Comments (3)
kltm
commented on September 12, 2024
1
@vanaukenk It looks like the diff is done, but no changes?
from noctua.
vanaukenk
commented on September 12, 2024
Yes, thanks @kltm - I noticed our empty diff.
Looking over ontology work since the 8th, however, this seems to make sense.
from noctua.
kltm
commented on September 12, 2024
"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.
from noctua.
Related Issues (20)
- can import PRO entities, but annotations are not associated
- Cannot import existing MF annotation HOT 3
- Ability to edit exisiting activity units without deleting and recreating HOT 4
- Existing term not available in Noctua HOT 1
- 2024-07-11 HOT 5
- annotate a MF activity unit on a specific sub-part of a complex HOT 10
- Disappearing URS HOT 4
- Pathway collapsed into a single position HOT 2
- 2024-07-25 HOT 4
- Auto import has_part entities for complexes
- Large numbers of entities are not exporting to the API HOT 11
- 2024-08-08 HOT 5
- Ability to distingush "unknown" steps from "constitutively upstream" HOT 4
- Abiity to add 'during' phase to a model HOT 3
- Question: can't locate complexes specified in our GPI HOT 12
- Question: Will new gene names be picked up by Noctua automatically
- 2024-09-12 HOT 5
- Annotatable entities should all be findable in the same search box
- 2024-09-26
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from noctua.