问题：

OWLAPI错误地使用OBO解析器处理n-三元文件

严易安

2023-03-14

我们有一个使用OWLAPI解析本体的包装器。

我们试图在这里解析它:https://github.com/ncbo/owlapiwrapper/blob/master/src/main/java/org/stanford/ncbo/oapiwrapper/ontologyparser.java#L637

我们面临两个案例：

运行mvn测试时：解析工作正常

我尝试了多种方法：

禁止OBO解析器。我尝试了多种语法，但没有一种奏效；包装器继续使用OBO解析器）

conf.setBannedParsers("org.obolibrary.oboformat.parser.OBOFormatParser");
conf.setBannedParsers("o.o.oboformat.parser.OBOFormatParser");
conf.setBannedParsers("OBOFormatParser");

避免使用不同的owlapi依赖项。与这里的文档一样，owlapi：Parser not found，如果从Jar运行，我尝试只使用owlapi-distribution来避免任何冲突

<dependency>
  <groupId>net.sourceforge.owlapi</groupId>
  <artifactId>owlapi-distribution</artifactId>
  <version>4.3.1</version>
</dependency>

当应用程序打包为jar（包含依赖项）并且运行jar解析NTriple文件时。则返回org.semanticweb.owlapi.rdf.turtle.parser.ParseException失败：遇到“ ”:genid1“”

导致问题的三个因素是:_:genid1.

当通过Maven测试在完全相同的文件上运行完全相同的解析器时（解析器是通过jUnit测试调用的，我们使用mvn test运行测试）。那么解析就会进行得很好。并成功提取了_:genid1节点给出的信息。

在第一种情况下，OWLAPI似乎无法解析空节点。在运行LoadOntologyFromontologyDocument之前，我使用VersionInfo.getVersionInfo()打印了OWLAPI版本：

对于jar版本（导致问题的原因）:OWL API（版本4.3.1)
测试版本（正在工作）:OWL API（版本4.3.1.2017-03-27T22:32:37Z)

更新2：

看来问题出在罐子楼。

在构建jar时，会覆盖一些依赖项，因此conf文件中并不包括所有的解析器

org.semanticweb.owlapi.rio.RioFunctionalSyntaxParserFactory
org.semanticweb.owlapi.rio.RioManchesterSyntaxParserFactory
org.semanticweb.owlapi.rio.RioOWLXMLParserFactory
org.semanticweb.owlapi.rio.RioFunctionalSyntaxParserFactory
org.semanticweb.owlapi.rio.RioManchesterSyntaxParserFactory
org.semanticweb.owlapi.rio.RioOWLXMLParserFactory

对于有空节点的NTriples文件，我们得到：

The following parsers were tried:
1) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@a4add54
2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@71454b9d
3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@67304a40
4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@61c9c3fd
6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@463b4ac8
16) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@11981797
17) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d

但对于RioTurtleDocumentFormat,它说：

Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
    Stack trace:
org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl)        
org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207)

因此，RioturtleDocumentFormatFactory似乎没有正确地包含在JAR中。

我还尝试使用maven-shade-plugin对jar进行打包，得到了同样的错误。

在禁止OBO解析器之后，log说它试图使用这些解析器解析文件：

The following parsers were tried:
1) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@2bb3058
2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@6bbe2511
3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@93cf163
4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@3d97a632
6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@784b990c
16) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@13f17eb4
17) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d

以下是RioTurtleDocumentFormatFactory的错误日志：

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
    Stack trace:
org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl)        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1156)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1112)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1068)
        org.stanford.ncbo.oapiwrapper.OntologyParser.findMasterFile(OntologyParser.java:708)
        org.stanford.ncbo.oapiwrapper.OntologyParser.internalParse(OntologyParser.java:651)
        org.stanford.ncbo.oapiwrapper.OntologyParser.parse(OntologyParser.java:630)
        org.stanford.ncbo.oapiwrapper.OntologyParserCommand.main(OntologyParserCommand.java:51)
No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl)        org.openrdf.rio.Rio.createParser(Rio.java:198)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1156)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1112)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1068)
        org.stanford.ncbo.oapiwrapper.OntologyParser.findMasterFile(OntologyParser.java:708)
        org.stanford.ncbo.oapiwrapper.OntologyParser.internalParse(OntologyParser.java:651)
        org.stanford.ncbo.oapiwrapper.OntologyParser.parse(OntologyParser.java:630)

