phyloref / phylo2owl

Tool to convert phylogenies to OWL ontologies
MIT License
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testShacl.jar should be compiled on Travis #14

Open gaurav opened 7 years ago

gaurav commented 7 years ago

Right now, it needs to be compiled locally because of a strange error on Travis (https://travis-ci.org/gaurav/phylo2owl/builds/177837977#L923). When we have more time, I'd like to look into this and figure out why it isn't working.

gaurav commented 7 years ago

I managed to get the JAR file compiling successfully on Travis, and the ensuing JAR file is executable. However, when given a set of shapes to validate, it gives an error message:

Exception in thread "main" java.lang.NoSuchMethodError: org.apache.jena.sparql.core.assembler.AssemblerUtils.registerModel(Lorg/apache/jena/rdf/model/Resource;Lorg/apache/jena/assembler/Assembler;)V at org.apache.jena.tdb.assembler.VocabTDB.init(VocabTDB.java:71) at org.apache.jena.tdb.assembler.VocabTDB.(VocabTDB.java:64) at org.apache.jena.tdb.assembler.AssemblerTDB.init(AssemblerTDB.java:25) at org.apache.jena.tdb.TDB.init(TDB.java:251) at org.apache.jena.tdb.sys.InitTDB.start(InitTDB.java:29) at org.apache.jena.system.JenaSystem.lambda$init$1(JenaSystem.java:111) at java.util.ArrayList.forEach(ArrayList.java:1249) at org.apache.jena.system.JenaSystem.forEach(JenaSystem.java:186) at org.apache.jena.system.JenaSystem.forEach(JenaSystem.java:163) at org.apache.jena.system.JenaSystem.init(JenaSystem.java:109) at org.apache.jena.rdf.model.ModelFactory.(ModelFactory.java:49) at org.topbraid.spin.util.JenaUtil.createDefaultModel(JenaUtil.java:311) at org.topbraid.spin.util.JenaUtil.(JenaUtil.java:74) at org.phyloref.phylo2owl.testShacl.main(testShacl.java:69)

I've figured out that the JAR files produced remotely and the one produced locally doesn't have exactly the same files in them, but they have all the files mentioned in the error message, so I'm still not sure what's causing this. Since we're fine producing JAR files locally for now, I'm going to hold off on this issue until it's needed.