This tool carries out data hub set up at the European Nucleotide Archive (ENA). For more information on the data hubs, see the COMPARE Data Hubs publication. As part of the set up procedure, a user/data hub coordinator does the following:
- Request an unused data hub.
- Provide their contact details with information on any consortium or institute or intended use of the hub. This includes providing a short and public description for the data hub.
- Define lists of data providers (they should have Webin accounts) and data consumers.
- Requests analysis and visualisation tools to be associated with the data hub.
Prior to running scripts, ensure the following have been completed:
- Complete the spreadsheet for data hub setup. This includes providing information regarding the data hub coordinator, the data hub, and listing data providers and data consumers. A template spreadsheet has been included in the repository
DH_Providers_Consumers.xlsx. - Include configuration information in
config.yaml, e.g.ADMIN_EMAIL: [email protected]. - Once cx_Oracle has been installed, define the folder path at the top of
assigner.pyor save as an environment variable -ORACLE_CLIENT_LIB.
To assign a data hub and link Webin account(s) to it, use assigner.py, providing a completed spreadsheet, with the unassigned data hub name and credentials.
python assigner.py -s DH_Providers_Consumers.xlsx -d <DATA HUB NAME> -p <DATA HUB PASSWORD>
Once a data hub has been assigned, to send emails to a list of providers and consumers, use emailer.py and provide a completed spreadsheet of data providers and consumers.
python emailer.py -s DH_Providers_Consumers.xlsx -d <DATA HUB NAME> -p <DATA HUB PASSWORD>
To run this tool, there are several requirements:
- cx_Oracle (https://cx-oracle.readthedocs.io/en/latest/user_guide/installation.html)
- Python 3.7+ (https://www.python.org/downloads/)
- Python Pandas (https://pandas.pydata.org/docs/getting_started/install.html)