1. In the Launcher, click the **Python 3 Notebook **icon, or click **File > New > Notebook**.
43 43  1. Create your Notebook.
44 44  
45 -[[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"]]
46 46  
47 47  = Launching the Terminal =
48 48  
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51 51  1. In the Launcher, click the **Terminal **icon, or click **File > New > Terminal**.
52 52  1. The terminal window opens.
53 53  
54 -[[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"]]
55 55  
56 56  Ubuntu is used to host Jupyter Notebook. Use the command cat /etc/os-release to determine to current version of Ubuntu:
57 57  
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188 188  
189 189  Afterwards, the environment will be listed when you open the Launcher to open a new Jupyter Notebook:
190 190  
191 -[[image:Project Workspace Jupyter view new Kernel 2023-07-11.png||height="25%" width="50%"]]
191 +[[image:1723798325144-485.png||height="436" width="867"]]
192 192  
193 193  
194 194  and also from each opened Notebook, e.g., via **Kernel > Change Kernel…** :
195 195  
196 -[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="32%" width="25%"]]
196 +[[image:1723798338447-469.png||height="317" width="247"]]
197 197  
198 198  = Installing New Python Packages =
199 199  
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283 283  * Open the login window and enter your HDC username and password (i.e. your EBRAINS account credentials).
284 284  * Grant access by clicking **Yes**.
285 285  
286 -[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="28%" width="30%"]]
286 +[[image:1723798355215-434.png||height="352" width="379"]]
287 287  
288 -[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="10%" width="30%"]]
288 +[[image:1723798365454-527.png||height="123" width="376"]]
289 289  
290 290  * After successful confirmation, return to the terminal in your JupyterHub browser tab.
291 291  
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368 368  
369 369  The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface:
370 370  
371 -[[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"]]
372 372  
373 373  
374 374  == Uploading Project Data from JupyterHub using the Pilot Command Line Interface ==
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409 409  Chemical Tracking Data rev.csv Chemical Tracking Data.csv
410 410  {{/code}}
411 411  
412 -[[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"]]
413 413  
414 414  ----
415 415  
416 -Copyright © 2023 [[Indoc Systems>>url:https://www.indocsystems.com]].
416 +Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
417 417  
418 418  HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
419 419  
420 -
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