Changes for page Using JupyterHub in HDC

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

From 1.3 to 1.2 From 2.1 to 1.7

From version 1.7

edited by Susan Evans
on 2023/07/11 14:05

Change comment: (Autosaved)

To version 1.3

edited by Susan Evans
on 2023/07/11 13:45

Change comment: (Autosaved)

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- Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png

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@@ -291,14 +291,26 @@
  When using the Pilot Command Line Interface in JupyterHub and the following actions are possible on the derivative files generated in JupyterHub:
++{table}
++**File Operation** | **Permitted in the **
++**Green Room**
++Word 1 | Word 2
++{table}
++
  |=(% colspan="1" rowspan="1" %)(((
  **File Operation**
++
++
  )))|=(% colspan="1" rowspan="1" %)(((
  **Permitted in the **
--**Green Room**
++**Green Room**
++
++
  )))|=(% colspan="1" rowspan="1" %)(((
  **Permitted in the **
--**Core**
++**Core**
++
++
  )))
  |(% colspan="1" rowspan="1" %)File upload
  (upload derivative output files from JupyterHub to the Green Room or Core storage)|(% colspan="1" rowspan="1" %)(((
@@ -313,85 +313,6 @@
  Yes
  )))
--== Downloading Project Data to JupyterHub using the Pilot Command Line Interface ==
--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.
--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}}.
--
--
--{{code language="none"}}
--collaborator4@jupyter-collaborator4:~$ pilotcli file sync --help
--Usage: pilotcli file sync [OPTIONS] [PATHS]... OUTPUT_PATH
--
--  Download files/folders from a given Project/folder/file in core zone.
--
--Options:
--  -z, --zone TEXT  Target Zone (i.e., core/greenroom)
--  --zip            Download files as a zip.
--  -i, --geid       Enable downloading by geid.
--  --help           Show this message and exit.
--{{/code}}
--
--=== Example ===
--
--Downloading a file from the Core to your Home Directory:
--
--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” {{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
--start downloading...
--Downloading Chemical Tracking Data.csv |██████████████████████████████ 100% 00:00
--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%"]]
--
--
--== 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~:// pilotcli file upload ./'Chemical Tracking Data rev.csv' -p indoctestproject/collaborator4 -z core -m "my workbench output, no additional sensitive data"
--
--When uploading data to the Core, you are reminded that you are bypassing the usual Green Room upload workflow. To confirm, type y at the prompt, or N 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}}
--
--
++

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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