OMERO-ARC

A plugin for omero-cli-transfer to export imaging projects from the OMERO database to ARC repositories.

Usage

Once installed, your can "pack" omero projects to ARC repositories.

If the ARC repository already exists, the OMERO project is added as a new study and connected assays. If the ARC repo does not exist, a new ARC repository is created.

Examples:

omero transfer pack --plugin arc Dataset:111 path/to/my/new/arc_repo
omero transfer pack --plugin arc Dataset:111 path/to/my/already/existing/arc_repo

Installation

Install Dependencies

• Install ARCCommander (and Git and Git LFS) as described here
• Install omero-cli-transfer as described here

Install omero-arc plugin

git clone git@github.com:cmohl2013/omero-arc.git
cd omero-arc
pip install omero-arc

Development Environment Setup

conda create -n myenv -c conda-forge python=3.8 zeroc-ice=3.6.5
conda activate myvenv

Installation

git clone git@github.com:cmohl2013/omero-arc.git
cd omero-arc
pip install -e .[dev] # installs optional dependencies including omero-cli-transfer
conda install pytest

Start OMERO test database

Launch OMERO test environment with docker-compose.

sudo chmod a+x .omero/compose # enure that compose is executable
sudo .omero/compose up

Run tests

OMERODIR="." ICE_CONFIG="test/ice.config" pytest