Changes for page Using JupyterHub in HDC
Last modified by Dennis Segebarth on 2024/10/02 18:14
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... ... @@ -340,9 +340,9 @@ 340 340 Reminder: Please follow Linux conventions for file management. If your filename contains spaces, wrap it in single or double quotes. 341 341 342 342 * //Filename~:// “Chemical Tracking Data.csv” 343 -* //Source~:// Project “Indoc Test Project”, “Core” storage zone, folder “collaborator4” {{code}}indoctestproject/collaborator4/Chemical Tracking Data.csv -z core{{/code}}344 -* //Destination: //user's Home directory in the Guacamole or JupyterHub VM {{code}}.{{/code}}345 -* //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 346 346 347 347 {{code language="none"}} 348 348 collaborator4@jupyter-collaborator4:~$ pilotcli file sync indoctestproject/collaborator4/'Chemical Tracking Data.csv' . -z core ... ... @@ -351,47 +351,10 @@ 351 351 File has been downloaded successfully and saved to: ./Chemical Tracking Data.csv 352 352 {{/code}} 353 353 354 -To confirm successful download, type {{code}}ls{{/code}} and verify the file "Chemical Tracking Data.csv" is stored in the Home folder. 355 355 356 -{{code language="none"}} 357 -collaborator4@jupyter-collaborator4:~$ ls 358 -'Chemical Tracking Data.csv' pilotcli 359 -{{/code}} 360 360 361 -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%"]] 364 364 358 +To confirm successful download, type ls and verify the file {{code}}Chemical Tracking Data.csv{{/code}} is stored in the Home folder. 365 365 366 -== Uploading Project Data from JupyterHub using the Pilot Command Line Interface == 367 - 368 -After analyzing Project data inside the JupyterHub, you can upload the generated outputs back into the Project via the Pilot Command Line Interface. 369 - 370 -=== Example === 371 - 372 -* //Filename//: Chemical Tracking Data rev.csv 373 -* //Source~:// user's Home directory in JupyterHub {{code}}.{{/code}} 374 -* //Destination//: Project “Indoc Test Project”, folder “collaborator4”, “Core” storage zone, 375 -{{code}}indoctestproject/collaborator4{{/code}} {{code}}-z core{{/code}} 376 -* //Command group/option~:// {{code}}file upload{{code}} 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" 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. 381 - 382 -{{code language="none"}} 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" 384 -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 385 -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 386 -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. 387 -To cancel this transfer, enter [n/No] 388 -To confirm and proceed with the data transfer, enter [y/Yes] 389 - [y/N]: y 390 -Starting upload of: ./Chemical Tracking Data rev.csv 391 -Pre-upload complete. 392 -Uploading Chemical Tracking Data rev.csv: |██████████████████████████████ 100% 00:00 393 -Upload Time: 2.92s for 1 files 394 -All uploading jobs have finished. 395 -{{/code}} 396 - 397 - 360 +[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]