agr_java_software

Modules

• agr_java_core - Shared library (Neo4j entities, Elasticsearch utilities, configuration)
• agr_api - REST API server
• agr_indexer - Elasticsearch site index builder
• agr_variant_indexer - Elasticsearch variant index builder
• agr_elasticsearch_util - Elasticsearch utility tools
• agr_api_tester - API integration tests
• agr_schema_validation - LinkML schema validation
• agr_intermine_data_extractor - InterMine data extraction

How to setup and build the API on a local system

1. Install docker, maven and java 11
2. Start up a Neo4j database image: docker run -it -p 7474:7474 -p 7687:7687 --env NEO4J_AUTH=none -e NEO4J_dbms_memory_pagecache_size=8g -e NEO4J_dbms_memory_heap_maxSize=6g ${REG}/agr_neo4j_data_image:build
3. Change directory into the agr_java_software directory
4. Build the API: make api
5. Change directory into agr_java_software/agr_api
6. Copy app.properties.defaults to app.properties and customize the configuration as needed. If developing locally with a local Neo4j instance, remove:
   • NEO4J_HOST=build.alliancegenome.org
7. Start app server: make run (for debug mode use make debug and remote connect to port 5045)
8. Call API endpoints, e.g. http://localhost:8080/api/gene/MGI:109583/alleles