2024-08-22

[kltm]

• [x] Send reminder email to go-consortium mailing list
• [x] Run noctua-models-migration pipeline for (@vanaukenk) (automated to day before) to get report
  http://skyhook.berkeleybop.org/noctua-models-migrations/reports/
• [x] Refresh minerva code with latest from minerva master
• [ ] Run replaced_by term update on blazegraph (@vanaukenk)
• [x] Cycle minerva to get latest ontology
• [x] Update NEO
• [x] Prep ticket for next outage

[kltm]

@vanaukenk It looks like the diff is done, but no changes?

[vanaukenk]

Yes, thanks @kltm - I noticed our empty diff. Looking over ontology work since the 8th, however, this seems to make sense.

[kltm]

"Run replaced_by term update on blazegraph" item failed.

SOP command

cd ~/local/src/git/noctua && time java -Xmx8G -jar ../minerva/minerva-cli/bin/minerva-cli.jar --dump-owl-models -j /tmp/blazegraph.jnl -f ~/local/src/git/noctua-models/models/

Failed with:

2024-08-22 16:51:16,543 WARN  (com.bigdata.rdf.ServiceProviderHook:171) Running.
2024-08-22 16:51:16,543 WARN  (com.bigdata.rdf.ServiceProviderHook:171) Running.
2024-08-22 16:51:23,586 WARN  (com.bigdata.rdf.lexicon.ResolveBlobsTask:109) No such term: BlobIV(-665520983:0:L)
2024-08-22 16:51:23,586 WARN  (com.bigdata.rdf.lexicon.ResolveBlobsTask:109) No such term: BlobIV(-665520983:0:L)
2024-08-22 16:51:23,597 ERROR (com.bigdata.relation.accesspath.BlockingBuffer:1517) java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.IllegalArgumentException
java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.IllegalArgumentException
    at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:?]
    at java.util.concurrent.FutureTask.get(FutureTask.java:191) ~[?:?]
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454) [minerva-cli.jar:?]
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710) [minerva-cli.jar:?]
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563) [minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365) [minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341) [minerva-cli.jar:?]
    at cutthecrap.utils.striterators.Striterator.hasNext(Striterator.java:89) [minerva-cli.jar:?]
    at com.bigdata.striterator.CloseableIteratorWrapper.hasNext(CloseableIteratorWrapper.java:69) [minerva-cli.jar:?]
    at com.bigdata.rdf.sail.Bigdata2SesameIteration.hasNext(Bigdata2SesameIteration.java:78) [minerva-cli.jar:?]
    at info.aduna.iteration.ExceptionConvertingIteration.hasNext(ExceptionConvertingIteration.java:78) [minerva-cli.jar:?]
    at org.openrdf.repository.RepositoryResult.hasNext(RepositoryResult.java:66) [minerva-cli.jar:?]
    at org.openrdf.repository.sail.SailRepositoryConnection.exportStatements(SailRepositoryConnection.java:254) [minerva-cli.jar:?]
    at org.openrdf.repository.base.RepositoryConnectionBase.export(RepositoryConnectionBase.java:173) [minerva-cli.jar:?]
    at org.geneontology.minerva.BlazegraphMolecularModelManager.dumpStoredModel(BlazegraphMolecularModelManager.java:812) [minerva-cli.jar:?]
    at org.geneontology.minerva.BlazegraphMolecularModelManager.dumpAllStoredModels(BlazegraphMolecularModelManager.java:769) [minerva-cli.jar:?]
    at org.geneontology.minerva.cli.CommandLineInterface.modelsToOWL(CommandLineInterface.java:455) [minerva-cli.jar:?]
    at org.geneontology.minerva.cli.CommandLineInterface.main(CommandLineInterface.java:225) [minerva-cli.jar:?]
Caused by: java.lang.RuntimeException: java.lang.IllegalArgumentException
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:260) ~[minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197) ~[minerva-cli.jar:?]
    at java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[?:?]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[?:?]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[?:?]
    at java.lang.Thread.run(Thread.java:829) ~[?:?]
Caused by: java.lang.IllegalArgumentException
    at com.bigdata.rdf.model.BigdataStatementImpl.<init>(BigdataStatementImpl.java:88) ~[minerva-cli.jar:?]
    at com.bigdata.rdf.model.BigdataValueFactoryImpl.createStatement(BigdataValueFactoryImpl.java:619) ~[minerva-cli.jar:?]
    at com.bigdata.rdf.model.BigdataValueFactoryImpl.createStatement(BigdataValueFactoryImpl.java:71) ~[minerva-cli.jar:?]
    at com.bigdata.rdf.store.BigdataStatementIteratorImpl.resolveChunk(BigdataStatementIteratorImpl.java:226) ~[minerva-cli.jar:?]
    at com.bigdata.rdf.store.BigdataStatementIteratorImpl.resolveChunk(BigdataStatementIteratorImpl.java:33) ~[minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:241) ~[minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197) ~[minerva-cli.jar:?]
    at java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[?:?]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[?:?]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[?:?]
    at java.lang.Thread.run(Thread.java:829) ~[?:?]
2024-08-22 16:51:23,597 ERROR (com.bigdata.relation.accesspath.BlockingBuffer:1517) java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.IllegalArgumentException
java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.IllegalArgumentException
    at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:?]
    at java.util.concurrent.FutureTask.get(FutureTask.java:191) ~[?:?]
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454) [minerva-cli.jar:?]
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710) [minerva-cli.jar:?]
