iBridges Dataverse

This package provides a Dataverse plugin for the iBridges CLI and GUI.
It allows you to create Dataverse datasets and upload iRODS data objects.

Dependencies

• Python 3.9+
• HTTPX
• PyDataverse
• iBridges and iBridges GUI (ibridges, ibridgesgui)

All dependencies are installable via pip.

Highlights

• Automatic checksum verification during upload
• Git‑like workflow: stage files first, upload later
• Shared state between CLI and GUI — switch freely without losing progress

⚠️ Important Notes

• Only files smaller than 9 GB are transferred.

• All iRODS data is downloaded locally before being uploaded to Dataverse.

  Files are downloaded one by one into a temporary directory, uploaded to Dataverse, and then deleted.
  You therefore need at least 9 GB of free disk space.
  If an upload fails, the temporary file is not deleted, so files may accumulate.

Installation

Install from PyPI

pip install ibridgesdvn

Install the CLI from GitHub

pip install git+https://github.com/iBridges-for-iRODS/ibridges-plugin-dataverse.git

Install both GUI and CLI

pip install git+https://github.com/iBridges-for-iRODS/ibridges-plugin-dataverse.git
pip install "ibridgesdvn[gui]"

This installs the Python package ibridgesdvn.

CLI Commands

Starting the iBridges CLI (ibridges -h) shows the additional Dataverse commands:

ibridgesdvn commands:
    dv-add-file        Stage iRODS files for upload.
    dv-cleanup         Clean up local Dataverse logs.
    dv-create-ds       Create a new Dataverse dataset.
    dv-draft           Show or delete draft datasets.
    dv-init            Store a Dataverse API token.
    dv-push            Upload staged files.
    dv-rm-file         Remove staged files.
    dv-setup           Manage Dataverse configurations.
    dv-status          Show pending uploads and drafts.
    dv-switch          Switch Dataverse configuration.

If you use the iBridges GUI, a Dataverse view becomes available.

The Dataverse View

1. Configure your Dataverse connection
   Add or remove Dataverse configurations.

2. Select a Dataverse collection
   If you don’t have a dataset yet, click Create New Dataset to generate one and obtain its DOI.

3. Select iRODS data objects
   Use the right-hand browser to select files.
   Click << to stage them for upload.
   You may remove entries at any time.

When ready, click Upload to Dataverse.
After upload, open the dataset in your browser to finalize publication.

Dataverse Commands

Configuring a Dataverse Instance

List or create Dataverse configurations:

ibridges dv-setup dvnl-demo https://demo.dataverse.nl

Activate a configuration and store an API token:

ibridges dv-init dvnl-demo
Your Dataverse token for dvnl-demo :
  demo -> https://demo.dataverse.org
* dvnl-demo -> https://demo.dataverse.nl

Switch between configurations:

ibridges dv-switch https://demo.dataverse.org
* demo -> https://demo.dataverse.org
  dvnl-demo -> https://demo.dataverse.nl

You may use URLs or aliases interchangeably.

Note: These setup commands are available only in the CLI, not in the shell.
All other commands work in both.

Creating a Dataset

You can create a dataset using a Dataverse dataset.json:

ibridges shell
ibshell:research-christine> dv-create-ds UUscience --metajson ibridgescontrib/ibridgesdvn/dataset.json
Dataset with pid 'doi:10.80227/PDVNL/RZQRAK' created.

Save the dataset identifier (e.g., 10.80227/PDVNL/RZQRAK) — you will need it for staging and uploading files.

Alternatively, create minimal metadata interactively:

ibshell:research-christine> dv-create-ds UUscience

This opens a short questionnaire for the required fields.

Browsing Files and Staging Them

Browse iRODS collections:

ibshell:research-christine> ls my_books

Stage files for upload:

ibshell:research-christine> dv-add-file 10.80227/PDVNL/RZQRAK irods:my_books/AdventuresSherlockHolmes.txt irods:my_books/DonQuixote.txt

All iRODS paths must be prefixed with irods:.
Relative paths are supported.

View the staging summary:

{'https://demo.dataverse.nl': {'add_file': [...]}}

Remove staged files:

ibshell:research-christine> dv-rm-file 10.80227/PDVNL/RZQRAK irods:my_books/DonQuixote.txt

Check status:

ibshell:research-christine> dv-status

Check opened drafts:

ibshell:research-christine> dv-draft

Uploading Data

Upload staged files:

ibshell:research-christine> dv-push 10.80227/PDVNL/RZQRAK

Files are downloaded to a temporary directory, uploaded to Dataverse, and removed locally if successful.

After upload, the status becomes empty:

ibshell:research-christine> dv-status