paxdb-service-orthology-storage

This is the pax-db.org orthology storage microservice. It consists of two docker images, one for 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

Versioning

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

License

MIT. See "LICENSE.txt".

Neo4j Dockerfile

A Dockerfile that produces a Docker Image for Neo4j.

Neo4j version

2.3.7

Usage

Build the image

To create the image paxdb/neo4j, execute the following command:

$ docker build -t paxdb/neo4j .

Run the image

To run the image and bind to host port 7474:

$ docker run -d --name neo4j -p 7474:7474 paxdb/neo4j

Once it's up and running open neo4j console, for example http://0.0.0.0:32768, and set the password.

Now create the second container to run the import:

sudo docker build -t paxdb/orthology-import -f Dockerfile.index .
sudo docker run --rm paxdb/orthology-import

Persistent data

The Neo4j server is configured to store data in the /data directory inside the container. You can map the container's /data volume to a volume on the host so the data becomes independent of the running container:

$ mkdir -p /tmp/neo4j
$ docker run -d \
    --name neo4j \
    -p 7474:7474 \
    -v /tmp/neo4j:/data \
    paxdb/neo4j