Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2024/10/02 18:14
From version 3.1
edited by Susan Evans
on 2023/07/11 14:11
Change comment: There is no comment for this version
To version 1.7
edited by Susan Evans
on 2023/07/11 14:05
Change comment: (Autosaved)

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1 -{{box cssClass="floatinginfobox" title="Table of Contents"}}
2 -{{toc depth="2"/}}
3 -{{/box}}
4 -
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 8  = How it Works =
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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="9%" width="25%"]]
22 +[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="10%" width="30%"]]
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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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="32%" width="25%"]]
188 +[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="64%" width="50%"]]
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="28%" width="30%"]]
278 +[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="46%" width="50%"]]
284 284  
285 -[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="10%" width="30%"]]
280 +[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="16%" width="50%"]]
286 286  
287 287  * After successful confirmation, return to the terminal in your JupyterHub browser tab.
288 288  
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378 378  * //Source~:// user's Home directory in JupyterHub {{code}}.{{/code}}
379 379  * //Destination//: Project “Indoc Test Project”, folder “collaborator4”, “Core” storage zone,
380 380  {{code}}indoctestproject/collaborator4{{/code}} {{code}}-z core{{/code}}
381 -* //Command group/option~:// {{code}}file upload{{/code}}
376 +* //Command group/option~:// {{code}}file upload{{code}}
382 382  * //User message// (for upload back to the Core): “my workbench output, no additional sensitive data"
383 -* //Command~:// {{code}}pilotcli file upload ./'Chemical Tracking Data rev.csv' -p{{/code}} {{code}}indoctestproject/collaborator4 -z core -m "my workbench output, no additional sensitive data"{{/code}}
378 +* //Command~:// pilotcli file upload ./'Chemical Tracking Data rev.csv' -p indoctestproject/collaborator4 -z core -m "my workbench output, no additional sensitive data"
384 384  
385 -When uploading data to the Core, you are reminded that you are bypassing the usual Green Room upload workflow. To confirm, type {{code}}y{{/code}} at the prompt, or {{code}}N{{/code}} to cancel.
380 +When uploading data to the Core, you are reminded that you are bypassing the usual Green Room upload workflow. To confirm, type y at the prompt, or N to cancel.
386 386  
387 387  {{code language="none"}}
388 388  collaborator4@jupyter-collaborator4:~$ pilotcli file upload ./'Chemical Tracking Data rev.csv' -p indoctestproject/collaborator4 -z core -m "my workbench output, no additional sensitive data"
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399 399  All uploading jobs have finished.
400 400  {{/code}}
401 401  
402 -After completing the upload, you can confirm the new file “Chemical Tracking Data rev.csv" exists in the correct directory using the pilotcli file list command and/or in the Portal File Explorer.
403 403  
404 -{{code language="none"}}
405 -collaborator4@jupyter-collaborator4:~$ pilotcli file list indoctestproject/collaborator4 -z core
406 -Chemical Tracking Data rev.csv Chemical Tracking Data.csv
407 -{{/code}}
408 -
409 -[[image:Jupyterhub file upload back to core v2.4.11 2023-05-25 1926.png||height="13%" width="50%"]]
410 -
411 -----
412 -
413 -Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
414 -
415 -HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].
416 -
Jupyterhub file upload back to core v2.4.11 2023-05-25 1926.png
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