Mapping tutorial, Ontop CI

[CFGrote]

This PR

• adds instructions for adding ontop mappings based on the ome_core owl ontology.
• additions to CI
  • java installation
  • ontop-cli installation
  • omero-py installation (through miniconda)
  • mapping omero ports to host on same port numbers (patching the docker files in .omero/)
  • launching docker in dev mode (.omero/docker dev start_up)
  • a script to insert data into the spun up omero
  • a properties file to run ontop against the test infra omero

Currently, the script to insert data fails with

source ci_utils/insert_data.sh
InternalException: Failed to connect: Ice.ConnectionLostException:
recv() returned zero
Error: Process completed with exit code 44.

This does not happen if run live on a PC. @joshmoore, do you have any clue what may be the cause?

[joshmoore]

This does not happen if run live on a PC. @joshmoore, do you have any clue what may be the cause?

Though I don't know of many who are testing .omero/docker dev start_up, I don't seeing anything wrong. I'm wondering if you are hitting some resource limit. Have you tried to check/print the logs?

[CFGrote]

Yeah, was thinking the same. I'll see if i can run a single omero command directly from the CI

[joshmoore]

Should we merge #2 with the hope of getting CI running here?

[CFGrote]

Should we merge #2 with the hope of getting CI running here?

honestly, I don't think that will change anything. Actually, #2 has become redundant after the work done today, @marimeireles planned to revoke it but probably forgot about it in the end.

[joshmoore]

Once the file exists, though, it should start running. I imagine, though, it's running on your fork, so you have sufficient visibility.

[CFGrote]

ah, now I understand. yes, it's running on my fork.

On 10/12/24 00:09, Josh Moore wrote:

Once the file exists, though, it should start running. I imagine, though, it's running on your fork, so you have sufficient visibility.

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[joshmoore]

InternalException: Failed to connect: Ice.ConnectionLostException:

Ah, I understand, @CFGrote. Looking at your fork reminded me: yeah, yaml line is a separate shell invocation. Since dev start_up uses an EXIT trap, when that shell exits, everything gets spun down:

https://github.com/ome/omero-test-infra/blob/master/docker#L63

You can set NOCLEAN=true to prevent the clean up.

[joshmoore]

.... but dev always sets NOCLEAN 😕

https://github.com/ome/omero-test-infra/blob/master/docker#L280

[CFGrote]

I thought I was doing just that in line 25 of https://github.com/CFGrote/omero-ontop-mappings/actions/runs/11299919172/workflow

[CFGrote]

It's getting late, I'll check out. :wave:

[CFGrote]

Argh. I just can't get a running omero that responds to omero cli commands issued on host system in gh CI. Kind of giving up here. @marimeireles, I suggest you take my scripts from ci_utils and put them into your docker compose. Maybe we're more lucky if data insertion, ontop and querying take place inside the container.