如何使用TDB和reasoner配置Apache Fuseki？删除数据集上的错误

Question

上下文

尽管有很多关于这个问题的问题/答案，但我仍然很难配置Apache .

我正在尝试配置一个Apache Fuseki实例，并激活了TDB和OWL推理器，用于测试我的应用程序。我需要创建一个数据集，执行我的测试，并以编程的方式删除数据集。

设置

我使用stain/jena-fuseki码头映像运行Apache。

我在3.10.0版中运行了Jena Fuseki。

bash-4.3# ./fuseki-server -version
Jena:       VERSION: 3.10.0
Jena:       BUILD_DATE: 2018-12-30T15:45:57+0000
TDB:        VERSION: 3.10.0
TDB:        BUILD_DATE: 2018-12-30T15:45:57+0000
Fuseki:     VERSION: 3.10.0
Fuseki:     BUILD_DATE: 2018-12-30T15:45:57+0000

碱基配置

我使用折叠shiro.ini文件。我允许每个人都可以完全访问，这只是一个测试实例。

bash-4.3# cat /fuseki/shiro.ini 

[main]
# Development
ssl.enabled = false
plainMatcher=org.apache.shiro.authc.credential.SimpleCredentialsMatcher
iniRealm.credentialsMatcher = $plainMatcher

[users]
admin=mysupersecurepassword

[roles]

[urls]
## Control functions open to anyone
/$/status = anon
/$/ping   = anon

# Everything else
/**=anon

我使用默认的config.ttl文件：

bash-4.3# cat /fuseki/config.ttl 
# Licensed under the terms of http://www.apache.org/licenses/LICENSE-2.0
## Fuseki Server configuration file.

@prefix :        <#> .
@prefix fuseki:  <http://jena.apache.org/fuseki#> .
@prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
@prefix ja:      <http://jena.hpl.hp.com/2005/11/Assembler#> .

[] rdf:type fuseki:Server ;
   .

我想做什么？

为了测试我的应用程序，我尝试创建一个数据集，执行测试，并以编程方式删除数据集。为此，我使用Fuseki HTTP管理协议。

我遵循以下步骤：

• POST /$/datasets创建数据集。
• POST /dataset_name/data上传数据文件。
• (执行我的应用程序测试)
• POST /dataset_name?update=DROP+ALL删除数据。
• DELETE /$/datasets/dataset_name删除数据集。

步骤1：

使用卷发：

curl -F 'files[]=@dataset.ttl' http://localhost:3030/$/datasets

我使用以下dataset.ttl文件：

@prefix fuseki: <http://jena.apache.org/fuseki#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix : <#> .


# Custom code
tdb:GraphTDB rdfs:subClassOf ja:Model .

# Setup service
:service rdf:type fuseki:Service ;
    rdfs:label                          "TDB dataset_name" ;
    fuseki:name                         "dataset_name" ;
    fuseki:dataset                      :dataset ;
    fuseki:serviceQuery                 "query", "sparql" ;
    fuseki:serviceUpdate                "update" ;
    fuseki:serviceUpload                "upload" ;
    fuseki:serviceReadWriteGraphStore   "data" ;
    fuseki:serviceReadGraphStore        "get" ;
.

# Setup Assembler model with reasoner
:dataset rdf:type ja:RDFDataset;
    ja:defaultGraph :modelInf ;
.
:modelInf rdf:type ja:InfModel;
    ja:baseModel :tdbGraph ;
    ja:reasoner [ 
        ja:reasonerURL <http://jena.hpl.hp.com/2003/OWLFBRuleReasoner> 
    ] ;
.

# TDB dataset used for RDF storage
:tdbGraph rdf:type tdb:GraphTDB;
    tdb:location "/fuseki/databases/dataset_name" ;
.

Jena Fuseki日志

[2019-10-23 14:41:00] Admin      INFO  [6] POST http://localhost:3030/$/datasets
[2019-10-23 14:41:00] Admin      INFO  [6] Filename: dataset.ttl, Content-Type=application/octet-stream, Charset=null => Turtle : Count=19 Triples=19 Quads=0
[2019-10-23 14:41:00] Admin      INFO  [6] Create database : name = /dataset_name
[2019-10-23 14:41:02] Admin      INFO  [6] 200 OK (1.894 s)

一切都好:P

第2步：

使用卷发：

curl -F 'files[]=@data.rdf' http://localhost:3030/dataset_name/data
{ 
  "count" : 1524 ,
  "tripleCount" : 1524 ,
  "quadCount" : 0
}

