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monarch-initiative / phenol

phenol: Phenotype ontology library
https://phenol.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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org/yaml/snakeyaml/Yaml not found #358

Closed pnrobinson closed 2 years ago

pnrobinson commented 2 years ago

Somehow this dependency is "leaking" (this is with latest dev version)

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)
(...)

see also https://github.com/monarch-initiative/phenol/issues/333 https://github.com/monarch-initiative/phenol/pull/336

ielis commented 2 years ago

@pnrobinson is this still an issue in v2.0.0-RC1?

pnrobinson commented 2 years ago

I will investigate. This was an attempt to deal with that https://github.com/monarch-initiative/phenol/pull/336 I think that the CurieUtilBuilder is also something that we should either copy paste into phenol or remove since it is just 2 classes and not modular (yet). I tried a slightly different implementation that might be faster, but I did not profile it.