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 1.3
edited by Susan Evans
on 2023/07/11 13:45
Change comment: (Autosaved)

Summary

Details

Page properties
Content
... ... @@ -1,8 +6,3 @@
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 =
... ... @@ -24,7 +24,7 @@
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.
... ... @@ -190,7 +190,7 @@
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  
... ... @@ -280,9 +280,9 @@
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  
... ... @@ -296,14 +296,26 @@
296 296  
297 297  When using the Pilot Command Line Interface in JupyterHub and the following actions are possible on the derivative files generated in JupyterHub:
298 298  
294 +{table}
295 +**File Operation** | **Permitted in the **
296 +**Green Room**
297 +Word 1 | Word 2
298 +{table}
299 +
299 299  |=(% colspan="1" rowspan="1" %)(((
300 300  **File Operation**
302 +
303 +
301 301  )))|=(% colspan="1" rowspan="1" %)(((
302 302  **Permitted in the **
303 -**Green Room**
306 +**Green Room**
307 +
308 +
304 304  )))|=(% colspan="1" rowspan="1" %)(((
305 305  **Permitted in the **
306 -**Core**
311 +**Core**
312 +
313 +
307 307  )))
308 308  |(% colspan="1" rowspan="1" %)File upload 
309 309  (upload derivative output files from JupyterHub to the Green Room or Core storage)|(% colspan="1" rowspan="1" %)(((
... ... @@ -318,99 +318,6 @@
318 318  Yes
319 319  )))
320 320  
321 -== Downloading Project Data to JupyterHub using the Pilot Command Line Interface ==
322 322  
323 -After logging into the Pilot Command Line Interface, you can download data from the Project Core into the JupyterHub environment to start your data analyses.
324 324  
325 -File related commands are grouped in the {{code}}file{{/code}} category. To view the full list of commands in this category, type {{code}}pilotcli file --help{{/code}}. To download project data, use the file sync command. To view the full list of commands in this category, type {{code}}pilotcli file sync --help{{/code}}.
326 -
327 -
328 -{{code language="none"}}
329 -collaborator4@jupyter-collaborator4:~$ pilotcli file sync --help
330 -Usage: pilotcli file sync [OPTIONS] [PATHS]... OUTPUT_PATH
331 -
332 - Download files/folders from a given Project/folder/file in core zone.
333 -
334 -Options:
335 - -z, --zone TEXT Target Zone (i.e., core/greenroom)
336 - --zip Download files as a zip.
337 - -i, --geid Enable downloading by geid.
338 - --help Show this message and exit.
339 -{{/code}}
340 -
341 -=== Example ===
342 -
343 -Downloading a file from the Core to your Home Directory:
344 -
345 -Reminder: Please follow Linux conventions for file management. If your filename contains spaces, wrap it in single or double quotes.
346 -
347 -* //Filename~:// “Chemical Tracking Data.csv”
348 -* //Source~:// Project “Indoc Test Project”, “Core” storage zone, folder “collaborator4” {{code}}indoctestproject/collaborator4/Chemical Tracking Data.csv -z core{{/code}}
349 -* //Destination: //user's Home directory in the Guacamole or JupyterHub VM {{code}}.{{/code}}
350 -* //Command group/option: //{{code}}file sync{{/code}}
351 -
352 -{{code language="none"}}
353 -collaborator4@jupyter-collaborator4:~$ pilotcli file sync indoctestproject/collaborator4/'Chemical Tracking Data.csv' . -z core
354 -start downloading...
355 -Downloading Chemical Tracking Data.csv |██████████████████████████████ 100% 00:00
356 -File has been downloaded successfully and saved to: ./Chemical Tracking Data.csv
357 -{{/code}}
358 -
359 -To confirm successful download, type {{code}}ls{{/code}} and verify the file "Chemical Tracking Data.csv" is stored in the Home folder.
360 -
361 -{{code language="none"}}
362 -collaborator4@jupyter-collaborator4:~$ ls
363 -'Chemical Tracking Data.csv' pilotcli
364 -{{/code}}
365 -
366 -The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface:
367 -
368 -[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]
369 -
370 -
371 -== Uploading Project Data from JupyterHub using the Pilot Command Line Interface ==
372 -
373 -After analyzing Project data inside the JupyterHub, you can upload the generated outputs back into the Project via the Pilot Command Line Interface.
374 -
375 -=== Example ===
376 -
377 -* //Filename//: Chemical Tracking Data rev.csv
378 -* //Source~:// user's Home directory in JupyterHub {{code}}.{{/code}}
379 -* //Destination//: Project “Indoc Test Project”, folder “collaborator4”, “Core” storage zone,
380 -{{code}}indoctestproject/collaborator4{{/code}} {{code}}-z core{{/code}}
381 -* //Command group/option~:// {{code}}file upload{{/code}}
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}}
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.
386 -
387 -{{code language="none"}}
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"
389 -You are about to transfer data directly to the PILOT Core! In accordance with the PILOT Terms of Use, please confirm that you have made your best efforts to
390 -pseudonymize or anonymize the data and that you have the legal authority to transfer and make this data available for dissemination and use within the PILOT .If you
391 -need to process the data to remove sensitive identifiers, please cancel this transfer and upload the data to the Green Room to perform these actions.
392 -To cancel this transfer, enter [n/No]
393 -To confirm and proceed with the data transfer, enter [y/Yes]
394 - [y/N]: y
395 -Starting upload of: ./Chemical Tracking Data rev.csv
396 -Pre-upload complete.
397 -Uploading Chemical Tracking Data rev.csv: |██████████████████████████████ 100% 00:00
398 -Upload Time: 2.92s for 1 files
399 -All uploading jobs have finished.
400 -{{/code}}
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 -
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/]].
416 416  
Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.sgevans
Size
... ... @@ -1,1 +1,0 @@
1 -35.0 KB
Content
Jupyterhub file upload back to core v2.4.11 2023-05-25 1926.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.sgevans
Size
... ... @@ -1,1 +1,0 @@
1 -507.5 KB
Content