This repository holds a Python package with wrappers and methods designed to work with the Status DB instance of CouchDB at NGI Stockholm. It can be used to retrieve information about project, samples, flow cells and anything else stored in the database.
This code was originally part of the scilifelab GitHub repository. It has been moved into it's own package here to make maintenance simpler.
To use this package, you need to install it. Clone the repository (remember to fork it if you're intending to make any changes) and download. Then, install the package with the following:
python setup.py install
Swap install for develop if you're going to change any code, to
avoid having to reinstall every time you make a change.
Finally, you need a config file with the information that the package requires to connect to the database. This is held within a config file in your home directory:
~/.ngi_config/statusdb.yaml
This file should be yaml formatted and look like this:
statusdb:
username: <login as user>
password: <password to use>
url: <full url of the database>Once installed, you can import the package into any other Python script. For example:
from statusdb.db import connections as statusdb
p = statusdb.ProjectSummaryConnection()
proj = p.get_entry('Testing_project')
samples = proj['samples']- Panneerselvam Senthilkumar and Phil Ewels
- Pulled code into own repository and updated methods.
- Per Unneberg
- Wrote original code, as part of the scilifelab repository.
- Chuan Wang
- Port scripts to support Python 3.