ONTOP for OMERO

This repository contains the code to create a virtual knowledge graph for OMERO using ontop-vkg mappings.

Development

For development, the omero-test-infra docker-compose file can be used. Follow these step to set it up:

Get omero-test-infra

In the root of this repository:

git clone https://github.com/ome/omero-test-infra .omero

Patch the port mapping configuration

We need to access omero's postgresql database. Inside the container, it runs on port 5432 but is not mapped to the host. We patch the docker-compose file to have the database served on postgresql://localhost:15432.

cp utils/portmapping.patch .omero
cd .omero
patch -p1 < portmapping.patch
cd ..

Add ontop database user

This step must be redone every time after resetting the test infrastructure.

utils/setup_ontop_dbuser.short

Get omero-py

Install omero-py via pip or from conda-forge. The script /utils/install_omero-py.sh/ downloads and installs miniconda to the user's home directory and install omero-py as well as pytest and rdflib into the base environment.

source utils/install_omero-py.sh

Launch omero-test-infra

.omero/docker dev start_up

Populate omero with test data.

We need something to play with, so let's create some projects and datasets, import a few images and annotate with key-value pairs (map annotations) and tags.

utils/insert_data.sh

Launch ontop endpoint

Assuming ontop is in your path:

ontop endpoint --mapping ontop/omemap.obda \
               --ontology ontop/omemap.ttl \
               --properties ontop/omemap.properties \
               --xml-catalog ontop/catalog-v001.xml \
               --dev

The commandline arguments point to the mappings file, mapping ontology, database connection details (properties), ontology import catalog, respectively. The --dev flag starts ontop int development mode. Edits to the mappings or ontology will trigger a restart of the endpoint. By default, the ontop endpoint is served at http://localhost:8080/sparql , the query editor is at http://localhost:8080 . Use the --port option to configure a different port.

Run tests

Finally,

pytest

will run the python test suite.

Reset database

To restart from a blank omero-test-infra (without images, datasets, projects, or annotations), run

.omero/docker srv

Don't forget to restart it according to above.

Acknowledgments

This project was developed with support from the Biohackathon 2024.