Merge LIMS

This project merges tables from two MySQL databases (lims and labbench) into a combined database (lims_merge).

Prerequisites

• Java 11 or later
  Verify with:

  java -version

• Maven 3.6+
  Verify with:

  mvn -v

• Access to the MySQL servers for lims, labbench, and the merge target (lims_merge).

Setup

1. Clone the repository

   git clone <repo_url>
   cd merge_lims

2. Configure environment variables
   Copy the example .env file and fill in your connection details:

   cp env.example .env

   Example .env:

   SRC_HOST=127.0.0.1
   SRC_PORT=your_port
   SRC_USER=your_username
   SRC_PASS=your_password
   SRC_SCHEMA=lims
   
   DST_HOST=<do_host>
   DST_PORT=<do_port>
   DST_USER=<do_user>
   DST_PASS=<do_password>
   DST_SCHEMA=lims_merge

3. Ensure the merge schema exists
   If needed, create the destination schema from the LIMS schema:

   mysql -h <MERGE_HOST> -P <MERGE_PORT> -u <MERGE_USER> -p --ssl-mode=REQUIRED      -e "CREATE DATABASE IF NOT EXISTS lims_merge;"

Build

Compile the project with Maven:

mvn clean package

This produces:

target/merge-subset-1.0-SNAPSHOT.jar

Run

Execute the merge:

java -jar target/merge-subset-1.0-SNAPSHOT.jar

The tool will:

• Connect to both source databases (lims and labbench).
• Copy shared/global tables to the merge schema.
• Merge plate-level data according to project logic.

Notes

• You must have read access to lims and labbench schemas and write access to the merge schema.
• Use --no-data dumps to clone structure if the merge schema is missing.
• Errors like “table doesn’t exist” usually mean you haven’t created the target schema.