OMERO Server Container
======================

The OMERO server container serves as the master node for the entire platform, handling core OMERO functionality with minimal but important customizations.

Overview
--------

Based on the official ``openmicroscopy/omero-server`` image, this container acts as the central coordination point for:

* Core OMERO server functionality
* Script execution coordination  
* Database management
* Ice grid management for distributed processing

Key Customizations
------------------

Script Installation
~~~~~~~~~~~~~~~~~~~

The container automatically installs three sets of scripts during build:

**1. BIOMERO Scripts**
   - Source: `NL-BioImaging/biomero-scripts <https://github.com/NL-BioImaging/biomero-scripts>`_
   - Location: ``/opt/omero/server/OMERO.server/lib/scripts/biomero/``
   - Purpose: Slurm-based image analysis workflows

**2. OMERO.figure Script**
   - Source: `ome/omero-figure <https://raw.githubusercontent.com/ome/omero-figure/refs/heads/master/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py>`_
   - Location: ``/opt/omero/server/OMERO.server/lib/scripts/omero/figure_scripts/``
   - Purpose: PDF export functionality for figures

**3. Labels2ROIs Script**
   - Source: `Cellular-Imaging-Amsterdam-UMC/label2rois <https://raw.githubusercontent.com/Cellular-Imaging-Amsterdam-UMC/label2rois/main/Labels2Rois.py>`_
   - Location: ``/opt/omero/server/OMERO.server/lib/scripts/omero/util_scripts/``
   - Purpose: Convert BIOMERO label images to OMERO ROIs

Automated Configuration Restoration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

**Configuration Backup/Restore System**
   - Script: ``00-restore-config.sh``
   - Purpose: Enables stateless container redeployments by automatically restoring OMERO configuration from backup
   - Location: ``/OMERO/backup/omero.config``
   - Benefit: No manual configuration needed after container (re)creation

**LDAP Integration Ready**
   - Config: ``01-ldap-config.omero``
   - Purpose: Pre-configured LDAP settings for enterprise authentication
   - Customizable via environment variables. Placeholder for now.

Dockerfile Key Changes
----------------------

.. code-block:: dockerfile

   # Install required scripts for analysis workflows
   RUN cd /opt/omero/server/OMERO.server/lib/scripts/ && \
       git clone --depth 1 --branch ${BIOMERO_VERSION} \
       https://github.com/NL-BioImaging/biomero-scripts.git biomero

   # Configuration restoration on startup
   ADD server/00-restore-config.sh* /startup/
   ADD server/01-ldap-config.omero /opt/omero/server/config/

Development Guidelines
----------------------

Configuration Changes
~~~~~~~~~~~~~~~~~~~~~

**Programmatic Configuration**: Always make configuration changes through scripts or environment variables to maintain stateless deployments:

.. code-block:: bash

   # Example: Add new configuration via startup script
   echo "config set -- omero.my.setting 'value'" >> /opt/omero/server/config/02-my-config.omero

**Environment Variables**: Use docker-compose environment variables for dynamic configuration:

.. code-block:: yaml

   environment:
     CONFIG_omero_db_host: "${POSTGRES_HOST}"
     CONFIG_omero_db_name: "${POSTGRES_DB}"

Adding New Scripts
~~~~~~~~~~~~~~~~~

To add additional OMERO scripts:

1. **Via Git Repository** (recommended for script collections):

.. code-block:: dockerfile

   RUN cd /opt/omero/server/OMERO.server/lib/scripts/ && \
       git clone https://github.com/your-org/your-scripts.git

2. **Via Direct Download** (for individual scripts):

.. code-block:: dockerfile

   RUN curl -o /opt/omero/server/OMERO.server/lib/scripts/path/script.py \
       https://raw.githubusercontent.com/your-org/repo/main/script.py

Testing Changes
~~~~~~~~~~~~~~~

1. **Build and test locally**:

.. code-block:: bash

   docker-compose -f docker-compose-dev.yml build omeroserver
   docker-compose -f docker-compose-dev.yml up -d omeroserver

2. **Verify script installation**:

.. code-block:: bash

   docker-compose exec omeroserver omero script list

3. **Check configuration**:

.. code-block:: bash

   docker-compose exec omeroserver omero config get

Related Documentation
---------------------

* :doc:`../architecture` - Overall system architecture
* :doc:`omeroweb` - Web interface development
* :doc:`biomeroworker` - Worker node development
* `OMERO Developer Documentation <https://omero.readthedocs.io/en/stable/developers/>`_