Go to https://sd2e.org
Once you have access to SD2E, login to the Jupyter Hub:
https://jupyter.sd2e.org/hub/login
- Startup your Jupyter Server by selecting the green 'My Server' button
- Once Started, under the 'Files' menu at the top right is an 'Upload' and 'New' pulldown
- From the new pulldown select 'Terminal'
- The sd2nb program is available as an interactive command.
- Get basic usage information
% sd2nb usage
usage: sd2nb command notebook (modifier)
sd2nb list - Show available notebooks
sd2nb search keyword - Find notebooks matching 'keyword'
sd2nb get notebook - Import a notebook to /Users/mwvaughn/tacc-work/sd2nb/
sd2nb share notebook (username) - Default is to share with everyone
sd2nb unshare notebook (username) - Default is to unshare with everyone
sd2nb shares notebook - List shares for a given notebook
sd2nb update notebook (delete) - Update or delete a shared notebook
IMPORTANT: If sharing/unsharing a notebook with spaces, please include "double quotes" around the notebook name
Version: 0.1.0 | Help: support@sd2e.org- List and search shared notebooks available to you
# List available notebooks
% sd2nb list
gzynda-test_notebook
vaughn-SD2E-App-ETL-Job-Submission-AgavePy-v0.1.0 vaughn-SharedNotebook
# Search (exact match case insensitive)
% sd2nb search etl
vaughn-SD2E-App-ETL-Job-Submission-AgavePy-v0.1.0 - Retrieve a shared notebook from the repository
% sd2nb get sd2eadm-ReadMeRNA_execution_script
[INFO] 2017-10-13T16:17:10Z - Importing to /home/jupyter/tacc-work/sd2nb...
######################################################################### 100.0%
[INFO] 2017-10-13T16:17:15Z - Done
# The notebook is copied to your personal persistent storage area. You're free
# to move it, rename it, edit it, etc.
% ls /home/jupyter/tacc-work/sd2nb
sd2eadm-ReadMeRNA_execution_script.ipynb- Share one of your notebooks with individual users
IMPORTANT: If your notebook has spaces in the name, please put the notebook name in double quotes, it will replace spaces with underscores.
# Share with a user
# cd to a directory containing a notebook you want to share (first time only)
% sd2nb share "Shared Notebook.ipynb" gzynda
File/folder does not exist
[INFO] 2017-10-13T15:59:24Z - Sharing as vaughn-SharedNotebook.ipynb...
[INFO] 2017-10-13T15:59:28Z - Done
[INFO] 2017-10-13T15:59:34Z - READ granted on vaughn-SharedNotebook.ipynb to gzynda
# Share with another user
# Once a notebook is uploaded to the repository you can share with more people
% sd2nb share SharedNotebook.ipynb jchuah
[INFO] 2017-10-13T16:00:07Z - READ granted on vaughn-SharedNotebook.ipynb to jchuah- Share your notebook with everyone
# Share with everyone
# If you want a notebook to be readable by everyone in the SD2 program, simply share
# it without specifying a user name.
% sd2nb share SharedNotebook.ipynb
[INFO] 2017-10-13T16:16:17Z - READ granted on vaughn-SharedNotebook.ipynb to everyone
# See who you have shared a notebook with:
% sd2nb shares SD2E-App-ETL-Job-Submission-AgavePy
John Fonner jfonner
Authorized Users public
- Update a shared notebook
# Update the repository copy of a given notebook
cd $HOME/directory-where-notebook-lives
% sd2nb update SharedNotebook
# Users who have downloaded a copy of the previous version won't currently be notified
# that a new version is available. Use the shares command to find out who you might
# need to notify of an updated notebook version.
- Delete a shared notebook
% sd2nb update SharedNotebook delete
# This will not delete any local copies other users have made, nor will it
# delete your local version of the notebook- Get immediate help by emailing support@sd2e.org
- Suggest improvements, fixes, or features at the project GitHub repository
SD2nb relies on bashids, a pure-bash implementation of the hashid algorithm, to generate short universal identifiers.