Virtual Biospecimen Repository (VBR) Python Library

This is a package for working with the TACC Virtual Biospecimen Repository database.

Installation

git clone https://github.com/A2CPS/python-vbr
cd python-vbr
pip install --user .

Usage

Connect to VBR Database

VBR is built atop the Tapis V3 pgrest service. The VBR constructor requires an active, valid Tapis API client to be passed in its constructor.

>>> import vbr
>>> from tapipy.tapis import Tapis
>>> t = Tapis(base_url='https://a2cps.tapis.io', username='<username>', password='<password>')
>>> d = vbr.VBR(t)
>>> d.list_tables()
[{'table_id': 33, 'table_name': 'organization', 'root_url': 'organization', 'primary_key': 'organization_id'}]

It is also possible to configure a VBR connection using the environment variables VBR_HOST, VBR_DATABASE, VBR_USERNAME, and VBR_PASSWORD.

>>> import vbr
>>> t = vbr.client.connection.TapisUserEnv()
>>> d = vbr.VBR(t)
>>> d.list_tables()
[{'table_id': 33, 'table_name': 'organization', 'root_url': 'organization', 'primary_key': 'organization_id'}]

Direct Operations

The client property of a VBR class instance is a standard tapipy connection. It supports all documented tapipy functions. API methods tailored to the VBR are described later.

>>> resp = d.client.pgrest.get_in_collection(collection='organization', item='1')

VBRRecord Table Classes

Each VBR table is represented by a table class. You can find a comprehensive list of these via help(vbr.tableclasses). You can find signature for instantiating each table class via the fields() classmethod.

Examples coming soon

Validation

The Table parent class implements basic validation at object construction time.

Examples coming soon

Retrieve a Record

Examples coming soon

Create a Record

Examples coming soon

Update a Record

Examples coming soon

Delete a Record

Examples coming soon

Utility functions

Coming soon

Contributing

Coming soon