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GFBio Data Submission and Brokerage System

DOI

Description

The system provides the central entry point for the submission services provided by GFBio e.V. for the long-term data archival and publication of biodiversity, ecology and environmental science data. Users can submit their data to one or more of the GFBio data centers. Submissions can be performed either via a web-based user interface or over a REST API, where the latter is suitable for high-throughput programmatic submissions.

The system requires a working connection to an JIRA Service Management (server/data center) instance, since all communication with the users is organised via JIRA issues.

Developer Guide

Settings

Moved to settings

Basic Commands

Setting Up Your Users

  • To create a normal user account, just go to Sign Up and fill out the form. Once you submit it, you'll see a " Verify Your E-mail Address" page. Go to your console to see a simulated email verification message. Copy the link into your browser. Now the user's email should be verified and ready to go.

  • To create an superuser account, use this command::

    $ python manage.py createsuperuser

For convenience, you can keep your normal user logged in on Chrome and your superuser logged in on Firefox (or similar), so that you can see how the site behaves for both kinds of users.

Type checks

Running type checks with mypy:

  $ mypy gfbio_submissions

Test coverage

To run the tests, check your test coverage, and generate an HTML coverage report::

$ coverage run -m pytest
$ coverage html
$ open htmlcov/index.html

Running tests with py.test

$ pytest

Live reloading and Sass CSS compilation

Moved to Live reloading and SASS compilation.

Celery

This app comes with Celery.

To run a celery worker:

cd gfbio_submissions
celery -A config.celery_app worker -l info

Please note: For Celery's import magic to work, it is important where the celery commands are run. If you are in the same folder with manage.py, you should be right.

Contact Us

Please email any questions and comments to our Service Helpdesk (info@gfbio.org).

  • This work was supported by the German Research Foundation (DFG) within the project “Establishment of the National Research Data Infrastructure (NFDI)” in the consortium NFDI4Biodiversity (project number 442032008).
  • This work was supported by the German Research Foundation (DFG) within the project "German Federation for Biological Data e.V.: Concept for a sustainable research data management of environmental data for Germany." (project number 408180549).
  • This work was supported by the German Research Foundation (DFG) within the project "German Federation for the Curation of Biological Data (GFBio)" (project number 229241684).