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monarch-initiative / phenol

phenol: Phenotype ontology library
https://phenol.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
23 stars 4 forks source link

org.yaml.snakeyaml #296

Closed pnrobinson closed 4 years ago

pnrobinson commented 4 years ago

When using phenol as a library, this seems to get introduced as an additional dependency

Exception in thread "main" java.lang.NoClassDefFoundError: org/yaml/snakeyaml/Yaml
    at org.monarchinitiative.phenol.io.utils.CurieUtilBuilder.generate(CurieUtilBuilder.java:56)
    at org.monarchinitiative.phenol.io.utils.CurieUtilBuilder.<clinit>(CurieUtilBuilder.java:22)
    at org.monarchinitiative.phenol.io.OntologyLoader.loadOntology(OntologyLoader.java:35)
    at org.jax.l2o.Lirical2Overlap.initDiseaseMap(Lirical2Overlap.java:66)
    at org.jax.l2o.Lirical2Overlap.<init>(Lirical2Overlap.java:25)
    at org.jax.l2o.Main.call(Main.java:36)

Investigate why this isn't being inlcuded in the phenol uberjar any ideas @julesjacobsen

pnrobinson commented 4 years ago

Sorry, this was not related to phenol.

pnrobinson commented 4 years ago

Still getting this with tukaani but only on Mac?

caused by: java.lang.ClassNotFoundException: org.tukaani.xz.XZInputStream
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    ... 22 more

The same thing applies to org/tukaani/xz

julesjacobsen commented 4 years ago

Which class is this being thrown from? It might be a transitive dependency which has been excluded?

pnrobinson commented 4 years ago

unclear what happened, but it is now working.