Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2024/10/02 18:14
From version 1.2
edited by Susan Evans
on 2023/07/11 13:40
Change comment: (Autosaved)
To version 1.6
edited by Susan Evans
on 2023/07/11 14:00
Change comment: (Autosaved)

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222 222  1. In the Jupyterhub Terminal, type {{code}}pilotcli{{/code}} to launch the latest version of the Pilot Command Line Interface.
223 223  1. Use the {{code}}pilotcli --help{{/code}} at any time to show the welcome message again.
224 224  
225 +{{code language="none"}}
226 +collaborator4@jupyter-collaborator4:~$ pilotcli
227 +Usage: pilotcli [OPTIONS] COMMAND [ARGS]...
225 225  
229 + What's new (Version 2.2.0):
230 +
231 + 1. CLI supports to perform multi-threading upload for file/folders
232 +
233 + 2. CLI supports to perform resumable upload for single file
234 +
235 +
236 +
237 +Options:
238 + --help Show this message and exit.
239 +
240 +Commands:
241 + container_registry Container Registry Actions.
242 + dataset Dataset Actions.
243 + file File Actions.
244 + project Project Actions.
245 + use_config Config Actions.
246 + user User Actions.
247 +{{/code}}
248 +
249 +== Logging into the Pilot Command Line Interface ==
250 +
251 +Users are required to login with platform credentials before performing any tasks through Pilot Command Line Interface.
252 +
253 +* Use the command {{code}}pilotcli user login{{/code}} to log into the Pilot Command Line Interface.
254 +
255 +{{code language="none"}}
256 +collaborator4@jupyter-collaborator4:~$ pilotcli user login
257 +Please, access https://iam.staging.pilot.indocresearch.com/realms/pilot/device?user_code=XXXX-XXXX to proceed
258 + ▄▄▄▄▄▄▄ ▄ ▄▄ ▄ ▄▄▄▄ ▄ ▄▄▄▄▄▄▄
259 + █ ▄▄▄ █ ▄ ▄███ ▀▀ █▀ ▀██▄ █ ▄▄▄ █
260 + █ ▄ ▀ ▄ ▀▄ ▀▀ ▄█▀▄▀ ▀▀▄█▄▄▀ █████▄▄▀▄
261 + ▄▄▄▄▄▄▄ ▀ ▀█▄ ▀▄ ██▀█ ▄▀▄▄ █ ▄ █▀▄▄▄
262 + █ ▄▄▄ █ █▀█▄▀ █▀ █▀▀█ ▀▄█▄█▄▄▄█▀▄█
263 + █ ███ █ █▀██▀▄ █▀▄▄▀▀█▄▀▀█▄▀█ ▀ ▀▄▀██
264 + █▄▄▄▄▄█ ▄▀▄▄██▄▄▀▄ ▀▀▄ ▄▄▀▀▀▄ █▄▄▄█
265 +
266 + Waiting validation finish...
267 +{{/code}}
268 +
269 +* (((
270 +You’ll be asked to validate your HDC user account using one of the provided methods.
271 +
272 +* Copy and paste the provided validation link into a new browser tab or
273 +* Scan the QR code with your mobile device.
274 +)))
275 +* Open the login window and enter your HDC username and password (i.e. your EBRAINS account credentials).
276 +* Grant access by clicking **Yes**.
277 +
278 +[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="46%" width="50%"]]
279 +
280 +[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="16%" width="50%"]]
281 +
282 +* After successful confirmation, return to the terminal in your JupyterHub browser tab.
283 +
284 +{{code language="none"}}
285 +Welcome to the Command Line Tool!
286 +{{/code}}
287 +
288 +* You’re now ready to start using the Pilot Command Line Interface to work with your Project data in JupyterHub.
289 +
290 +== Zone Restrictions when using Pilot Command Line Interface in JupyterHub ==
291 +
292 +When using the Pilot Command Line Interface in JupyterHub and the following actions are possible on the derivative files generated in JupyterHub:
293 +
294 +|=(% colspan="1" rowspan="1" %)(((
295 +**File Operation**
296 +)))|=(% colspan="1" rowspan="1" %)(((
297 +**Permitted in the **
298 +**Green Room**
299 +)))|=(% colspan="1" rowspan="1" %)(((
300 +**Permitted in the **
301 +**Core**
302 +)))
303 +|(% colspan="1" rowspan="1" %)File upload 
304 +(upload derivative output files from JupyterHub to the Green Room or Core storage)|(% colspan="1" rowspan="1" %)(((
305 +Yes
306 +)))|(% colspan="1" rowspan="1" %)(((
307 +Yes
308 +)))
309 +|(% colspan="1" rowspan="1" %)File download
310 +(download files from Green Room or Core into JupyterHub)|(% colspan="1" rowspan="1" %)(((
311 +**No**
312 +)))|(% colspan="1" rowspan="1" %)(((
313 +Yes
314 +)))
315 +
316 +== Downloading Project Data to JupyterHub using the Pilot Command Line Interface ==
317 +
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.
319 +
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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