Upgrade Jena version to 3.16.0

[awoods]

Related to: https://jira.lyrasis.org/browse/VIVO-1943

What does this pull request do?

Upgrades Jena from 3.11.0 to 3.16.0

What's new?

No functional change

How should this be tested?

A successful build indicates success

Additional Notes:

Based on the comment in the jena-users, I do not expect this upgrade will fix the issue in VIVO-1943.
However, the upgrade should generally be useful. I am happy to follow-up with another commit that adds the patch mentioned in the ticket regarding the use of Syntax.syntaxARQ.

Interested parties

@VIVO-project/vivo-committers

[brianjlowe]

This actually fixes VIVO-1943. With 50K insert batches, the master branch immediately throws StackOverflowExceptions. With this pull request applied, works fine.

[sarbajitdutta]

This actually fixes VIVO-1943. With 50K insert batches, the master branch immediately throws StackOverflowExceptions. With this pull request applied, works fine.

@brianjlowe How are you doing the batch inserts? Have you used the VIVO Update api for 50k inserts? I had some problem with SDB direct when I was using v3 Jena libraries. It went away when I updated to 3.16.0 for ReCiter-Connect.

[brianjlowe]

@sarbajitdutta My testing was exclusively using the VIVO SPARQL Update API. This was a series of INSERT DATA { GRAPH <...> { ... } } requests to the API where each request contained 50000 serialized triples.

[sarbajitdutta]

@brianjlowe @awoods I tried the fix but for big publications it fails with this message. Also, I did not set the maxPostSize in tomcat server.xml for 8080 port. By default it fails and it vivo.all.log it says this
2020-12-03 14:47:02,645 ERROR [BasicAuthenticator] Trying to check for valid fields on a null user.

reactor.netty.http.client.PrematureCloseException: Connection prematurely closed BEFORE response

2020-12-03 14:47:03.743  INFO 87121 --- [pool-3-thread-4] r.c.v.s.p.s.VivoPublicationsServiceImpl  : Api Exception

reactor.core.Exceptions$ReactiveException: reactor.netty.http.client.PrematureCloseException: Connection prematurely closed BEFORE response
        at reactor.core.Exceptions.propagate(Exceptions.java:393) ~[reactor-core-3.3.10.RELEASE.jar:3.3.10.RELEASE]
        at reactor.core.publisher.BlockingSingleSubscriber.blockingGet(BlockingSingleSubscriber.java:97) ~[reactor-core-3.3.10.RELEASE.jar:3.3.10.RELEASE]
        at reactor.core.publisher.Mono.block(Mono.java:1680) ~[reactor-core-3.3.10.RELEASE.jar:3.3.10.RELEASE]
        at reciter.connect.vivo.api.client.VivoClient.vivoUpdateApi(VivoClient.java:60) ~[classes/:na]
        at reciter.connect.vivo.sdb.publications.service.VivoPublicationsServiceImpl.importPublications(VivoPublicationsServiceImpl.java:435) [classes/:na]
        at reciter.connect.vivo.sdb.publications.service.VivoPublicationsServiceImpl.publicationsExist(VivoPublicationsServiceImpl.java:752) [classes/:na]
        at reciter.connect.vivo.sdb.publications.service.VivoPublicationsServiceImpl$1.call(VivoPublicationsServiceImpl.java:926) [classes/:na]
        at reciter.connect.vivo.sdb.publications.service.VivoPublicationsServiceImpl$1.call(VivoPublicationsServiceImpl.java:1) [classes/:na]
        at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_91]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_91]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_91]
        at java.lang.Thread.run(Thread.java:745) [na:1.8.0_91]
        Suppressed: java.lang.Exception: #block terminated with an error
                at reactor.core.publisher.BlockingSingleSubscriber.blockingGet(BlockingSingleSubscriber.java:99) ~[reactor-core-3.3.10.RELEASE.jar:3.3.10.RELEASE]
                ... 10 common frames omitted
Caused by: reactor.netty.http.client.PrematureCloseException: Connection prematurely closed BEFORE response
        Suppressed: reactor.core.publisher.FluxOnAssembly$OnAssemblyException: 
Error has been observed at the following site(s):
        |_ checkpoint ⇢ Request to POST http://localhost:8080/api/sparqlUpdate [DefaultWebClient]