Changes for page Using JupyterHub in HDC

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

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1 +{{box cssClass="floatinginfobox" title="Table of Contents"}}
2 +{{toc depth="2"/}}
3 +{{/box}}
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1 1  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/]].
2 2  
3 3  = How it Works =
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19 19  
20 20  = Launching JupyterHub =
21 21  
22 -[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="10%" width="30%"]]
27 +[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="9%" width="25%"]]
23 23  
24 24  1. Launch your Project and click the **JupyterHub icon** in the left menu bar.
25 25  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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185 185  
186 186  and also from each opened Notebook, e.g., via **Kernel > Change Kernel…** :
187 187  
188 -[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="64%" width="50%"]]
193 +[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="32%" width="25%"]]
189 189  
190 190  = Installing New Python Packages =
191 191  
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275 275  * Open the login window and enter your HDC username and password (i.e. your EBRAINS account credentials).
276 276  * Grant access by clicking **Yes**.
277 277  
278 -[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="46%" width="50%"]]
283 +[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="28%" width="30%"]]
279 279  
280 -[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="16%" width="50%"]]
285 +[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="10%" width="30%"]]
281 281  
282 282  * After successful confirmation, return to the terminal in your JupyterHub browser tab.
283 283  
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373 373  * //Source~:// user's Home directory in JupyterHub {{code}}.{{/code}}
374 374  * //Destination//: Project “Indoc Test Project”, folder “collaborator4”, “Core” storage zone,
375 375  {{code}}indoctestproject/collaborator4{{/code}} {{code}}-z core{{/code}}
376 -* //Command group/option~:// {{code}}file upload{{code}}
381 +* //Command group/option~:// {{code}}file upload{{/code}}
377 377  * //User message// (for upload back to the Core): “my workbench output, no additional sensitive data"
378 -* //Command~:// pilotcli file upload ./'Chemical Tracking Data rev.csv' -p indoctestproject/collaborator4 -z core -m "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}}
379 379  
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.
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.
381 381  
382 382  {{code language="none"}}
383 383  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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394 394  All uploading jobs have finished.
395 395  {{/code}}
396 396  
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.
397 397  
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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