README.md

This is the [pax-db.org][http://pax-db.org] protein search microservice.

Installation

Versioning

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

License

MIT. See "LICENSE.txt".

Usage

build the image

docker build . -t paxdb5_0

run container in interactive mode and build index into /data folder

docker run -it --network=host --user=root --restart=always --name paxdb_search_lucene_index_ct --entrypoint /bin/bash paxdb5_0

cd /srv/paxdb && mvn -P build-index install

copy built index into host directory to be served

docker cp $containerID:/data/lucene_index_5_0 [host_data_directory]

serve the paxdb-search API

docker run -it --user=paxdb --restart=always -p 127.0.0.1:[host_port]:[docker_port]/tcp --name [] --entrypoint /bin/bash -v [host_data_directory]:/data/lucene_index_5_0 paxdb5_0

Update procedure

The process of updating to a new version is as follows:

1. update versions in pom.xml and update other parameters in paxdb.properties (possibly also hibernate.properties)
2. sql schema with tables species, proteins, proteins_names in localhost
3. global replace with new sql schema (e.g. paxdb5_0)
4. global replace /opt/paxdb/[version_no] with new [version_no]