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 1.1
edited by Susan Evans
on 2023/07/11 13:35
Change comment: (Autosaved)

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180 180  
181 181  Afterwards, the environment will be listed when you open the Launcher to open a new Jupyter Notebook:
182 182  
183 -[[image:Project Workspace Jupyter view new Kernel 2023-07-11.png||height="25%" width="50%"]]
184 184  
185 185  
186 -and also from each opened Notebook, e.g., via **Kernel > Change Kernel…** :
187 187  
188 -[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="64%" width="50%"]]
189 189  
190 -= Installing New Python Packages =
191 -
192 -We highly recommend the use of virtual environments when installing new packages (see //Creating a Python Virtual Environment and Registering a Kernel// above for more details). Consequently, we recommend installing new packages via commands in the JupyterHub terminal in the corresponding virtual environments, instead of installing packages from within Jupyter Notebooks.
193 -
194 -Depending on the IT policies, outbound traffic may need to go through a proxy. If so, users will be required to provide the proxy command line argument such as pip, curl, wget, etc.
195 -
196 -For example:
197 -
198 -{{code language="none"}}
199 -pip install my_package
200 -{{/code}}
201 -
202 -If you are using conda to manage python packages:
203 -
204 -{{code language="none"}}
205 -conda install my_package
206 -{{/code}}
207 -
208 -The above information is provided as examples only. Please refer to documentation provided by your IT department with respect to proxy configuration.
209 -
210 -= Using the Pilot Command Line Interface in a JupyterHub Terminal =
211 -
212 -The Pilot Command Line Interface (CLI) is deployed within JupyterHub as extension resource. Project members can use the Pilot Command Line Interface in a JupyterHub terminal to download Project data from the Core for further analysis, and upload the derivative outputs back to the Green Room or Core.
213 -
214 -The Home Directory is your default directory. When you download a copy of your Core files to JupyterHub, the files persists in the JupyterHub environment until deleted by you, so you can return to the session and continue your work at a later time without the need to retrieve the data from the Core again.
215 -
216 -The following sections focus on getting started with basic pilotcli commands in JupyterHub. For additional pilotcli commands and usage, see the article //Working with HDC Project Files in the Command Line Interface//.
217 -
218 -== Launching Pilot Command Line Interface ==
219 -
220 -1. Launch your Project and click the **JupyterHub** icon in in the workspace icon group.
221 -1. Click the **Terminal **launcher icon to open the Terminal.
222 -1. In the Jupyterhub Terminal, type {{code}}pilotcli{{/code}} to launch the latest version of the Pilot Command Line Interface.
223 -1. Use the {{code}}pilotcli --help{{/code}} at any time to show the welcome message again.
224 -
225 -{{code language="none"}}
226 -collaborator4@jupyter-collaborator4:~$ pilotcli
227 -Usage: pilotcli [OPTIONS] COMMAND [ARGS]...
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 - █▄▄▄▄▄█ ▄▀▄▄██▄▄▀▄ ▀▀▄ ▄▄▀▀▀▄ █▄▄▄█
265 265  
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 -{table}
295 -**File Operation** | **Permitted in the **
296 -**Green Room**
297 -Word 1 | Word 2
298 -{table}
299 -
300 -|=(% colspan="1" rowspan="1" %)(((
301 -**File Operation**
302 -
303 -
304 -)))|=(% colspan="1" rowspan="1" %)(((
305 -**Permitted in the **
306 -**Green Room**
307 -
308 -
309 -)))|=(% colspan="1" rowspan="1" %)(((
310 -**Permitted in the **
311 -**Core**
312 -
313 -
314 -)))
315 -|(% colspan="1" rowspan="1" %)File upload 
316 -(upload derivative output files from JupyterHub to the Green Room or Core storage)|(% colspan="1" rowspan="1" %)(((
317 -Yes
318 -)))|(% colspan="1" rowspan="1" %)(((
319 -Yes
320 -)))
321 -|(% colspan="1" rowspan="1" %)File download
322 -(download files from Green Room or Core into JupyterHub)|(% colspan="1" rowspan="1" %)(((
323 -**No**
324 -)))|(% colspan="1" rowspan="1" %)(((
325 -Yes
326 -)))
327 -
328 -
329 -
330 -
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