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 9.1
edited by Dennis Segebarth
on 2024/08/16 08:54
Change comment: Deleted image "Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png"

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1 +XWiki.dsegebarth
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1 +{{box cssClass="floatinginfobox" title="Table of Contents"}}
2 +{{toc depth="2"/}}
3 +{{/box}}
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5 +
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  
8 +[[image:1723798240534-407.png||height="189" width="291"]]
9 +
10 +
3 3  = How it Works =
4 4  
5 5  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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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%"]]
30 +[[image:1723798257792-201.png||height="121" width="349"]]
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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34 34  1. In the Launcher, click the **Python 3 Notebook **icon, or click **File > New > Notebook**.
35 35  1. Create your Notebook.
36 36  
37 -[[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"]]
38 38  
39 39  = Launching the Terminal =
40 40  
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43 43  1. In the Launcher, click the **Terminal **icon, or click **File > New > Terminal**.
44 44  1. The terminal window opens.
45 45  
46 -[[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"]]
47 47  
48 48  Ubuntu is used to host Jupyter Notebook. Use the command cat /etc/os-release to determine to current version of Ubuntu:
49 49  
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180 180  
181 181  Afterwards, the environment will be listed when you open the Launcher to open a new Jupyter Notebook:
182 182  
183 -[[image:Project Workspace Jupyter view new Kernel 2023-07-11.png||height="25%" width="50%"]]
191 +[[image:1723798325144-485.png||height="436" width="867"]]
184 184  
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%"]]
196 +[[image:1723798338447-469.png||height="317" width="247"]]
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%"]]
286 +[[image:1723798355215-434.png||height="352" width="379"]]
279 279  
280 -[[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"]]
281 281  
282 282  * After successful confirmation, return to the terminal in your JupyterHub browser tab.
283 283  
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360 360  
361 361  The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface:
362 362  
363 -[[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"]]
364 364  
365 365  
366 366  == Uploading Project Data from JupyterHub using the Pilot Command Line Interface ==
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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}}
384 +* //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"
386 +* //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.
388 +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  
405 +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  
407 +{{code language="none"}}
408 +collaborator4@jupyter-collaborator4:~$ pilotcli file list indoctestproject/collaborator4 -z core
409 +Chemical Tracking Data rev.csv Chemical Tracking Data.csv
410 +{{/code}}
411 +
412 +[[image:1723798397694-530.png||height="217" width="863"]]
413 +
414 +----
415 +
416 +Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
417 +
418 +HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
419 +
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