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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

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)}));

Installation

npm install paxdb-service-orthology-storage

Storage build

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

API Frontend

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

Versioning

All versions are <major>.<minor>.<patch>, where major and minor follow pax-db.org versions.

License

MIT. See "LICENSE.txt".