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Unichem2index

Small tool for information replication between Unichem's DB and an ElasticSearch index.

How to use

After installing oracle's oracle-instaclient on your machine run:

unichem2index -eshost="http://0.0.0.0:9200" -oraconn=hr/hr@localhost:1521:XE

Configuration File

# Oracle Connection String for Unichems DB
oracleconn: 'hr/hr@oradb:1521/xe'

# ElasticSearch host, index and type
elastichost: 'http://elasticsearch:9200'
index: Unichem
type: Compound

# Query parameters for extraction
querystart: 2 # Starting number, useful to resume stoped extractions
querylimit: 5 # Amount of records fetch on each query
# Elastic Bulk add parameters
bulklimit: 2 # Limit of records to add for each Bulk worker
maxbulkcalls: 4 # Maximum number of worker at one time

logpath: ''

Flags

  • eshost (Mandatory): ElasticSearch host, e.g.: -eshost="http://0.0.0.0:9200". This will override the ES host on the config file.
  • oraconn (Mandatory): Oracle DB connection string, e.g.: -oraconn=hr/hr@localhost:1521:XE. This will override the Oracle Connection Strin on the config file (oraclenconn).
  • v: Software version
  • d: Debug log level

NOTE: Setting the log level to Debug will greatly decrease performance

How to build

A Go installation its required in order to compile Unichem2index, it can be downloaded from here.

make build
  1. Build the binary using docker-compose up golangBuilder
  2. Build the docker image using docker-compose build unichem
  3. docker push chembl/unichem2index:latest

Dockerized

To run it on Docker its required to download oracle's instant client files and place them on the Docker folder, e.g.:

Docker/oracle-instantclient18.3-basic-18.3.0.0.0-1.x86_64.rpm
Docker/oracle-instantclient18.3-devel-18.3.0.0.0-1.x86_64.rpm
Docker/oracle-instantclient18.3-sqlplus-18.3.0.0.0-1.x86_64.rpm

Make sure to place your config.yaml file inside the Docker folder as well. config.yaml example