rcsb.exdb 1.35

RCSB Python ExDB data extraction and loading workflows

py-rcsb_exdb

RCSB exchange database extraction and loading workflow tools

Introduction

This module contains a collection of utility classes for extracting data from the RCSB exchange database and subsequently reloading processed or integrated data.

Installation

Download the library source software from the project repository:

git clone --recurse-submodules https://github.com/rcsb/py-rcsb_exdb.git

Optionally, run test suite (Python versions 2.7 and 3.7) using tox:

tox

Installation is via the program pip. To run tests from the source tree, the package must be installed in editable mode (i.e. -e):

pip install -e . --extra-index-url https://pypi.anaconda.org/OpenEye/simple

# or using uv

uv pip install -e .

Installing in Ubuntu Linux (tested in 18.04)

You will need a few packages, before pip install . can work:

sudo apt install flex bison

Installing on macOS

To use and develop this package on macOS requires a number of packages that are not distributed as part of the base macOS operating system. The following steps provide one approach to creating the development environment for this package. First, install the Apple XCode package and associate command-line tools. This will provide essential compilers and supporting tools. The HomeBrew package manager provides further access to a variety of common open source services and tools. Follow the instructions provided by at the HomeBrew site to install this system. Once HomeBrew is installed, you can further install the MongoDB packages which are required to support the ExDB tools. HomeBrew also provides a variety of options for managing a Python virtual environments.