Adding docs

[marimeireles]

Hi Josh,

I've been reading omero-rdf code because I'm looking into building a similar tool to scrape data from the electronic notebook system (and possibly build a more generic tool for extracting data).

I thought I might write some small "how to use" docs for omero-rdf.

from omero.plugins.rdf import RdfControl
from omero.cli import CLI

def main():
    # OMERO server connection details
    host = 'localhost'
    port = 4064
    username = 'your_username'
    password = 'your_password'

    # Image ID to export as RDF
    image_id = 123

    # Create an instance of the CLI class
    cli = CLI()

    # Login to the OMERO server
    cli.invoke(["login", host, "-u", username, "-w", password, "-p", str(port)])

    # Create an instance of the RdfControl class
    rdf_control = RdfControl(cli)

    # Set up the arguments for exporting the RDF
    args = Namespace(
        target=[f"Image:{image_id}"],
        pretty=True,
        ellide=False,
        trim_whitespace=False
    )

    # Run the action to export RDF
    rdf_control.action(args)

    # Logout from the OMERO server
    cli.invoke(["logout"])

if __name__ == "__main__":
    main()

This is an improved (by chatgpt) version of the script I first wrote to use omero-rdf, though, I'm not entirely sure if that's how it's supposed to be used?

I also could try to add some little introduction on how to build a plugin, which might be helpful for #11.

Please let me know whether I'm on the right path and if docs would be helpful here. :)

[joshmoore]

This is really interesting, @marimeireles! It's like ChatGPT read the implementation and did something that would be technically correct, but not optimal (and not something that I think any human has ever done).

With OMERO plugins, there are usually two styles of access:

• CLI based, i.e. from Bash
• Library based

For the second, we really should do some refactoring so that you don't need any of the boilerplate above. i.e., our goal would be something like:

from omero.gateway import BlitzGateway
from omero_rdf import RdfLibrary

with BlitzGateway("root","omero","xx.xxx.xxx.xx") as conn:
    lib = RdfLibrary(connection)
    # Load whatever you want here.

For #11, I think you are most interested in something like https://github.com/German-BioImaging/omero-rdf/blob/main/src/omero_rdf/idr_annotations.py