Thank you Andy!
Unfortunately, the cause is still unclear to me; could someone help me to
decipher this :
Thank you very much, in advance!
08:18:21 INFO Fuseki :: [1587] 200 OK (24 ms)
08:18:29 INFO Admin :: [1588] Compact dataset /iremus
08:18:29 INFO Server :: Task : 9 : Compact
08:18:29 INFO Server :: [Task 9] starts : Compact
08:18:29 INFO Compact :: [1588] >>>> Start compact /iremus
08:18:30 WARN Compact :: [1588] **** Exception in compact
org.apache.jena.tdb2.TDBException: NodeTableTRDF/Read
at
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:102)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:52)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:208)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:133)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:52)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:65)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:107)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:103)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:52)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.atlas.iterator.Iter$IterMap.lambda$forEachRemaining$0(Iter.java:432)
~[fuseki-server.jar:5.0.0]
at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]
at org.apache.jena.atlas.iterator.Iter$IterMap.forEachRemaining(Iter.java:432)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.atlas.iterator.IteratorWrapper.forEachRemaining(IteratorWrapper.java:52)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.CopyDSG.lambda$copy$0(CopyDSG.java:38)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.system.Txn.exec(Txn.java:77) ~[fuseki-server.jar:5.0.0]
at org.apache.jena.system.Txn.executeWrite(Txn.java:125)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.CopyDSG.lambda$copy$1(CopyDSG.java:36)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.system.Txn.exec(Txn.java:77) ~[fuseki-server.jar:5.0.0]
at org.apache.jena.system.Txn.executeRead(Txn.java:115)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.CopyDSG.copy(CopyDSG.java:35)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.sys.DatabaseOps.lambda$compaction$3(DatabaseOps.java:431)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.dboe.transaction.txn.TransactionalSystemControl.execReadOnlyDatabase(TransactionalSystemControl.java:45)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.DatabaseOps.compaction(DatabaseOps.java:419)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.DatabaseOps.compact(DatabaseOps.java:359)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.DatabaseMgr.compact(DatabaseMgr.java:81)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.fuseki.ctl.ActionCompact$CompactTask.run(ActionCompact.java:109)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.fuseki.async.AsyncPool.lambda$submit$0(AsyncPool.java:66)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.fuseki.async.AsyncTask.call(AsyncTask.java:100)
~[fuseki-server.jar:5.0.0]
at java.base/java.util.concurrent.FutureTask.run(Unknown Source) ~[?:?]
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
~[?:?]
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
~[?:?]
at java.base/java.lang.Thread.run(Unknown Source) [?:?]
Caused by: org.apache.thrift.protocol.TProtocolException: Unrecognized type 0
at org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:140)
~[fuseki-server.jar:5.0.0]
at org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:53)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:432)
~[fuseki-server.jar:5.0.0]
at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:238)
~[fuseki-server.jar:5.0.0]
at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:227)
~[fuseki-server.jar:5.0.0]
at org.apache.thrift.TUnion.read(TUnion.java:145) ~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:82)
~[fuseki-server.jar:5.0.0]
... 32 more
08:18:30 ERROR Server :: Exception in task 9 execution
org.apache.jena.tdb2.TDBException: NodeTableTRDF/Read
at
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:102)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:52)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:208)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:133)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:52)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:65)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:107)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:103)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:52)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.atlas.iterator.Iter$IterMap.lambda$forEachRemaining$0(Iter.java:432)
~[fuseki-server.jar:5.0.0]
at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]
at org.apache.jena.atlas.iterator.Iter$IterMap.forEachRemaining(Iter.java:432)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.atlas.iterator.IteratorWrapper.forEachRemaining(IteratorWrapper.java:52)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.CopyDSG.lambda$copy$0(CopyDSG.java:38)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.system.Txn.exec(Txn.java:77) ~[fuseki-server.jar:5.0.0]
at org.apache.jena.system.Txn.executeWrite(Txn.java:125)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.CopyDSG.lambda$copy$1(CopyDSG.java:36)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.system.Txn.exec(Txn.java:77) ~[fuseki-server.jar:5.0.0]
at org.apache.jena.system.Txn.executeRead(Txn.java:115)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.CopyDSG.copy(CopyDSG.java:35)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.sys.DatabaseOps.lambda$compaction$3(DatabaseOps.java:431)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.dboe.transaction.txn.TransactionalSystemControl.execReadOnlyDatabase(TransactionalSystemControl.java:45)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.DatabaseOps.compaction(DatabaseOps.java:419)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.sys.DatabaseOps.compact(DatabaseOps.java:359)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.tdb2.DatabaseMgr.compact(DatabaseMgr.java:81)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.fuseki.ctl.ActionCompact$CompactTask.run(ActionCompact.java:109)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.fuseki.async.AsyncPool.lambda$submit$0(AsyncPool.java:66)
~[fuseki-server.jar:5.0.0]
at org.apache.jena.fuseki.async.AsyncTask.call(AsyncTask.java:100)
~[fuseki-server.jar:5.0.0]
at java.base/java.util.concurrent.FutureTask.run(Unknown Source) ~[?:?]
