Changes for page Using JupyterHub in HDC
Last modified by Dennis Segebarth on 2024/10/02 18:14
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... ... @@ -222,139 +222,4 @@ 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]... 228 228 229 - 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%"]]
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