Issue 17611
checklist imports fail - verbatim usage exceptions
17611
Reporter: mdoering
Assignee: mdoering
Type: Bug
Summary: checklist imports fail - verbatim usage exceptions
Priority: Minor
Resolution: Fixed
Status: Closed
Created: 2015-06-02 16:11:44.398
Updated: 2015-06-08 15:10:48.829
Resolved: 2015-06-08 15:10:48.805
Description: INFO [2015-06-02 15:57:46,460+0200] [pool-10-thread-2] org.gbif.checklistbank.cli.importer.Importer: Start importing checklist 80b4b440-eaca-4860-aadf-d0dfdd3e856e
INFO [2015-06-02 15:57:47,525+0200] [pool-10-thread-2] org.gbif.checklistbank.cli.common.NeoConfiguration: Starting embedded neo4j database from /home/crap/neo/80b4b440-eaca-4860-aadf-d0dfdd3e856e
INFO [2015-06-02 15:57:49,067+0200] [pool-10-thread-2] org.gbif.checklistbank.cli.importer.Importer: First synced usage key for dataset 80b4b440-eaca-4860-aadf-d0dfdd3e856e is 143141905
INFO [2015-06-02 15:58:30,185+0200] [pool-10-thread-3] org.gbif.checklistbank.cli.importer.Importer: Start importing checklist 9e11f45e-f496-42e5-a1a6-9415907a3717
INFO [2015-06-02 15:58:30,294+0200] [pool-10-thread-3] org.gbif.checklistbank.cli.common.NeoConfiguration: Starting embedded neo4j database from /home/crap/neo/9e11f45e-f496-42e5-a1a6-9415907a3717
INFO [2015-06-02 15:58:30,320+0200] [pool-10-thread-3] org.gbif.checklistbank.cli.importer.Importer: First synced usage key for dataset 9e11f45e-f496-42e5-a1a6-9415907a3717 is 143144329
ERROR [2015-06-02 15:58:41,696+0200] [pool-10-thread-2] org.gbif.checklistbank.cli.importer.Importer: Failed to sync Periclimenes Costa taxonID '9363' from dataset 80b4b440-eaca-4860-aadf-d0dfdd3e856e
ERROR [2015-06-02 15:58:41,696+0200] [pool-10-thread-3] org.gbif.checklistbank.cli.importer.Importer: Failed to sync Hemigrammus barrigonae Eigenmann & Henn, 1914 taxonID 'urn:lsid:catalogueoflife.org:taxon:2c131000-4661-11e1-9b0d-e752e483e0da:col20120124' from dataset 9e11f45e-f496-42e5-a1a6-9415907a3717
ERROR [2015-06-02 15:58:41,696+0200] [pool-10-thread-2] org.gbif.checklistbank.cli.importer.Importer: Aborting sync of dataset 80b4b440-eaca-4860-aadf-d0dfdd3e856e
ERROR [2015-06-02 15:58:41,696+0200] [pool-10-thread-3] org.gbif.checklistbank.cli.importer.Importer: Aborting sync of dataset 9e11f45e-f496-42e5-a1a6-9415907a3717
ERROR [2015-06-02 15:58:41,712+0200] [pool-10-thread-2] org.gbif.checklistbank.cli.common.RabbitBaseService: Failed to process dataset 80b4b440-eaca-4860-aadf-d0dfdd3e856e
java.lang.ArrayIndexOutOfBoundsException: -1
at com.esotericsoftware.kryo.util.IntArray.pop(IntArray.java:175) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at com.esotericsoftware.kryo.Kryo.reference(Kryo.java:848) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:553) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:683) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.utils.VerbatimNameUsageMapperKryo.read(VerbatimNameUsageMapperKryo.java:68) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.neo.NeoMapper.readVerbatim(NeoMapper.java:351) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.importer.Importer.syncDataset(Importer.java:90) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.importer.Importer.run(Importer.java:69) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.importer.ImporterService.process(ImporterService.java:57) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.importer.ImporterService.process(ImporterService.java:26) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.common.RabbitBaseService.handleMessage(RabbitBaseService.java:96) [checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.common.RabbitBaseService.handleMessage(RabbitBaseService.java:27) [checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.common.messaging.MessageConsumer.handleCallback(MessageConsumer.java:101) [checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.common.messaging.MessageConsumer.handleDelivery(MessageConsumer.java:65) [checklistbank-cli.jar:2.16-SNAPSHOT]