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563) [minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365) [minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341) [minerva-cli.jar:?]
    at cutthecrap.utils.striterators.Striterator.hasNext(Striterator.java:89) [minerva-cli.jar:?]
    at com.bigdata.striterator.CloseableIteratorWrapper.hasNext(CloseableIteratorWrapper.java:69) [minerva-cli.jar:?]
    at com.bigdata.rdf.sail.Bigdata2SesameIteration.hasNext(Bigdata2SesameIteration.java:78) [minerva-cli.jar:?]
    at info.aduna.iteration.ExceptionConvertingIteration.hasNext(ExceptionConvertingIteration.java:78) [minerva-cli.jar:?]
    at org.openrdf.repository.RepositoryResult.hasNext(RepositoryResult.java:66) [minerva-cli.jar:?]
    at org.openrdf.repository.sail.SailRepositoryConnection.exportStatements(SailRepositoryConnection.java:254) [minerva-cli.jar:?]
    at org.openrdf.repository.base.RepositoryConnectionBase.export(RepositoryConnectionBase.java:173) [minerva-cli.jar:?]
    at org.geneontology.minerva.BlazegraphMolecularModelManager.dumpStoredModel(BlazegraphMolecularModelManager.java:812) [minerva-cli.jar:?]
    at org.geneontology.minerva.BlazegraphMolecularModelManager.dumpAllStoredModels(BlazegraphMolecularModelManager.java:769) [minerva-cli.jar:?]
    at org.geneontology.minerva.cli.CommandLineInterface.modelsToOWL(CommandLineInterface.java:455) [minerva-cli.jar:?]
    at org.geneontology.minerva.cli.CommandLineInterface.main(CommandLineInterface.java:225) [minerva-cli.jar:?]
Caused by: java.lang.RuntimeException: java.lang.IllegalArgumentException
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:260) ~[minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197) ~[minerva-cli.jar:?]
    at java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[?:?]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[?:?]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[?:?]
    at java.lang.Thread.run(Thread.java:829) ~[?:?]
Caused by: java.lang.IllegalArgumentException
    at com.bigdata.rdf.model.BigdataStatementImpl.<init>(BigdataStatementImpl.java:88) ~[minerva-cli.jar:?]
    at com.bigdata.rdf.model.BigdataValueFactoryImpl.createStatement(BigdataValueFactoryImpl.java:619) ~[minerva-cli.jar:?]
    at com.bigdata.rdf.model.BigdataValueFactoryImpl.createStatement(BigdataValueFactoryImpl.java:71) ~[minerva-cli.jar:?]
    at com.bigdata.rdf.store.BigdataStatementIteratorImpl.resolveChunk(BigdataStatementIteratorImpl.java:226) ~[minerva-cli.jar:?]
    at com.bigdata.rdf.store.BigdataStatementIteratorImpl.resolveChunk(BigdataStatementIteratorImpl.java:33) ~[minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:241) ~[minerva-cli.jar:?]
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197) ~[minerva-cli.jar:?]
    at java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[?:?]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[?:?]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[?:?]
    at java.lang.Thread.run(Thread.java:829) ~[?:?]
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.IllegalArgumentException
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
    at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
    at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
    at cutthecrap.utils.striterators.Striterator.hasNext(Striterator.java:89)
    at com.bigdata.striterator.CloseableIteratorWrapper.hasNext(CloseableIteratorWrapper.java:69)
    at com.bigdata.rdf.sail.Bigdata2SesameIteration.hasNext(Bigdata2SesameIteration.java:78)
    at info.aduna.iteration.ExceptionConvertingIteration.hasNext(ExceptionConvertingIteration.java:78)
    at org.openrdf.repository.RepositoryResult.hasNext(RepositoryResult.java:66)
    at org.openrdf.repository.sail.SailRepositoryConnection.exportStatements(SailRepositoryConnection.java:254)
    at org.openrdf.repository.base.RepositoryConnectionBase.export(RepositoryConnectionBase.java:173)
    at org.geneontology.minerva.BlazegraphMolecularModelManager.dumpStoredModel(BlazegraphMolecularModelManager.java:812)
    at org.geneontology.minerva.BlazegraphMolecularModelManager.dumpAllStoredModels(BlazegraphMolecularModelManager.java:769)
    at org.geneontology.minerva.cli.CommandLineInterface.modelsToOWL(CommandLineInterface.java:455)
    at org.geneontology.minerva.cli.CommandLineInterface.main(CommandLineInterface.java:225)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.IllegalArgumentException
    at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
    at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
    ... 15 more
Caused by: java.lang.RuntimeException: java.lang.IllegalArgumentException
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:260)
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.lang.IllegalArgumentException
    at com.bigdata.rdf.model.BigdataStatementImpl.<init>(BigdataStatementImpl.java:88)
    at com.bigdata.rdf.model.BigdataValueFactoryImpl.createStatement(BigdataValueFactoryImpl.java:619)
    at com.bigdata.rdf.model.BigdataValueFactoryImpl.createStatement(BigdataValueFactoryImpl.java:71)
    at com.bigdata.rdf.store.BigdataStatementIteratorImpl.resolveChunk(BigdataStatementIteratorImpl.java:226)
    at com.bigdata.rdf.store.BigdataStatementIteratorImpl.resolveChunk(BigdataStatementIteratorImpl.java:33)
    at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:241)
    ... 5 more

real    0m8.908s
user    0m21.474s
sys 0m1.359s

Restarting as-is on production filesystem.