/clinvar_blacklight

A blacklight indexing and viewing system for clinvar data

Primary LanguageRubyGNU General Public License v3.0GPL-3.0

README

This is an experimental prototype for indexing ClinVar data into Blacklight

This project takes data downloaded from the NCBI FTP Site, indexes that data into solr, and provides a Blacklight based interface for interacting with the data.

Getting the Data

$ ftp ftp.ncbi.nlm.nih.gov/ (enter 'anonymous' for the login and your email address for the password)

ftp > cd pub/clinvar/xml
ftp > get ClinVarFullRelease_00-latest.xml.gz
ftp > exit
$ gunzip ClinVarFullRelease_00-latest.xml.gz

Requirements

  • Ruby 2.3
  • Blacklight 6
  • Ruby gems documented via Gemfile

Tests

  • Run rake ci to run tests
  • CI build via travis-ci.org

To do:

  • Ruby version

  • System dependencies

  • Configuration

  • Database creation

  • Database initialization

  • How to run the test suite

  • Services (job queues, cache servers, search engines, etc.)

  • Deployment instructions

  • ...