This is the pax-db.org orthology storage API service.
Essentially there're two packages here, one for the storage (neo4j) and another for the front-end (node.js express).
Storage consists of two docker images, one for storage (neo4j) and another to import data.
As a bonus it exports an npm module which exposes the API. Example usage:
const opts = {server:'http://neo4j:7474',user:'neo4j',pass:'secret'};
const orth = require('paxdb-service-orthology-storage')(opts);
orth.count('Protein').then(numProteins => console.log(`num proteins: ${numProteins}`);
orth.loadOrthologs('9606.ENSP00000356969', 'PRIMATES', 'BRAIN').
then(cogs => console.log(`orthologs: ${JSON.stringify(cogs)}));
npm install paxdb-service-orthology-storage
docker build -t paxdb/orthology-indexer -f Dockerfile.index .
Need to create a tmp neo4j for data indexing. The Neo4j server is configured
to store data in the /data directory inside the container. We'll map the
container's /data volume to a volume on the host and use it later to build the final image:
docker run -d --name paxdb_tmp_neo --log-driver=json-file \
--env=NEO4J_AUTH=none \
--env=NEO4J_dbms_memory_pagecache_size=1024M \
--env=NEO4J_dbms_memory_heap_maxSize=2048M \
-p 27474:7474 \
-v /tmp/paxdb-orthology-neo4j:/data \
neo4j:3.1.6
Now create the second container to run the import:
# docker run --rm --env=NEO4J_PORT=37890 paxdb/orthology-indexer
docker run --rm --link paxdb_tmp_neo:neo4j paxdb/orthology-indexer
Once it's done, stop neo4j and create the other image with the neo4j data:
docker stop paxdb_tmp_neo
mv /tmp/paxdb-orthology-neo4j neo4j
docker build -t paxdb/orthology-storage:4.1.0 -f Dockerfile.storage .
docker rm -v paxdb_tmp_neo
docker service create --limit-memory 2g --limit-cpu 1.0 --detach \
--with-registry-auth --name paxdb-orthology-storage_4_1 \
--mount type=bind,source=/tmp/paxdb-neo4j_database-v4.1.0,destination=/data \
-p 13006:7474 orthology-storage:4.1.0
docker build -t paxdb/orthology-api:4.1.0 -f Dockerfile.front .
docker service create --limit-memory 1g --limit-cpu 1.0 --detach \
--with-registry-auth --env NEO4J_URL=http://localhost:13006 \
--env NEO4J_PASS=ssssecret --name paxdb-orthology-api_4 \
-p 13007:3000 paxdb/orthology-api:4.1.0
All versions are <major>.<minor>.<patch>, where major and minor follow
pax-db.org versions.
MIT. See "LICENSE.txt".