Changes for page Using JupyterHub in HDC
Last modified by Dennis Segebarth on 2024/10/02 18:14
From version 2.1
edited by Susan Evans
on 2023/07/11 14:10
on 2023/07/11 14:10
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... ... @@ -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 = ... ... @@ -345,9 +345,9 @@ 345 345 Reminder: Please follow Linux conventions for file management. If your filename contains spaces, wrap it in single or double quotes. 346 346 347 347 * //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}}343 +* //Source~:// Project “Indoc Test Project”, “Core” storage zone, folder “collaborator4” indoctestproject/collaborator4/Chemical Tracking Data.csv -z core 344 +* //Destination: //user's Home directory in the Guacamole or JupyterHub VM . 345 +* //Command group/option: //file sync 351 351 352 352 {{code language="none"}} 353 353 collaborator4@jupyter-collaborator4:~$ pilotcli file sync indoctestproject/collaborator4/'Chemical Tracking Data.csv' . -z core ... ... @@ -356,61 +356,10 @@ 356 356 File has been downloaded successfully and saved to: ./Chemical Tracking Data.csv 357 357 {{/code}} 358 358 359 -To confirm successful download, type {{code}}ls{{/code}} and verify the file "Chemical Tracking Data.csv" is stored in the Home folder. 360 360 361 -{{code language="none"}} 362 -collaborator4@jupyter-collaborator4:~$ ls 363 -'Chemical Tracking Data.csv' pilotcli 364 -{{/code}} 365 365 366 -The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface: 367 367 368 -[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]] 369 369 358 +To confirm successful download, type ls and verify the file {{code}}Chemical Tracking Data.csv{{/code}} is stored in the Home folder. 370 370 371 -== 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 - 360 +[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]
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