ort: Reference file is wrong on option analyzer/skipExcluded

Here’s some more context from the log:

Writing analyzer result to '/output/analyzer-result.json'.
14:26:15.280 [main] INFO  org.ossreviewtoolkit.cli.commands.AnalyzerCommand - Wrote ORT result to 'analyzer-result.json' (0.30 MiB) in 449.990072ms.
The analysis took 26.618897436s.
Found 2 project(s) and 223 package(s) in total (not counting excluded ones).
Applied 0 curation(s) from 3 provider(s).
Resolved issues: 0 errors, 0 warnings, 0 hints.
Unresolved issues: 0 errors, 1 warning, 0 hints.

real	0m31.670s
user	0m0.063s
sys	0m0.069s
* Finish analyzer at 2023-02-16 14:26

* Updating .ort.yml file at [/ort/eclipsefdn-ort/conf/repositories/ecd.che/che/].
Exception in thread "main" com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException: Unrecognized field "skip_excluded" (class org.ossreviewtoolkit.model.config.AnalyzerConfiguration), not marked as ignorable (5 known properties: "sw360_configuration", "allow_dynamic_versions", "disabled_package_managers", "enabled_package_managers", "package_managers"])
 at [Source: (File); line: 57, column: 6] (through reference chain: org.ossreviewtoolkit.model.OrtResult["analyzer"]->org.ossreviewtoolkit.model.AnalyzerRun["config"]->org.ossreviewtoolkit.model.config.AnalyzerConfiguration["skip_excluded"])
	at com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException.from(UnrecognizedPropertyException.java:61)
	at com.fasterxml.jackson.databind.DeserializationContext.handleUnknownProperty(DeserializationContext.java:1127)
	at com.fasterxml.jackson.databind.deser.std.StdDeserializer.handleUnknownProperty(StdDeserializer.java:2023)
	at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.handleUnknownProperty(BeanDeserializerBase.java:1700)
	at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.handleUnknownProperties(BeanDeserializerBase.java:1650)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeUsingPropertyBased(BeanDeserializer.java:540)
	at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.deserializeFromObjectUsingNonDefault(BeanDeserializerBase.java:1405)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserializeFromObject(BeanDeserializer.java:352)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:185)
	at com.fasterxml.jackson.databind.deser.SettableBeanProperty.deserialize(SettableBeanProperty.java:542)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeWithErrorWrapping(BeanDeserializer.java:564)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeUsingPropertyBased(BeanDeserializer.java:439)
	at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.deserializeFromObjectUsingNonDefault(BeanDeserializerBase.java:1405)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserializeFromObject(BeanDeserializer.java:352)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:185)
	at com.fasterxml.jackson.databind.deser.SettableBeanProperty.deserialize(SettableBeanProperty.java:542)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeWithErrorWrapping(BeanDeserializer.java:564)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer._deserializeUsingPropertyBased(BeanDeserializer.java:439)
	at com.fasterxml.jackson.databind.deser.BeanDeserializerBase.deserializeFromObjectUsingNonDefault(BeanDeserializerBase.java:1405)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserializeFromObject(BeanDeserializer.java:352)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:185)
	at com.fasterxml.jackson.databind.deser.DefaultDeserializationContext.readRootValue(DefaultDeserializationContext.java:323)
	at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4674)
	at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3514)
	at org.ossreviewtoolkit.helper.utils.UtilsKt.readOrtResult(Utils.kt:367)
	at org.ossreviewtoolkit.helper.commands.repoconfig.GenerateScopeExcludesCommand.run(GenerateScopeExcludesCommand.kt:61)
	at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:198)
	at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:211)
	at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:211)
	at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:18)
	at com.github.ajalt.clikt.core.CliktCommand.parse(CliktCommand.kt:400)
	at com.github.ajalt.clikt.core.CliktCommand.parse$default(CliktCommand.kt:397)
	at com.github.ajalt.clikt.core.CliktCommand.main(CliktCommand.kt:415)
	at com.github.ajalt.clikt.core.CliktCommand.main(CliktCommand.kt:440)
	at org.ossreviewtoolkit.helper.HelperMainKt.main(HelperMain.kt:67)

* Start scanner at 2023-02-16 14:26
docker run -v /data/results/ecd.che/che/202302161425:/output -v /data/cache/ort/:/ort_cache/ -v /ort/eclipsefdn-ort/conf:/home/ort/.ort/config/ --rm -e JAVA_OPTS=-Xmx10g --env-file /ort/eclipsefdn-ort/run_env.txt ort --info scan -f JSON --scanners ScanCode -i /output/analyzer-result.json -o /output

So the UnrecognizedPropertyException occurs after writing the analyzer result but before running the scanner. Apparently you’re running the GenerateScopeExcludesCommand from the helper-cli in between, and for some reason is does not seem to cope with the new AnalyzerConfiguration. Can it be that your helper-cli build is older than the cli build?

Yes, unless you’re explicitly using UploadResultToPostgresCommand, analyzer results don’t end up in the DB, and the DB does not have to be reinitialized.

$ docker run ort --version
eb34b0dd11-dirty

Which AFAICT was committed yesterday.