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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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json output bug #620

Closed seoanezonjic closed 1 year ago

seoanezonjic commented 1 year ago

When the RC2 version is set with output json, if the phenopacket has not age data (I think that with sex data could occur the same) lirical breaks with: 12:59:18.044 [main] ERROR o.m.l.c.c.AbstractPrioritizeCommand - Error: Cannot invoke org.monarchinitiative.lirical.core.model.Age.equals(Object)" because the return value of org.monarchinitiative.lirical.core.analysis.AnalysisData.age()" is null However, if the json output is not requested there is no error. I think that age or sex data should be NOT mandatory to json output. In my case I lack of this data with the HPO profiles that I'm analysing. Thank you in advance

ielis commented 1 year ago

Hi, thanks for reporting the bug. As you suggested, there was an issue in the JSON writer which expected the age to always be non-null. However, the age field can be null based on the AnalysisData contract.

I fixed the bug in #621 and the updated code is available in the latest LIRICAL.

I will close this since it is very likely that #620 fixed the error. However, please feel free to reopen if the error persists.

seoanezonjic commented 1 year ago

Hi @ielis I've enabled again the json output and I've realised that my version was old so I've followed the link https://thejacksonlaboratory.github.io/LIRICAL/latest/setup.html The documentation describes a RC3 version but when I go to releases or I compile the code following the instructions, I get a RC2 jar file and the error described in this issue persists. What am I doing wrong?