csr limitation

[pnrobinson]

When trying to load maxo.json, I get this:

java.lang.RuntimeException: org.monarchinitiative.phenol.graph.csr.InsufficientWidthException: 
Unable to encode 159 relation types using 15 slots

I am guessing that for our purposes, we are only interested in is_a relations (in many cases) and that we could offer an option to ignore some relations? I haven't looked in the code, but what is the reason for limiting to 15 slots?

[ielis]

Looks weird, a possible bug, since the code should be using Long (64 slots) to encode the relationship types. So, 15 slots sounds like a bug.

On the other hand, if there indeed are 159 relation types in MAxO, we'll have to either just use is_a or rework the code. I thought 64 bits would be enough for our use cases..

There is nothing too special about your code, right? I should just download the latest MAxO and try to load it to replicate the bug, right?

[ielis]

FWIW, MAxO v2023-10-03 can now be loaded by running this on the latest develop:

  Path path = Path.of("path/to/maxo.json");
  CurieUtil curieUtil = CurieUtilBuilder.defaultCurieUtil();
  OntologyLoaderOptions options = OntologyLoaderOptions.builder()
    .discardNonPropagatingRelationships(true)
    .forceBuild(true)
    .build();
  MinimalOntology maxo = MinimalOntologyLoader.loadOntology(path.toFile(), curieUtil, options, "MAXO");

However, there is a disconnected node MAXO:0001487, so the build fails unless .forceBuild(true) is set.

Please reopen if you run into troubles again..