Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2024/10/02 18:14

From 1.5 to 1.6 From 6.1 to 7.1

From version 1.6

edited by Susan Evans
on 2023/07/11 14:00

Change comment: (Autosaved)

To version 6.1

edited by Dennis Segebarth
on 2024/03/01 09:14

Change comment: There is no comment for this version

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- Jupyterhub file upload back to core v2.4.11 2023-05-25 1926.png
- Jupyterhub-Logo-300x100px cropped.png

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--XWiki.sgevans
++XWiki.dsegebarth

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++{{box cssClass="floatinginfobox" title="Table of Contents"}}
++{{toc depth="2"/}}
++{{/box}}
++
++
  JupyterHub is an open-source, multi-user version of Jupyter Notebook for performing analysis of Project files in the Core. More information can be found in the application documentation [[https:~~/~~/jupyter.org/>>https://jupyter.org/]].
++[[image:Jupyterhub-Logo-300x100px cropped.png||height="13%" width="20%"]]
++
++
  = How it Works =
  JupyterHub allows Project members to create or import Jupyter Notebooks into the Project Workspace environment, retrieve Project files from the Core, perform computational workflows on the data, and write the outputs back to the Core where they can be accessed by other Project members. JupyterHub spins up a new JupyterLab instance for each Project member.
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  = Launching JupyterHub =
--[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="10%" width="30%"]]
++[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="9%" width="25%"]]
 . Launch your Project and click the **JupyterHub icon** in the left menu bar.
 . Click **Sign in with Keycloak** to initiate your session. JupyterHub automatically authenticates with your existing username and password and launches your session - no additional sign-in is required.
@@ -185,7 +185,7 @@
  and also from each opened Notebook, e.g., via **Kernel > Change Kernel…** :
--[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="64%" width="50%"]]
++[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="32%" width="25%"]]
  = Installing New Python Packages =
@@ -275,9 +275,9 @@
  * Open the login window and enter your HDC username and password (i.e. your EBRAINS account credentials).
  * Grant access by clicking **Yes**.
--[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="46%" width="50%"]]
++[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="28%" width="30%"]]
--[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="16%" width="50%"]]
++[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="10%" width="30%"]]
  * After successful confirmation, return to the terminal in your JupyterHub browser tab.
@@ -340,9 +340,9 @@
  Reminder: Please follow Linux conventions for file management. If your filename contains spaces, wrap it in single or double quotes.
  * //Filename~:// “Chemical Tracking Data.csv”
--* //Source~:// Project “Indoc Test Project”, “Core” storage zone, folder “collaborator4” indoctestproject/collaborator4/Chemical Tracking Data.csv -z core
--* //Destination: //user's Home directory in the Guacamole or JupyterHub VM .
--* //Command group/option: //file sync
++* //Source~:// Project “Indoc Test Project”, “Core” storage zone, folder “collaborator4” {{code}}indoctestproject/collaborator4/Chemical Tracking Data.csv -z core{{/code}}
++* //Destination: //user's Home directory in the Guacamole or JupyterHub VM {{code}}.{{/code}}
++* //Command group/option: //{{code}}file sync{{/code}}
  {{code language="none"}}
  collaborator4@jupyter-collaborator4:~$ pilotcli file sync indoctestproject/collaborator4/'Chemical Tracking Data.csv' . -z core
@@ -351,10 +351,62 @@
  File has been downloaded successfully and saved to: ./Chemical Tracking Data.csv
  {{/code}}
++To confirm successful download, type {{code}}ls{{/code}} and verify the file "Chemical Tracking Data.csv" is stored in the Home folder.
++{{code language="none"}}
++collaborator4@jupyter-collaborator4:~$ ls
++'Chemical Tracking Data.csv'   pilotcli
++{{/code}}
++The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface:
++[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]
--To confirm successful download, type ls and verify the file {{code}}Chemical Tracking Data.csv{{/code}} is stored in the Home folder.
--[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]
++== Uploading Project Data from JupyterHub using the Pilot Command Line Interface ==
++
++After analyzing Project data inside the JupyterHub, you can upload the generated outputs back into the Project via the Pilot Command Line Interface.
++
++=== Example ===
++
++* //Filename//: Chemical Tracking Data rev.csv
++* //Source~:// user's Home directory in JupyterHub {{code}}.{{/code}}
++* //Destination//: Project “Indoc Test Project”, folder “collaborator4”, “Core” storage zone,
++{{code}}indoctestproject/collaborator4{{/code}} {{code}}-z core{{/code}}
++* //Command group/option~:// {{code}}file upload{{/code}}
++* //User message// (for upload back to the Core): “my workbench output, no additional sensitive data"
++* //Command~:// {{code}}pilotcli file upload ./'Chemical Tracking Data rev.csv' -p{{/code}} {{code}}indoctestproject/collaborator4 -z core -m "my workbench output, no additional sensitive data"{{/code}}
++
++When uploading data to the Core, you are reminded that you are bypassing the usual Green Room upload workflow. To confirm, type {{code}}y{{/code}} at the prompt, or {{code}}N{{/code}} to cancel.
++
++{{code language="none"}}
++collaborator4@jupyter-collaborator4:~$ pilotcli file upload ./'Chemical Tracking Data rev.csv' -p indoctestproject/collaborator4 -z core -m "my workbench output, no additional sensitive data"
++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
++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
++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.
++To cancel this transfer, enter [n/No]
++To confirm and proceed with the data transfer, enter [y/Yes]
++ [y/N]: y
++Starting upload of: ./Chemical Tracking Data rev.csv
++Pre-upload complete.
++Uploading Chemical Tracking Data rev.csv:  |██████████████████████████████ 100% 00:00
++Upload Time: 2.92s for 1 files
++All uploading jobs have finished.
++{{/code}}
++
++After completing the upload, you can confirm the new file “Chemical Tracking Data rev.csv" exists in the correct directory using the pilotcli file list command and/or in the Portal File Explorer.
++
++{{code language="none"}}
++collaborator4@jupyter-collaborator4:~$ pilotcli file list indoctestproject/collaborator4 -z core
++Chemical Tracking Data rev.csv  Chemical Tracking Data.csv
++{{/code}}
++
++[[image:Jupyterhub file upload back to core v2.4.11 2023-05-25 1926.png||height="13%" width="50%"]]
++
++----
++
++Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
++
++HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
++
++

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