Jena Fuseki日志

[2019-10-23 14:44:52] Fuseki     INFO  [7] POST http://localhost:3030/dataset_name/data
[2019-10-23 14:44:53] Fuseki     INFO  [7] Filename: data.rdf, Content-Type=application/octet-stream, Charset=null => RDF/XML : Count=1524 Triples=1524 Quads=0
[2019-10-23 14:44:54] Fuseki     INFO  [7] 200 OK (1.858 s)

一切都好:P

步骤3：

测试我的应用程序(这里没用)

第4步：

使用卷发：

curl -d "update=DROP+ALL" -X POST http://localhost:3030/dataset_name/update
...
Update succeeded
...

Jena Fuseki日志

[2019-10-23 15:04:13] Fuseki     INFO  [67] POST http://localhost:3030/dataset_name/update
[2019-10-23 15:04:14] Fuseki     INFO  [67] 200 OK (268 ms)

一切都好:P

第5步：

使用卷发：

curl -X DELETE http://localhost:3030/$/datasets/dataset_name

Jena Fuseki日志

[2019-10-23 15:10:17] Admin      INFO  [92] DELETE http://localhost:3030/$/datasets/dataset_name
[2019-10-23 15:10:17] Admin      INFO  [92] DELETE ds=/dataset_name
[2019-10-23 15:10:17] Server     INFO  Shutting down data service for [, data, upload, query, get, update, sparql]
[2019-10-23 15:10:17] Admin      WARN  [92] RC = 500 : Not in a transaction
org.apache.jena.tdb.transaction.TDBTransactionException: Not in a transaction
        at org.apache.jena.tdb.transaction.DatasetGraphTransaction.get(DatasetGraphTransaction.java:140)
        at org.apache.jena.tdb.transaction.DatasetGraphTransaction.getDatasetGraphToQuery(DatasetGraphTransaction.java:86)
        at org.apache.jena.tdb.store.GraphTxnTDB.getDatasetGraphTDB(GraphTxnTDB.java:51)
        at org.apache.jena.tdb.store.GraphTDB.sync(GraphTDB.java:128)
        at org.apache.jena.tdb.store.GraphTDB.close(GraphTDB.java:133)
        at org.apache.jena.reasoner.BaseInfGraph.close(BaseInfGraph.java:445)
        at org.apache.jena.reasoner.rulesys.BasicForwardRuleInfGraph.close(BasicForwardRuleInfGraph.java:360)
        at org.apache.jena.reasoner.rulesys.FBRuleInfGraph.close(FBRuleInfGraph.java:710)
        at org.apache.jena.sparql.core.DatasetGraphMapLink.close(DatasetGraphMapLink.java:199)
        at org.apache.jena.fuseki.server.DataService.expel(DataService.java:223)
        at org.apache.jena.fuseki.server.DataService.shutdown(DataService.java:199)
        at org.apache.jena.fuseki.mgt.ActionDatasets.execDeleteItem(ActionDatasets.java:360)
        at org.apache.jena.fuseki.ctl.ActionContainerItem.execDelete(ActionContainerItem.java:105)
        at org.apache.jena.fuseki.ctl.ActionContainerItem.perform(ActionContainerItem.java:64)
        at org.apache.jena.fuseki.ctl.ActionCtl.executeLifecycle(ActionCtl.java:68)
        at org.apache.jena.fuseki.ctl.ActionCtl.executeAction(ActionCtl.java:62)
        at org.apache.jena.fuseki.ctl.ActionCtl.execCommonWorker(ActionCtl.java:53)
        at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:74)
        at org.apache.jena.fuseki.ctl.ActionContainerItem.doDelete(ActionContainerItem.java:52)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:713)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
        at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:865)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1655)
        at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:101)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1642)
        at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
        at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
        at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
        at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
        at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
        at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
        at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
        at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
        at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
        at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
        at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
        at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1642)
        at org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285)
        at org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1634)
        at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146)
        at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257)
        at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255)
        at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1340)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203)
        at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
        at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
        at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201)
        at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1242)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144)
        at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:690)
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
        at org.eclipse.jetty.server.Server.handle(Server.java:503)
        at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:364)
        at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:260)
        at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:305)
        at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103)
        at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:118)
        at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:765)
        at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:683)
        at java.lang.Thread.run(Thread.java:745)
[2019-10-23 15:10:17] Admin      INFO  [92] 500 Not in a transaction (65 ms)

这就是问题所在。有人能帮我解决这个问题吗？

思想/尝试

对于默认的dataset配置文件，我尝试使用相同的过程，但没有错误。因此，我认为这来自数据集配置文件。

在这里，我称之为默认数据集配置文件：

@prefix :      <http://base/#> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
@prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix fuseki: <http://jena.apache.org/fuseki#> .