RioTurtleDocumentFormat.class
RioTurtleDocumentFormatFactory.class
RioTurtleParserFactory.class
RioTurtleStorerFactory.class

META-INF/services/org.openrdf.rio.RDFParserFactory
META-INF/services/org.semanticweb.owlapi.io.LegacyOWLParserFactory
META-INF/services/org.semanticweb.owlapi.model.OWLOntologyManagerFactory
META-INF/services/org.semanticweb.owlapi.io.OWLParserFactory
META-INF/services/org.semanticweb.owlapi.model.OWLStorerFactory
META-INF/services/org.semanticweb.owlapi.model.OWLDocumentFormatFactory
META-INF/services/org.openrdf.rio.LanguageHandler
META-INF/services/org.openrdf.rio.DatatypeHandler
META-INF/services/org.openrdf.rio.RDFWriterFactory
META-INF/services/com.fasterxml.jackson.core.JsonFactory
META-INF/services/com.fasterxml.jackson.core.ObjectCodec
META-INF/services/org.apache.commons.logging.LogFactory
META-INF/services/javax.servlet.ServletContainerInitializer

org.semanticweb.owlapi.rio.RioFunctionalSyntaxParserFactory
org.semanticweb.owlapi.rio.RioManchesterSyntaxParserFactory
org.semanticweb.owlapi.rio.RioOWLXMLParserFactory
org.semanticweb.owlapi.rio.RioFunctionalSyntaxParserFactory
org.semanticweb.owlapi.rio.RioManchesterSyntaxParserFactory
org.semanticweb.owlapi.rio.RioOWLXMLParserFactory

org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory
org.semanticweb.owlapi.formats.N3DocumentFormatFactory
org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory
org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory
org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory
org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory
org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory
org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory
org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory
org.semanticweb.owlapi.formats.TrigDocumentFormatFactory
org.semanticweb.owlapi.formats.TrixDocumentFormatFactory
org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory
org.semanticweb.owlapi.formats.N3DocumentFormatFactory
org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory
org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory
org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory
org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory
org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory
org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory
org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory
org.semanticweb.owlapi.formats.TrigDocumentFormatFactory
org.semanticweb.owlapi.formats.TrixDocumentFormatFactory

因此org.semanticweb.owlapi.formats.RioturtleDocumentFormatFactory实际上列在一些Meta-INF/Services文件中，并且类包含在JAR中。但看起来罐子还是找不到。

我真的不明白OWLAPI是如何定义使用哪个解析器以及在哪里找到它们的。

更新4：

<plugin>
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-shade-plugin</artifactId>
  <version>2.3</version>
  <executions>
    <execution>
      <phase>package</phase>
      <goals>
        <goal>shade</goal>
      </goals>
      <configuration>
        <artifactSet>
          <includes>
            <include>net.sourceforge.owlapi:owlapi-api</include>
            <include>net.sourceforge.owlapi:owlapi-apibinding</include>
            <include>net.sourceforge.owlapi:owlapi-fixers</include>
            <include>net.sourceforge.owlapi:owlapi-impl</include>
            <include>net.sourceforge.owlapi:owlapi-oboformat</include>
            <include>net.sourceforge.owlapi:owlapi-parsers</include>
            <include>net.sourceforge.owlapi:owlapi-rio</include>
            <include>net.sourceforge.owlapi:owlapi-tools</include>
            <include>commons-cli:*</include>
            <include>commons-io:*</include>
            <include>org.slf4j:*</include>
            <include>net.sourceforge.owlapi:owlapi-osgidistribution</include>
            <include>com.google.inject:*</include>
            <include>javax.inject:*</include>
            <include>com.google.*</include>
            <include>aopalliance:*</include>
            <include>org.openrdf.sesame:*</include>
            <include>org.tukaani:*</include>
            <include>net.sf.trove4j:*</include>
            <include>org.apache.commons:commons-csv</include>
          </includes>
        </artifactSet>
        <transformers>
          <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
            <mainClass>org.stanford.ncbo.oapiwrapper.OntologyParserCommand</mainClass>
          </transformer>
        </transformers>
      </configuration>
    </execution>
  </executions>
</plugin>

