RCSB exchange database extraction and loading workflow tools
This module contains a collection of utility classes for extracting data from the RCSB exchange database and subsequently reloading processed or integrated data.
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 setuptools or tox:
python setup.py test
or simply run
toxInstallation 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 -r requirements.txt # OR: pip install -i https://pypi.anaconda.org/OpenEye/simple OpenEye-toolkits
pip install -e .You will need a few packages, before pip install . can work:
sudo apt install flex bison
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.
A convenience CLI exdb_exec_cli is provided for performing update and loading operations.
exdb_exec_cli --help
usage: exdb_exec_cli [-h] [--data_set_id DATA_SET_ID] [--full] [--etl_chemref]
[--etl_tree_node_lists] [--config_path CONFIG_PATH]
[--config_name CONFIG_NAME] [--db_type DB_TYPE]
[--read_back_check] [--num_proc NUM_PROC]
[--chunk_size CHUNK_SIZE]
[--document_limit DOCUMENT_LIMIT] [--debug] [--mock]
[--cache_path CACHE_PATH] [--rebuild_cache]
optional arguments:
-h, --help show this help message and exit
--data_set_id DATA_SET_ID
Data set identifier (default= 2019_14 for current
week)
--full Fresh full load in a new tables/collections (Default)
--etl_chemref ETL integrated chemical reference data
--etl_tree_node_lists
ETL tree node lists
--config_path CONFIG_PATH
Path to configuration options file
--config_name CONFIG_NAME
Configuration section name
--db_type DB_TYPE Database server type (default=mongo)
--read_back_check Perform read back check on all documents
--num_proc NUM_PROC Number of processes to execute (default=2)
--chunk_size CHUNK_SIZE
Number of files loaded per process
--document_limit DOCUMENT_LIMIT
Load document limit for testing
--debug Turn on verbose logging
--mock Use MOCK repository configuration for testing
--cache_path CACHE_PATH
Top cache path for external and local resource files
--rebuild_cache Rebuild cached files from remote resources
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For example, to construct and load tree nodes list data collections, the following command may be used:
exdb_exec_cli --mock --full --etl_tree_node_lists --rebuild_cache \
--cache_path ./CACHE \
--config_path ./rcsb/mock-data/config/dbload-setup-example.yml \
--config_name site_info_configuration >& LOGTREE \