A plugin for omero-cli-transfer to export imaging projects from the OMERO database to an ARC locally.
Once installed, your can "pack" omero projects to an ARC. The project metadata is mapped to studies in an ARC along with investigation metadata and the datasets are mapped to the assays. If there exits ISA metadata mapped to projects and datasets as described, with proper namespaces in omero key-value pair, the (meta)data is transfered from omero to the local ARC.
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
- Install
ARCCommander(and Git and Git LFS) as described here - Install
omero-cli-transferas described here
pip install omero-arc
conda create -n myenv -c conda-forge python=3.8 zeroc-ice=3.6.5
conda activate myvenv
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
Launch OMERO test environment with docker-compose.
sudo chmod a+x .omero/compose # enure that compose is executable
sudo .omero/compose up
OMERODIR="." ICE_CONFIG="test/ice.config" pytest
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