Plugin for omero-cli-transfer to export OMERO data to ARC repositories.
Project description
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-transferas 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
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