Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2024/10/02 18:14
From version 1.3
edited by Susan Evans
on 2023/07/11 13:45
Change comment: (Autosaved)
To version 1.6
edited by Susan Evans
on 2023/07/11 14:00
Change comment: (Autosaved)

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291 291  
292 292  When using the Pilot Command Line Interface in JupyterHub and the following actions are possible on the derivative files generated in JupyterHub:
293 293  
294 -{table}
295 -**File Operation** | **Permitted in the **
296 -**Green Room**
297 -Word 1 | Word 2
298 -{table}
299 -
300 300  |=(% colspan="1" rowspan="1" %)(((
301 301  **File Operation**
302 -
303 -
304 304  )))|=(% colspan="1" rowspan="1" %)(((
305 305  **Permitted in the **
306 -**Green Room**
307 -
308 -
298 +**Green Room**
309 309  )))|=(% colspan="1" rowspan="1" %)(((
310 310  **Permitted in the **
311 -**Core**
312 -
313 -
301 +**Core**
314 314  )))
315 315  |(% colspan="1" rowspan="1" %)File upload 
316 316  (upload derivative output files from JupyterHub to the Green Room or Core storage)|(% colspan="1" rowspan="1" %)(((
... ... @@ -325,6 +325,48 @@
325 325  Yes
326 326  )))
327 327  
316 +== Downloading Project Data to JupyterHub using the Pilot Command Line Interface ==
328 328  
318 +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.
329 329  
330 -
320 +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}}.
321 +
322 +
323 +{{code language="none"}}
324 +collaborator4@jupyter-collaborator4:~$ pilotcli file sync --help
325 +Usage: pilotcli file sync [OPTIONS] [PATHS]... OUTPUT_PATH
326 +
327 + Download files/folders from a given Project/folder/file in core zone.
328 +
329 +Options:
330 + -z, --zone TEXT Target Zone (i.e., core/greenroom)
331 + --zip Download files as a zip.
332 + -i, --geid Enable downloading by geid.
333 + --help Show this message and exit.
334 +{{/code}}
335 +
336 +=== Example ===
337 +
338 +Downloading a file from the Core to your Home Directory:
339 +
340 +Reminder: Please follow Linux conventions for file management. If your filename contains spaces, wrap it in single or double quotes.
341 +
342 +* //Filename~:// “Chemical Tracking Data.csv”
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 +
347 +{{code language="none"}}
348 +collaborator4@jupyter-collaborator4:~$ pilotcli file sync indoctestproject/collaborator4/'Chemical Tracking Data.csv' . -z core
349 +start downloading...
350 +Downloading Chemical Tracking Data.csv |██████████████████████████████ 100% 00:00
351 +File has been downloaded successfully and saved to: ./Chemical Tracking Data.csv
352 +{{/code}}
353 +
354 +
355 +
356 +
357 +
358 +To confirm successful download, type ls and verify the file {{code}}Chemical Tracking Data.csv{{/code}} is stored in the Home folder.
359 +
360 +[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]
Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png
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1 +XWiki.sgevans
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