Setting-up the environment

The package usage configuration files to define and build SQLite databases. Rather than supply each file individually the API will look for a directory with these files.

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/parser
mkdir ~/.clinvar_build_config/schema

Note: while the location and root directory name can be user defined, the subdirectories should called parser and schema.

Add to your path

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

Configuration Files

Copy the .cnf and .json files from this repository to your configuration directory. Moving the cnf file to the schema subdirectory and the JSON file to the parser 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 Type	Purpose	Used By	Format
`.cnf`	Database schema definition	`schema_generator`	Custom TOML-like
`.json`	XML parsing rules	`parser`	JSON