Import of zarr into OMERO merge-ci latest-ci

[pwalczysko]

On both merge-ci (on idr2-slot3) and latest-ci (on idr1-slot2), the import of ome.zarr files fails with the error below. The files were imported previously into OMERO successfully using the same servers and envs.

export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
source /home/omero/workspace/OMERO-server/.venv3/bin/activate
(.venv3) bash-4.2$ pwd
/uod/idr-scratch/petr-test/sub-resolutions
(.venv3) bash-4.2$ omero import --transfer=ln_s --skip=checksum --parallel-upload=10 -T Dataset:name:test-zarr LuCa-7color_Scan1.ome.zarr/ --depth=10

causes the following error reports (the error repeats several times, probably extra error for each subfolder of the ome.zarr)

``` 2022-08-05 09:07:17,137 40610 [ main] ERROR ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/sub-resolutions/LuCa-7color_Scan1.ome.zarr/0/2/0/3/0/4/0 java.lang.Exception: java.lang.NoClassDefFoundError: com/fasterxml/jackson/annotation/JsonKey at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:469) at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576) at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387) at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384) at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384) at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384) at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384) at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384) at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384) at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355) at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(CommandLineImporter.java:148) at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997) Caused by: java.lang.NoClassDefFoundError: com/fasterxml/jackson/annotation/JsonKey at com.fasterxml.jackson.databind.introspect.JacksonAnnotationIntrospector.hasAsKey(JacksonAnnotationIntrospector.java:1080) at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:495) at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:421) at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getPropertyMap(POJOPropertiesCollector.java:386) at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getProperties(POJOPropertiesCollector.java:233) at com.fasterxml.jackson.databind.introspect.BasicBeanDescription._properties(BasicBeanDescription.java:164) at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findProperties(BasicBeanDescription.java:239) at com.fasterxml.jackson.databind.deser.BasicDeserializerFactory._findCreatorsFromProperties(BasicDeserializerFactory.java:328) at com.fasterxml.jackson.databind.deser.BasicDeserializerFactory._constructDefaultValueInstantiator(BasicDeserializerFactory.java:272) at com.fasterxml.jackson.databind.deser.BasicDeserializerFactory.findValueInstantiator(BasicDeserializerFactory.java:223) at com.fasterxml.jackson.databind.deser.BeanDeserializerFactory.buildBeanDeserializer(BeanDeserializerFactory.java:261) at com.fasterxml.jackson.databind.deser.BeanDeserializerFactory.createBeanDeserializer(BeanDeserializerFactory.java:150) at com.fasterxml.jackson.databind.deser.DeserializerCache._createDeserializer2(DeserializerCache.java:414) at com.fasterxml.jackson.databind.deser.DeserializerCache._createDeserializer(DeserializerCache.java:349) at com.fasterxml.jackson.databind.deser.DeserializerCache._createAndCache2(DeserializerCache.java:264) at com.fasterxml.jackson.databind.deser.DeserializerCache._createAndCacheValueDeserializer(DeserializerCache.java:244) at com.fasterxml.jackson.databind.deser.DeserializerCache.findValueDeserializer(DeserializerCache.java:142) at com.fasterxml.jackson.databind.DeserializationContext.findRootValueDeserializer(DeserializationContext.java:591) at com.fasterxml.jackson.databind.ObjectMapper._findRootDeserializer(ObjectMapper.java:4733) at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4594) at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3561) at com.bc.zarr.ZarrUtils.fromJson(ZarrUtils.java:113) at com.bc.zarr.ZarrGroup.ensureZarrFormatIs2(ZarrGroup.java:120) at com.bc.zarr.ZarrGroup.validateGroupToBeOpened(ZarrGroup.java:111) at com.bc.zarr.ZarrGroup.open(ZarrGroup.java:102) at com.bc.zarr.ZarrGroup.open(ZarrGroup.java:95) at com.bc.zarr.ZarrGroup.open(ZarrGroup.java:87) at loci.formats.services.JZarrServiceImpl.getGroupAttr(JZarrServiceImpl.java:104) at loci.formats.in.ZarrReader.initFile(ZarrReader.java:164) at loci.formats.FormatReader.setId(FormatReader.java:1443) at loci.formats.ImageReader.setId(ImageReader.java:849) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) at loci.formats.ChannelFiller.setId(ChannelFiller.java:234) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) at loci.formats.Memoizer.setId(Memoizer.java:662) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427) ... 14 common frames omitted Caused by: java.lang.ClassNotFoundException: com.fasterxml.jackson.annotation.JsonKey at java.net.URLClassLoader.findClass(URLClassLoader.java:382) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 54 common frames omitted ```

cc @joshmoore @sbesson @dgault

[joshmoore]

When did it start, @pwalczysko? Do all files fail now?

[pwalczysko]

When did it start, @pwalczysko?

Detected during last week, say, Thursday or Wednesday. Not sure when did it start, could have started during my AL or even before, even June 2022 would be plausible.

Do all files fail now?

Yes, all ome.zarr files I tried, not only the ones I have created with bf2raw, but also the ones from the history of the bash on merge-ci, the same error. The error shows itself also with import -f.

[pwalczysko]

This seems to be fixed on merge-ci now, see user-3 https://merge-ci.openmicroscopy.org/web/webclient/?show=dataset-58969 for reimports.

[sbesson]

Is it okay to mark this as resolved? We might need to include this workflow in the functional tests ahead of the upcoming OMERO.server relases. /cc @jburel