Test OWL ZIP

[jamesaoverton]

See owlcs/owlapi#375 and recent commits to OWLAPI master: owlcs/owlapi@b583351

I think it would be helpful for us to test this before it's released.

1. Build OWLAPI from master.

2. See if OWLAPI master can open the ZIP files we're currently creating. If this doesn't work, try naming the zipped ontology root.owl.

3. Generate YAML index files and add them to the ZIP files. The "root" is the requested ontology. Make sure OWLAPI master can open them.

[beckyjackson]

See if OWLAPI master can open the ZIP files we're currently creating. If this doesn't work, try naming the zipped ontology root.owl.

I was able to get this working with a Gradle project, not yet with Clojure. I was getting a series of really annoying errors, so I switched to Java to make sure it actually works (I think it's something with dependencies). I was able to read BFO contained in bfo.zip and got this OWLOntology object:

Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/bfo.owl>)
VersionIRI(<http://purl.obolibrary.org/obo/bfo/2.0/bfo.owl>)))
[Axioms: 575 Logical Axioms: 52]
First 20 axioms: ...

I'll go get this working in Clojure now.

Generate YAML index files and add them to the ZIP files. The "root" is the requested ontology. Make sure OWLAPI master can open them.

Just to make sure I'm getting this correct... this is what we want for the OWLZipYaml:

ro: &ro {
   iri: 'http://purl.obolibrary.org/obo/ro.owl',
   versionIri:,
   path: ro.owl
   }
annotations: {
   iri: 'http://purl.obolibrary.org/obo/ro/annotations.owl',
   versionIri:,
   path: annotations.owl
   }
pato_import: {
   iri: 'http://purl.obolibrary.org/obo/ro/pato_import.owl',
   versionIri:,
   path: pato_import.owl
   }
# ... and rest of imports ...

roots:
 - <<: *ro

[beckyjackson]

Ok, that was easier than expected. I got it -kind of- working in Clojure. I get an exception, but it's not fatal and the ontology still loads:

DEBUG	Exception reading file 
org.xml.sax.SAXException
at org.semanticweb.owlapi.util.ZipIRIMapper.startElement(ZipIRIMapper.java:313)
... and rest of stack trace ...

I used ZipIRIMapper to get the IRI inside bfo.zip, and loaded it as an OWLOntology, and it returned the same data as the Java implementation. Not sure about the exception, but I'll start working towards building the OWLZipYaml.