Sample parser is throwing error that does not respect Phenopacket schema

[lacek]

Exomiser throws below error when provided sample YAML in phenopacket format with pedigree entry containing paternalId or maternalId of 0

java.lang.IllegalStateException: Failed to execute CommandLineRunner
        at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:771)
        at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:752)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:314)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1303)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1292)
        at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53)
Caused by: java.lang.IllegalArgumentException: Parent '0' not found for individual 'father'
        at org.monarchinitiative.exomiser.core.model.Pedigree.checkParent(Pedigree.java:73)
        at org.monarchinitiative.exomiser.core.model.Pedigree.validate(Pedigree.java:61)
        at org.monarchinitiative.exomiser.core.model.Pedigree.<init>(Pedigree.java:51)
        at org.monarchinitiative.exomiser.core.model.Pedigree.of(Pedigree.java:83)
        at org.monarchinitiative.exomiser.core.analysis.sample.PhenopacketPedigreeConverter.toExomiserPedigree(PhenopacketPedigr
eeConverter.java:56)
        at org.monarchinitiative.exomiser.core.analysis.sample.PhenopacketSampleConverter.findFamilyOrProbandOnlyPedigree(Phenop
acketSampleConverter.java:65)
        at org.monarchinitiative.exomiser.core.analysis.sample.PhenopacketSampleConverter.toExomiserSample(PhenopacketSampleConv
erter.java:49)
        at org.monarchinitiative.exomiser.core.analysis.sample.PhenopacketConverter.toSample(PhenopacketConverter.java:40)
        at org.monarchinitiative.exomiser.core.analysis.sample.Sample.from(Sample.java:56)
        at org.monarchinitiative.exomiser.core.analysis.JobParser.getSample(JobParser.java:120)
        at org.monarchinitiative.exomiser.core.analysis.JobParser.parseSample(JobParser.java:85)
        at org.monarchinitiative.exomiser.core.analysis.AnalysisParser.parseSample(AnalysisParser.java:99)
        at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:67)
        at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJob(ExomiserCommandLineRunner.java:79)
        at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJobs(ExomiserCommandLineRunner.java:62)
        at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:57)
        at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:768)
        ... 5 common frames omitted

Example entry that triggers the above error:

pedigree:
  persons:
    - familyId: 1234
      individualId: father
      paternalId: '0'
      maternalId: '0'
      sex: MALE
      affectedStatus: UNAFFECTED

According to the Phenopacket schema v1.0.0:

Individuals whose parents are not represented in the PED file are known as founders; their parents are represented by a zero (“0”) in the columns for mother and father.

I would therefore expect '0' to be a valid empty value.

As a workaround, I'm now omitting the fields paternalId and maternalId similar to the example provided in Phenopacket's documentation and Exomiser would not throw error. This is in fact does not conform to Phenopacket schema neither as both fields are "required".

I guess validating strictly according to Phenopacket schema (i.e. making paternalId and maternalId required) may break the practice/script/pipeline of existing Exomiser users. However, supporting string value of 0 should be acceptable.