at com.rabbitmq.client.impl.ConsumerDispatcher$4.run(ConsumerDispatcher.java:121) [checklistbank-cli.jar:2.16-SNAPSHOT]
at com.rabbitmq.client.impl.ConsumerWorkService$WorkPoolRunnable.run(ConsumerWorkService.java:76) [checklistbank-cli.jar:2.16-SNAPSHOT]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_75]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_75]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_75]
ERROR [2015-06-02 15:58:41,712+0200] [pool-10-thread-3] org.gbif.checklistbank.cli.common.RabbitBaseService: Failed to process dataset 9e11f45e-f496-42e5-a1a6-9415907a3717
com.esotericsoftware.kryo.KryoException: java.lang.ArrayIndexOutOfBoundsException: -1
Serialization trace:
extensions (org.gbif.api.model.checklistbank.VerbatimNameUsage)
at com.esotericsoftware.kryo.serializers.ObjectField.read(ObjectField.java:144) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:557) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:683) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.utils.VerbatimNameUsageMapperKryo.read(VerbatimNameUsageMapperKryo.java:68) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.neo.NeoMapper.readVerbatim(NeoMapper.java:351) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.importer.Importer.syncDataset(Importer.java:90) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.importer.Importer.run(Importer.java:69) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.importer.ImporterService.process(ImporterService.java:57) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.importer.ImporterService.process(ImporterService.java:26) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.common.RabbitBaseService.handleMessage(RabbitBaseService.java:96) [checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.checklistbank.cli.common.RabbitBaseService.handleMessage(RabbitBaseService.java:27) [checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.common.messaging.MessageConsumer.handleCallback(MessageConsumer.java:101) [checklistbank-cli.jar:2.16-SNAPSHOT]
at org.gbif.common.messaging.MessageConsumer.handleDelivery(MessageConsumer.java:65) [checklistbank-cli.jar:2.16-SNAPSHOT]
at com.rabbitmq.client.impl.ConsumerDispatcher$4.run(ConsumerDispatcher.java:121) [checklistbank-cli.jar:2.16-SNAPSHOT]
at com.rabbitmq.client.impl.ConsumerWorkService$WorkPoolRunnable.run(ConsumerWorkService.java:76) [checklistbank-cli.jar:2.16-SNAPSHOT]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_75]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_75]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_75]
Caused by: java.lang.ArrayIndexOutOfBoundsException: -1
at com.esotericsoftware.kryo.util.IntArray.add(IntArray.java:79) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at com.esotericsoftware.kryo.Kryo.readReferenceOrNull(Kryo.java:826) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:703) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
at com.esotericsoftware.kryo.serializers.ObjectField.read(ObjectField.java:125) ~[checklistbank-cli.jar:2.16-SNAPSHOT]
... 17 common frames omitted
^C
[crap@bla6 logs]$
]]>
Author: mdoering@gbif.org
Comment: Looks like a bad deploy issue. All tests and local imports run fine
Created: 2015-06-02 17:26:58.577
Updated: 2015-06-02 17:26:58.577
Author: mdoering@gbif.org
Comment: kryo threading problem https://github.com/gbif/checklistbank/commit/02b33ee1959dcae5bd5563adc5c62177ea40c2b2
Created: 2015-06-08 15:10:48.826
Updated: 2015-06-08 15:10:48.826