Configuration files

The ./resources/clinvar_config directory contains configuration files that drive both database schema generation and XML parsing for clinvar-build. Additionally, the directory includes the xsd file the configuration files were developed against.

How configuration works

A single set of JSON files (one per ClinVar record type) is used to both build the SQL schema as well as parse the XML files:

Concern	Module	What it reads
Database schema (CREATE TABLE, CREATE INDEX)	`schema_generator`	`sql/*.json`
XML parsing and database loading	`parser`	`sql/*.json`

Schema constraints (not_null, unique, defaults, foreign_key_constraint, _indexes) are annotations on the same entity definitions used for parsing. See sql/README.md for the full annotation reference.

Setting-up the directory

The parser and schema_generator modules look for configuration files using the environmental variable ${CLINVAR_BUILD_CONFIG}.

Create configuration directory

mkdir ~/.clinvar_build_config
mkdir ~/.clinvar_build_config/sql

Note: while the location and root directory name can be user defined, the sql subdirectory name must not be changed.

Add to your path

vim ~/.bashrc
export CLINVAR_BUILD_CONFIG="${HOME}/.clinvar_build_config"
source ~/.bashrc

Configuration files

Copy the .json files from the sql/ subdirectory in this directory (clinvar_build/resources/clinvar_config/sql) to your configuration directory’s sql/ subdirectory.

Fallback behavior

If the environmental variable is not found, clinvar-build will attempt to look for the location of the ./resources/clinvar_build_config directory among the installed package files as a fallback.

Configuration file types

File	Purpose
`sql/rcv_parse.json`	RCV entity definitions (parsing + schema)
`sql/vcv_parse.json`	VCV entity definitions (parsing + schema)