Containerization of Chemaxon JChem Postgres Cartridge

This is my attempt to fix the sample provided by chemaxon. Things made better:

• based on Debian 10 Buster (slim)
• Bump to Postgres 12
• Bump to Open JDK 11 (headless installation)
• Support for JPC 5+
• No initialization during build of the image. The Dockerfile respects POSTGRES_USER and POSTGRES_PASSWORD provided via environment on startup and creates a user and a database at first start, not earlier.

Getting started

• download JPC 5+ Debian/Ubuntu package (jchem-psql_<version>_amd64.deb) from Chemaxon's download page (you'll need a login)
• copy the downloaded file next to the Dockerfile, its name should match jchem-*.deb
• copy your license.cxl next to the Dockerfile
• build your container image: docker build -t jpc:latest .
• run a container from the built image: docker run -e POSTGRES_USER=jpcuser -e POSTGRES_PASSWORD=banana -p 5432:5432 jpc:latest

try it out

• connect to the database from a shell (with postgres-client installed) psql -h localhost -p 5432 -U jpcuser
• run some cartridge commands:

jpcuser=# CREATE table test(mol Molecule("sample"), id int);
CREATE TABLE

jpcuser=# insert into test(id, mol) values (1, 'c'), (2, 'cc'), (3, 'ccc');
INSERT 0 3

jpcuser=# select * from test;
 mol | id 
-----+----
 c   |  1
 cc  |  2
 ccc |  3
(3 rows)

jpcuser=# select * from test where mol |<| 'cc';
 mol | id 
-----+----
 c   |  1
 cc  |  2
(2 rows)

todo's

• clean shutdown. The postgres process get's killed on stop which might lead to data corruption
• support volumes for data and molecule types
• uncomment set -Eeo pipefail on entrypoint.sh. for some reason there is still a stderr output when PC start that lets the script fail