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OBASK Quick start

Prerequisites:

  1. Update to Docker Compose V2 (>= Docker Compose version v2.17) (see https://docs.docker.com/compose/install/linux/)

Create your project:

  1. Install cookiecutter

    bash python3 -m pip install --user cookiecutter

    or

    bash conda install cookiecutter

  2. Navigate to a folder where you want to create your new pipeline project and run the OBASK project template:

    bash cookiecutter gh:OBASKTools/obask-template

    or

    bash python3 -m cookiecutter gh:OBASKTools/obask-template

    Then provide your project_name when asked.

  3. Commit your project to GitHub. Be bold; if you are not satisfied with the result, you can delete the repository and create it again as many times as you want.

    • Navigate to your newly created project folder and initialize the git repository.

    bash git init -b main git add . git commit -m "First commit"

    • Create a new repository. The repo name should be the same as the project_name you provided to the template.

    • Do not initialize with a README (you already have one).

    • Click Create.

    • See the section under "…or push an existing repository from the command line." Follow the instructions there. For example, (make sure the location of your remote is exactly correct!).

    bash git remote add origin https://github.com/MyRepo/my_project_name.git git branch -M main git push -u origin main

  4. Customize your configs:

    Mandatory: - config/collectdata/vfb_fullontologies.txt - config/prod/neo4j2owl_config.yaml (see neo4j2owl configuration)

    Advanced: - collect/sparqls - dumps/sparqls for labels

Run your project:

When ready, run:

docker-compose up

Once the pipeline is complete, your services will be live at:
- Neo4J, http://localhost:7474/browser/
- Solr, http://localhost:8993/solr
- Ontology API, http://localhost:8007/ontology
- Triplestore, http://localhost:8080/rdf4j-workbench/repositories/obask/summary

Re-run your project

If you are not 100% happy with the output and want to do further configurations, you can safely shutdown and clean all services through:

docker-compose down

Then you can continue customizing your configurations and run the pipeline again to see them in action via:

docker-compose up

Troubleshooting

1- Dumps: Semantic tag labels should not contain a space character in the config/prod/neo4j2owl_config.yaml

1- Dumps: Parser Exception with a message similar to:

Caused by: org.semanticweb.owlapi.manchestersyntax.renderer.ParserException: Encountered RO_0002100 at line 1 column 1. Expected one of:
    Class name
    Object property name
    Data property name
    inverse
    not

This error indicates that the mentioned entity (in this case RO_0002100) is used in the config/prod/neo4j2owl_config.yaml, but it could not be found in any of the input ontologies (config/collectdata/vfb_fullontologies.txt). Problem in this case is a typographical error: RO_0002100 should be used in its curie form RO:0002100 in the config/prod/neo4j2owl_config.yaml.