Can't load SWEET, getting 403 error

[graybeal]

There's a ticket for this at ESIPFed/sweet#150, this is to reference that ticket as it affects BioPortal loading of SWEET.

[carueda]

In particular, this comment about the diagnosis of the problem: ESIPFed/sweet#150 (comment)

EDIT: I'd add here that this is not strictly speaking a bioportal/protege/owlapi issue -- the 403 is indeed reported from the SWEET server - the issue is that a certain "middleware" there (cloudflare) doesn't like the User-Agent:Java/1.8.0_40 request header sent from these clients.

[jvendetti]

As a temporary workaround to make SWEET 3.3.0 accessible in BioPortal, I performed the following steps:

1. Downloaded a local copy of sweetAll.ttl (and all associated imports) from the ESIPFed/sweet repository.
2. Downloaded a catalog-v00.xml file from ESIPFed that facilitates being able to open the local copy in Protege. See need catalog.xml file mapping sweet namespaces to local files  ESIPFed/sweet#147.
3. Used the Protege application (v 5.5.0) to merge all imports into a single ontology file, and uploaded that file to BioPortal.

The classes tab now displays a class hierarchy.

[jvendetti]

I modified my local dev environment to use Open JDK 12 (production BioPortal uses Java 8). With this newer version of Java, the following test case for loading SWEET:

File file = new File("/Users/jvendetti/Development/GitHub/sweet/src/sweetAll.ttl");
FileDocumentSource fileDocumentSource = new FileDocumentSource(file);
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(fileDocumentSource);

... doesn't result in the 403 responses. All unit tests pass in the owlapi_wrapper project against Java 12. I don't see any reason why we couldn't upgrade that portion of the codebase to the latest Java.

@alexskr - are you aware of any roadblocks with our production machines that would prevent us from upgrading to Open JDK 12?

[alexskr]

It would be better to use Open JDK 11 because it is LTS.

[graybeal]

Cloudflare has updated their settings and Protege doesn't have any more trouble with the SWEET ontology. Just need to confirm BioPortal works now and fix the auto-download setting.

[jvendetti]

I modified SWEET in BioPortal to use the load from URL functionality again (http://sweetontology.net/sweetALL). Processing completed successfully.