search

IHTSDO / snomed-owl-toolkit

The official SNOMED CT OWL Toolkit. OWL conversion, classification and authoring support.
Other
92 stars 19 forks source link

Contents of release-zipfile #4

Closed ronaldcornet closed 6 years ago

ronaldcornet commented 6 years ago

Two questions:

Which are the constraints regarding contents of the Snapshot.zip?

I get a 0-byte owl-files, but seemingly no errors:

Creating Ontology using the following options: Snapshot archives: [SnomedCT_InternationalRF2.zip] Delta archive: -none- Ontology URI: http://snomed.info/sct/900000000000207008 Ontology Version: 20180501 Include FSN Annotations: true

2018-05-01 14:51:15,037 [INFO ] [main] org.snomed.otf.owltoolkit.conversion.RF2ToOWLService - Loading RF2 files

I've tried both zipping the "Snapshot" folder from the release, as well as the "Terminology folder". Both gave the same result.

kaicode commented 6 years ago

Hi @ronaldcornet, The snomed-boot library within the owl toolkit is looking for the following files:

Plus some reference sets:

The can be in any folder within the zip and could be prefixed with "x" which is the format for technical previews.

If it can't find the concept, or description file you should get an error like:

FileNotFoundException: No Concept RF2 file found.

Feel free to email me your zip (via google drive or dropbox or something if it's too big) and I'll diagnose it.

kaicode commented 6 years ago

Here is example input and output using the international edition and an extension. https://gist.github.com/kaicode/2d53a48ee6f5173cbc2bd64f677dd4d0

If you are not getting this much output it's possible that you need to assign more memory. The process uses about 2g.

You can make sure java is getting enough memory using the Xms parameter: java -Xms2g -jar target/snomed-owl-toolkit-1.3.1-executable.jar ...other params

ronaldcornet commented 6 years ago

Argh, I had gzipped one of the .txt files (relationships), so the set of .txt files was incomplete. Now it works. It would be great if missing necessary files would be indicated. Sorry for this bug on my end!

kaicode commented 6 years ago

It's nice to hear it works on Windows. Thank you for testing.