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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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Problem parsing phenopacket #455

Closed justaddcoffee closed 4 years ago

justaddcoffee commented 4 years ago

Problem parsing a phenopacket from the wild: Willoughby-2018-WDR45-proband.txt

Possibly the problematic field datasetId is illegal, but we should probably recover gracefully if possible. 

/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/bin/java -Dfile.encoding=UTF-8 -jar /Users/jtr4v/IdeaProjects/LIRICAL/target/LIRICAL.jar phenopacket -p /Users/jtr4v/IdeaProjects/LIRICAL/example_data/pps/splicing/Willoughby-2018-WDR45-proband.json -o /Users/jtr4v/IdeaProjects/LIRICAL/example_data/output/ -x Willoughby-2018-WDR45-proband
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/jtr4v/IdeaProjects/LIRICAL/target/LIRICAL.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/Users/jtr4v/IdeaProjects/LIRICAL/target/lib/log4j-slf4j-impl-2.12.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.apache.logging.slf4j.Log4jLoggerFactory]
com.google.protobuf.InvalidProtocolBufferException: Cannot find field: datasetId in message org.phenopackets.schema.v1.core.Individual
    at com.google.protobuf.util.JsonFormat$ParserImpl.mergeMessage(JsonFormat.java:1417)
    at com.google.protobuf.util.JsonFormat$ParserImpl.merge(JsonFormat.java:1377)
    at com.google.protobuf.util.JsonFormat$ParserImpl.parseFieldValue(JsonFormat.java:1896)
    at com.google.protobuf.util.JsonFormat$ParserImpl.mergeField(JsonFormat.java:1587)
    at com.google.protobuf.util.JsonFormat$ParserImpl.mergeMessage(JsonFormat.java:1419)
    at com.google.protobuf.util.JsonFormat$ParserImpl.merge(JsonFormat.java:1377)
    at com.google.protobuf.util.JsonFormat$ParserImpl.merge(JsonFormat.java:1259)
    at com.google.protobuf.util.JsonFormat$Parser.merge(JsonFormat.java:407)
    at org.monarchinitiative.lirical.io.PhenopacketImporter.fromJson(PhenopacketImporter.java:60)
    at org.monarchinitiative.lirical.cmd.PhenopacketCommand.run(PhenopacketCommand.java:180)
    at org.monarchinitiative.lirical.Lirical.main(Lirical.java:149)
Exception in thread "main" org.monarchinitiative.lirical.exception.LiricalRuntimeException: Could not load phenopacket at /Users/jtr4v/IdeaProjects/LIRICAL/example_data/pps/splicing/Willoughby-2018-WDR45-proband.json
    at org.monarchinitiative.lirical.io.PhenopacketImporter.fromJson(PhenopacketImporter.java:65)
    at org.monarchinitiative.lirical.cmd.PhenopacketCommand.run(PhenopacketCommand.java:180)
    at org.monarchinitiative.lirical.Lirical.main(Lirical.java:149)

Process finished with exit code 1