feature/120-uv-vis-fluorescence-examples

[markdoerr]

In this PR we will add more common example datasets (to explore the capabilities of our framework):

UV-vis single sample, single measurement and microtiter plate example
UV-vis kinetics measurement example
corresponding Fluorescence measurement examples

Closes #120

[github-actions]

PR Preview Action v1.8.1
🚀 View preview at https://nfdi-de.github.io/chem-dcat-ap/pr-preview/pr-121/
Built to branch gh-pages at 2026-04-17 17:18 UTC. Preview will be ready when the GitHub Pages deployment is complete.

[markdoerr]

I added also a fluorescence kinetics measurement in a 96well microtiter plate to illustrate, how high-throughput measurements could be handled with DCAT-AP-chem.

[markdoerr]

after fixing the tests, the PR could be merged....
@dalito, @StroemPhi and @HendrikBorgelt, please review and comment.

[HendrikBorgelt]

hi @markdoerr.

Your test are currently failing because the testpipeline needs specific test file names to run correctly. Currentl, since we don't want to start every example from the dcat-ap root class, which should be cataloge, we choose the starting class, from which the test runner shall start, by naming the testfile after respective class, e.g. DatageneratingActivity-001, AnalysisDataset-001 a.s.o. If you change the names into e.g. NMR_Analysis_dataset, you would need to implement different testing mechanisms. While this is simple for the uv pytest command, the just test command, running the linkML inbuild _test_examples command, causes the issues here.
So for now, please make sure to just name your test files after the Startingclass, from which the data can be validated, followed by a dash and a number.

[markdoerr]

Thanks for the hint, @HendrikBorgelt ,
now I had time to look into how you call the tests - and understand the strange, brittle naming convention that was introduced :)
What was speaking against using the in-build LinkML validators, like, e.g.:
uv run linkml validate tests/data/valid/MTP96well-Kinetics-Fluorescence-Ex488nm-Em520nm-AnalysisDataset-001.yaml -s src/chem_dcat_ap/schema/chem_dcat_ap.yaml -C AnalysisDataset 2>&1 ?

They should be also programmatically callable (without a subprocess call) - if you have not done it before, I could have a look into it ....

[HendrikBorgelt]

the uv pytest running tests/test_data.py, can simply be modified, without larger issues.

however just test implements

uv run linkml-run-examples --input-formats json --input-formats yaml --output-formats json --output-formats yaml --counter-example-input-directory tests/data/invalid --input-directory tests/data/valid --output-directory examples/output --schema src/dcat_ap_plus/schema/dcat_ap_plus.yaml > examples/output/README.md

which I think causes an issue if you run it without the named schema files. I would need to do additional testing to check this. However, as far as I understand, this is the default test setup LinkML implements, so we should not deviate from this to much. (have a look at this issue linkml/linkml#2564)
We can add commands in the justfile to modify the cli command slightly. here you can find the available cli options.

But maybe we need to discuss this with @StroemPhi and @dalito in more detail.