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Exception while GET: Parsing of imported Ontology due to usage of ttl-parser together with xml-file #22

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keiligch opened this issue Sep 21, 2022 · 2 comments
Open

Exception while GET: Parsing of imported Ontology due to usage of ttl-parser together with xml-file #22

keiligch opened this issue Sep 21, 2022 · 2 comments

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@keiligch
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Server answer with stack trace

<body>Exception occured while processing /models
    <pre>Message: net.enilink.komma.core.KommaException: Invalid RDF data:
IRI included an unencoded space: '32' [line 1]
    net.enilink.komma.model.ModelUtil.readData(ModelUtil.java:644)
    net.enilink.komma.model.rdf4j.SerializableModelSupport$1.run(SerializableModelSupport.java:211)
    java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    java.base/java.lang.Thread.run(Thread.java:829)
Caught and thrown by:
Message: org.eclipse.rdf4j.rio.RDFParseException: IRI included an unencoded space: '32' [line 1]
    org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportError(RDFParserHelper.java:276)
    org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.reportError(AbstractRDFParser.java:584)
    org.eclipse.rdf4j.rio.turtle.TurtleParser.reportError(TurtleParser.java:1298)
    org.eclipse.rdf4j.rio.turtle.TurtleParser.parseURI(TurtleParser.java:900)
    org.eclipse.rdf4j.rio.turtle.TurtleParser.parseValue(TurtleParser.java:568)
    org.eclipse.rdf4j.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:395)
    org.eclipse.rdf4j.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:330)
    org.eclipse.rdf4j.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:200)
    org.eclipse.rdf4j.rio.turtle.TurtleParser.parse(TurtleParser.java:162)
    org.eclipse.rdf4j.rio.turtle.TurtleParser.parse(TurtleParser.java:125)
    net.enilink.komma.model.ModelUtil.readData(ModelUtil.java:642)
    net.enilink.komma.model.rdf4j.SerializableModelSupport$1.run(SerializableModelSupport.java:211)
    java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    java.base/java.lang.Thread.run(Thread.java:829)
</pre>
</body>

Process

  • posting a new model in ttl-format to the /models-endpoint . Ontology imports another ontology in rdf/xml which is accessable in the web (example ttl below)
  • sending GET with the same model as parameter -> only the first time server exception is thrown
  • sending GET again -> everything ok

Reason (most likely)
When sending GET request model is being parsed with the RDF4J.rio-TurtleParser, but also the imported rdf/xml. The first line of the xml is <?xml version="1.0" encoding="UTF-8"?> which probably is interpreted as an IRI by the turtle parser. The exception is thrown due to the space inbetween.
In my test, I could isolate the problematic ontology (no further imports, so the mistake is certainly from there): http://spinrdf.org/sp

HTTP Code for testing (insert domain address)

POST /models?model=http://example.com/test HTTP/1.1
Host: {my own domain}
Content-Type: text/turtle

@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .

<http://www.example.com/test#> rdf:type owl:Ontology ;
                                owl:imports <http://spinrdf.org/sp> .
@kenwenzel
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We should use IURIConverter.contentDescription at

https://github.com/komma/komma/blob/22424c4a21394d510455f1148c99faa41ffcc755/bundles/core/net.enilink.komma.model/src/main/java/net/enilink/komma/model/base/ModelSupport.java#L729

if neither a mime type nor a content description are contained within the options map.

@kenwenzel
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The response from http://spinrdf.org/sp does not declare a Content-Type header:
image

Therefore, we cannot determine the correct parser upfront. A solution would be to use some sort of trial and error mechanism to guess the correct mime type.
See also https://github.com/apache/any23/blob/master/mime/src/main/java/org/apache/any23/mime/TikaMIMETypeDetector.java

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@kenwenzel @keiligch