但它不会改变jar中的meta-inf/services/org.openrdf.rio.rdfParserFactory文件中的任何内容

可能是因为我需要添加net.sourceforge.owlapi:owlapi-osgidistribute，这会覆盖RDFParserFactory文件。但没有包含它，我得到了一个java.lang.noClassDefoundError：org/semanticweb/owlapi/model/owlannotationvalue

公羊兴文

2023-03-14

这里有几个问题合谋：

OwlonTologyLoaderConfiguration是一个不可变的类。setter生成一个修改的对象，而不是调用对象的更改。
有两个OBO解析器

要解决此问题,请使用：

conf = conf.setBannedParsers(
    "org.coode.owlapi.obo12.parser.OBO12ParserFactory org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParserFactory");

manager.getOntologyConfigurator().withBannedParsers("...");

OWLOntologyDocumentSource source = 
    new FileDocumentSource(fileName, new NTriplesDocumentFormat());

第二个更新：POM有多个包含解析器列表的JAR。尝试替换

<dependency>
  <groupId>net.sourceforge.owlapi</groupId>
  <artifactId>owlapi-distribution</artifactId>
  <version>4.3.1</version>
</dependency>

<dependency>
  <groupId>net.sourceforge.owlapi</groupId>
  <artifactId>owlapi-rio</artifactId>
  <version>4.3.1</version>
</dependency>

<dependency>
  <groupId>net.sourceforge.owlapi</groupId>
  <artifactId>owlapi-compatibility</artifactId>
  <version>4.3.1</version>
</dependency>

与

<dependency>
  <groupId>net.sourceforge.owlapi</groupId>
  <artifactId>owlapi-osgidistribution</artifactId>
  <version>4.3.1</version>
</dependency>

更新：我已经签出了您用来复制问题的项目。为了调试它，我尝试一次添加一个OWLAPI依赖项，直到错误停止发生--在这样做的过程中，我发现以下文件的内容：

问题是，在重新打包owlapi-distribution及其依赖项时，服务内部的文件没有按照预期进行合并。

你应该可以通过使用shade插件在你的重新打包修复。作为一个示例，我在这里粘贴了Owlapi-Distributation所做的工作--您需要更改排除列表，因为您可能不想排除任何依赖项。

        <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-shade-plugin</artifactId>
            <version>2.3</version>
            <executions>
                <execution>
                    <phase>package</phase>
                    <goals>
                        <goal>shade</goal>
                    </goals>
                    <configuration>
                        <artifactSet>
                            <includes>
                                <include>net.sourceforge.owlapi:owlapi-api</include>
                                <include>net.sourceforge.owlapi:owlapi-apibinding</include>
                                <include>net.sourceforge.owlapi:owlapi-fixers</include>
                                <include>net.sourceforge.owlapi:owlapi-impl</include>
                                <include>net.sourceforge.owlapi:owlapi-oboformat</include>
                                <include>net.sourceforge.owlapi:owlapi-parsers</include>
                                <include>net.sourceforge.owlapi:owlapi-rio</include>
                                <include>net.sourceforge.owlapi:owlapi-tools</include>
                            </includes>
                            <excludes>
                                <exclude>org.apache.felix:org.osgi.core</exclude>
                                <exclude>org.openrdf.sesame:*</exclude>
                                <exclude>com.fasterxml.jackson.core:*</exclude>
                                <exclude>com.github.jsonld-java:*</exclude>
                                <exclude>com.fasterxml.jackson.core:*</exclude>
                                <exclude>org.apache.httpcomponents:*</exclude>
                                <exclude>commons-codec:commons-codec:*</exclude>
                                <exclude>org.slf4j:*</exclude>
                                <exclude>org.semarglproject:*</exclude>
                                <exclude>com.google.guava:*</exclude>
                                <exclude>com.google.inject:*</exclude>
                                <exclude>javax.inject:*</exclude>
                                <exclude>aopalliance:*</exclude>
                                <exclude>com.google.inject.extensions:*</exclude>
                                <exclude>com.google.code.findbugs:*</exclude>
                                <exclude>org.slf4j:slf4j-api</exclude>
                                <exclude>commons-io:*</exclude>
                                <exclude>org.tukaani:*</exclude>
                                <exclude>net.sf.trove4j:*</exclude>
                            </excludes>
                        </artifactSet>
                        <transformers>
                            <transformer
                                implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
                        </transformers>
                    </configuration>
                </execution>
            </executions>
        </plugin>

OWLAPI错误地使用OBO解析器处理n-三元文件

共有1个答案

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