Stream: implementers
Topic: java validator bugs?
Patrick Werner (Jun 12 2019 at 13:18):
1. When validating a whole folder each file should be validated if it is a valid resource. I just tested it and had some tsv(csv) files in the folder and got:
[Fatal Error] :1:1: Content is not allowed in prolog.
.. not a resource: ./12345_789_somatic_snv.tsv
Exception in thread "main" java.lang.Exception: Unable to find/resolve/read -ig ./12345_789_somatic_snv.tsv
at org.hl7.fhir.r5.validation.ValidationEngine.loadIgSource(ValidationEngine.java:446)
at org.hl7.fhir.r5.validation.ValidationEngine.loadContent(ValidationEngine.java:780)
at org.hl7.fhir.r5.validation.ValidationEngine.validate(ValidationEngine.java:812)
at org.hl7.fhir.r5.validation.Validator.main(Validator.java:436)
2. I also get a stack trace on syntax errors:
Exception in thread "main" org.hl7.fhir.exceptions.FHIRException: Unable to find type Count for element valueCount with path Observation.component.value[x]
at org.hl7.fhir.r5.elementmodel.Property.getChildProperties(Property.java:309)
at org.hl7.fhir.r5.elementmodel.XmlParser.parseChildren(XmlParser.java:241)
at org.hl7.fhir.r5.elementmodel.XmlParser.parseChildren(XmlParser.java:317)
at org.hl7.fhir.r5.elementmodel.XmlParser.parseChildren(XmlParser.java:317)
at org.hl7.fhir.r5.elementmodel.XmlParser.parse(XmlParser.java:178)
at org.hl7.fhir.r5.elementmodel.XmlParser.parse(XmlParser.java:162)
at org.hl7.fhir.r5.elementmodel.XmlParser.parse(XmlParser.java:134)
at org.hl7.fhir.r5.validation.InstanceValidator.validate(InstanceValidator.java:586)
at org.hl7.fhir.r5.validation.ValidationEngine.validate(ValidationEngine.java:902)
at org.hl7.fhir.r5.validation.ValidationEngine.validate(ValidationEngine.java:816)
at org.hl7.fhir.r5.validation.Validator.main(Validator.java:436)
it would be better to catch these, report the error and continue with the validation
Patrick Werner (Jun 12 2019 at 13:30):
3.: for every example file i get:
error: Read off end of file: 4642092 / 2147483596:7
Grahame Grieve (Jun 12 2019 at 13:35):
the first error is - I try to read unknown files in case they are resources, and the xml library generates that log message internally
Grahame Grieve (Jun 12 2019 at 13:36):
I don't know what's with the second or third - can I reproduce?
Patrick Werner (Jun 18 2019 at 12:19):
error 1: the validator exits after the stacktrace, would be nice to catch that parser exception
error 2: Observation doesn't allow valueCount which was used here
error 3: i've attached the example causing the error NGS_ObsVariant_SNV_12345_009_FGFR1.xml
Patrick Werner (Jun 18 2019 at 12:21):
validated with latest java validator: "java -jar ~/Downloads/org.hl7.fhir.validator.jar . -version 4.0.0"
Patrick Werner (Jun 18 2019 at 14:10):
Found another improvable Error message:
Element 'Observation.component[10].valueCodeableConcept.system': minimum required = 1, but only found 0
Here the profile constrains component.value[x] to Quantity, the validator doesn't recognize the wrong data type.
Last updated: Apr 12 2022 at 19:14 UTC