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
~[?:?]
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
~[?:?]
at java.base/java.lang.Thread.run(Unknown Source) [?:?]
Caused by: org.apache.thrift.protocol.TProtocolException: Unrecognized type 0
at org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:140)
~[fuseki-server.jar:5.0.0]
at org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:53)
~[fuseki-server.jar:5.0.0]
at
org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:432)
~[fuseki-server.jar:5.0.0]
at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:238)
~[fuseki-server.jar:5.0.0]
at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:227)
~[fuseki-server.jar:5.0.0]
at org.apache.thrift.TUnion.read(TUnion.java:145) ~[fuseki-server.jar:5.0.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:82)
~[fuseki-server.jar:5.0.0]
---
Thomas Bottini
IReMus — Institut de Recherche en Musicologie UMR 8223
________________________________
De : Andy Seaborne <a...@apache.org>
Envoyé : mardi 2 juillet 2024 22:34:32
À : users@jena.apache.org
Objet : Re: Docker & compacting a dataset
Hi Thomas,
There should be a log file somewhere and that usually has more information.
Andy
On 02/07/2024 12:47, BOTTINI Thomas wrote:
> Hello ;
>
> I run fuseki with a Docker compose and a Docker image (inspired by
> https://hub.docker.com/r/secoresearch/fuseki/).
> Here is a fragment of the docker-compose.yml :
>
> fuseki:
> build: ./fuseki-docker
> ports:
> - 3030:3030
> volumes:
> - ./fuseki-data:/fuseki-base/databases
> - ./fuseki-configuration:/fuseki-base/configuration
>
>
> I want/need/try to compact a dataset :
>
> $ http POST localhost:3030/$/compact/iremus?deleteOld=true -a admin:XYZ
>
> HTTP/1.1 200 OK
> Content-Encoding: gzip
> Content-Length: 56
> Content-Type: application/json;charset=utf-8
> Date: Tue, 02 Jul 2024 11:43:11 GMT
> Expires: Thu, 01 Jan 1970 00:00:00 GMT
> Fuseki-Request-Id: 30
> Location: /$/compact/iremus/4
> Set-Cookie: JSESSIONID=node01py6j2rduedd7jwqpre5qkctr29.node0; Path=/
> Set-Cookie: rememberMe=deleteMe; Path=/; Max-Age=0; Expires=Mon, 01-Jul-2024
> 11:43:11 GMT; SameSite=lax
> Vary: Accept-Encoding, Origin
>
> {
> "requestId": 30,
> "taskId": "4"
> }
>
> The task fails immediately :
>
> $ http localhost:3030/$/tasks -a admin:XYZ
>
> {
> "finished": "2024-07-02T11:43:11.487+00:00",
> "started": "2024-07-02T11:43:11.069+00:00",
> "success": false,
> "task": "Compact",
> "taskId": "4"
> }
>
> How can I find the reasons of this failure? Could it be something related to
> the Docker volume?
>
> Thank you very much, in advance,
>
> Best regards
>
> --
> 💾 Thomas Bottini
> Institut de Recherche en Musicologie — IReMus UMR822
>