:service_tdb_all        a                   fuseki:Service ;
        rdfs:label                          "TDB2 dataset_name" ;
        fuseki:dataset                      :tdb_dataset_readwrite ;
        fuseki:name                         "dataset_name" ;
        fuseki:serviceQuery                 "query" , "sparql" ;
        fuseki:serviceReadGraphStore        "get" ;
        fuseki:serviceReadWriteGraphStore   "data" ;
        fuseki:serviceUpdate                "update" ;
        fuseki:serviceUpload                "upload" .

:tdb_dataset_readwrite  a                   tdb2:DatasetTDB2 ;
        tdb2:location                       "/fuseki/databases/dataset_name" .

对于如何正确配置Jena Fuseki，我找不到任何清晰的文档。许多例子可以找到，但日期从一些年，不知道他们是否仍然是最新的。也没有解释它们到底是如何工作的，所以很难把它加到具体的案例中。

如果有任何文档/教程解释什么是"ja:RDFDataset“、"ja:InfModel”和其他"ja:things“，以及它们是如何工作的，我们将不胜感激。

我仍然从本体/triplestore/链接数据开始，而这些文档并不是最容易阅读的：

• https://jena.apache.org/documentation/assembler/
• https://jena.apache.org/documentation/javadoc/jena/org/apache/jena/assembler/JA.html

我尝试了不同的配置示例，并且总是在步骤1或步骤5中出现错误。

示例

配置：

@prefix : <#> .
@prefix fuseki: <http://jena.apache.org/fuseki#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .

[] rdf:type fuseki:Server ;
    fuseki:services (
        <#service>
    ) .

## ---------------------------------------------------------------
## Service with only SPARQL query on an inference model.
## Inference model base data in TDB.

<#service> rdf:type fuseki:Service ;
    fuseki:name "dataset_name" ;
    fuseki:serviceQuery "query" , "sparql" ;
    fuseki:serviceUpdate "update" ;
    fuseki:serviceUpload "upload" ;
    fuseki:serviceReadWriteGraphStore "data" ;
    fuseki:serviceReadGraphStore "get" ;
    fuseki:dataset <#dataset>  ;
    .

<#dataset> rdf:type ja:RDFDataset ;
    ja:defaultGraph <#model> ;
    . 

<#model> rdf:type ja:InfModel ;
    ja:baseModel <#tdbGraph> ;
    ja:reasoner [
        ja:reasonerURL <http://jena.hpl.hp.com/2003/OWLFBRuleReasoner> ;
    ] ;
    .

<#tdbGraph> rdf:type tdb:GraphTDB ;
    tdb:dataset <#tdbDataset> ;
    .

<#tdbDataset> rdf:type tdb:DatasetTDB ;
    tdb:location "/fuseki/databases/dataset_name" ;
    .

步骤1出错。

Fuseki日志：

[2019-10-23 15:20:51] Admin      INFO  [93] POST http://localhost:3030/$/datasets
[2019-10-23 15:20:51] Admin      INFO  [93] Filename: dataset.ttl, Content-Type=text/turtle, Charset=null => Turtle : Count=23 Triples=23 Quads=0
[2019-10-23 15:20:51] Admin      INFO  [93] Create database : name = /dataset_name
[2019-10-23 15:20:51] Admin      WARN  [93] RC = 500 : cannot find a most specific type for :tdbGraph, which has as possibilities: ja:Model tdb:GraphTDB.
org.apache.jena.assembler.exceptions.AmbiguousSpecificTypeException: cannot find a most specific type for :tdbGraph, which has as possibilities: ja:Model tdb:GraphTDB.

Answer 1

完整服务器使用其中一个模板为通过UI或协议创建的数据库提供删除。无法以这种方式删除推送服务器的任意配置文件；即使它们可以从服务器断开链接，也可能会留下一些不利于测试的内容(它们是任意的附件文件)。

对于测试，有一种更简单的方法。为每个测试拆分一个服务器，要么是脚本化的，要么是来自Java (JUnit等)。服务器的"Fuseki“版本启动和停止非常快。因此，使用所需的配置启动服务器--如果数据相当小，您可以使用内存中的TDB数据库(位置是"--mem--")来处理数据。

这将在服务器退出时完成清除，从而使测试完全隔离。