openRDF.org Issue Tracker

[SES-652] Calling RDFFormat.getFileExtensions() returns MIME Types

Wed, 17 Dec 2008 13:56:39 +0100 (CET)

Calling RDFFormat.getFileExtensions() returns the same as RDFFormat.getMIMETypes. This is due to a copy+paste bug in http://repo.aduna-software.org/svn/info.aduna/commons/lang/trunk/src/main/java/info/aduna/lang/FileFormat.java:
/**
* Gets the file format's file extensions.
*
* @return An unmodifiable list of file extension strings, e.g. "text".
*/
public List<String> getFileExtensions() {
return Collections.unmodifiableList(mimeTypes);
}

[SES-424] Rio should be aware of the .owl extension

Dependency — Thu, 20 Mar 2008 20:45:24 +0100 (CET)

Often OWL ontologies that are written in RDF/XML have the .owl file name extension. However, this extension is not recognized by Rio.

[SES-425] RDF/XML writer needs to encode "carriage return" characters in literal values

Thu, 4 Oct 2007 12:09:13 +0200 (CEST)

XML parsers are required to normalize any end-of-line character sequences in XML documents to a single LF (line feed) character[1]. Due to this, any CR (carriage return) characters and CR-LF combinations that are part of RDF literal values will be replaced with LF characters by the XML parser, effectively changing the RDF literal value. To prevent this, any CR characters in RDF literals should be encoded using the entity 

[1] http://www.w3.org/TR/REC-xml/#sec-line-ends

[SES-452] Add support for @base directive to Turtle parser

Thu, 20 Mar 2008 20:15:26 +0100 (CET)

Dave Beckett added an @base directive to the Turtle specification on 2007/09/12. Support for this directive should be added to the Turtle parser.

[SES-496] Update Turtle parser to 20 November 2007 specification

Thu, 20 Mar 2008 20:16:30 +0100 (CET)

Dave Beckett recently updated the Turtle spec. The changes brings the spec closer to how Sesame's Turlte parser treats Turtle data: canonicalization of integers and boolean is no longer required and white space is optional where possible.

[SES-531] turtle parser fails on prefixed symbols containing '.'

Mon, 30 Jun 2008 17:40:02 +0200 (CEST)

Uploading a Turtle file containing prefixed URIs with '.' incorrectly complains.

For example, loading

@prefix : <http://example.com/> .
:sym.1 a :symbol .

produces the error "Malformed document: Illegal predicate value: ".1"^^http://www.w3.org/2001/XMLSchema#decimal". Using the same example, but ":sym1" rather than ":sym.1", loads correctly. The error also occurs with URIs like "foo:sym.1".

I believe these are valid URIs according to the spec (and Redland's Rapper handles them).

[SES-534] Allow arbitrary SAX ContentHandler's to be used with RDFXMLWriter

Fri, 4 Jul 2008 16:07:41 +0200 (CEST)

Instead of writing directly to a java.io.Writer, RDFXMLWriter could write to a org.xml.sax.ContentHandler to allow arbitrary SAX ContentHandlers to be used. The current behaviour can be implemented by using info.aduna.xml.SAXWriter as the default content handler.

[SES-573] Write relative URIs for subjects where possible

Tue, 2 Dec 2008 19:54:15 +0100 (CET)

Allow serialised RDF output to be written with relative URLs for subjects that are located along with the output RDF. This allows the RDF to be resolved after the files have been moved along with their metadata. e.g., an index.rdf included in an archive.

See this post for a rough sample written as a separate class:
http://openrdf.org/forum/mvnforum/viewthread?thread=296&offset=10#6416

[SES-655] TurtleParser should report BNode object statement before reporting its subject statements

Fri, 19 Dec 2008 00:44:39 +0100 (CET)

The Turtle parser reports the type and properties of implicit blank nodes before reporting what the statement of the resource that references it. This order prevents a PrettyWriter-like handler from creating a readable syntax. This can be seen in the repository manager that reads in configuration templates and writes them back out in the order the statements were parsed.

This is also a problem for writing to the federation. Since all statements of a BNodes can only exist in one members and some members maybe configured to only accept certain subject URIs, it is important to know which resources will link to the BNode before adding it to a member.

This can be fixed by changing the method parseImplicitBlank to take a BNode as a parameter and calling it after the first statement (s, p, BNode) has been reported.

[SES-666] RDF/XML Parser logs to standard error

Wed, 1 Apr 2009 12:11:04 +0200 (CEST)

RDFXMLParser should set an error handler for XML parser, otherwise the default XML parser error handler is used which outputs to standard error (without using a/the logging framework).

[SES-761] Rio parser should use long instead of int for line numbers

Related — Fri, 20 May 2011 05:08:34 +0200 (CEST)

The current rio parsers use ints for line numbers. For very large files, this may cause problems. Changing this will require small changes in client code as well, as the interfaces ParseErrorListener and ParseLocationListener will have to be adapted.

[SES-777] Turtle parser does not initiate handleComment RDFHandler events

Thu, 9 Jun 2011 08:53:37 +0200 (CEST)

The RDFHandler.handleComment(String comment) is never invoked for a TurtleParser.

[SES-539] XML Literal normalization

Related — Mon, 31 Oct 2011 15:54:52 +0100 (CET)

XML literal normalization is not implemented yet.

[SES-679] RDF/XML parser fails on relative URIs in rdf:datatype

Related — Tue, 13 Mar 2012 15:21:48 +0100 (CET)

Trying to parse the following document:

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://example.com/#">
  <Foo>
    <bar rdf:datatype="hello">Zyzzyx</bar>
  </Foo>
</rdf:RDF>

I get:

org.openrdf.rio.RDFParseException: Not a valid (absolute) URI: hello [line 3, column 37]

The problem is the value "hello" for rdf:datatype, Rio expects an absolute URI. Section 2.14 of the RDF/XML spec says however that rdf:datatype can contain relative URIs which are to be resolved in the usual way.

[SES-960] RDF Parsers Incorrectly Resolves Relative Query URIs

Related — Tue, 13 Mar 2012 15:22:05 +0100 (CET)

The expect triple from the RDF/XML below is <http://example.com/file.rdf?qs> dc:ttile "This should be file.rdf?qs". However, the local part of the base is dropped when resolving relative query strings, such as "?qs".

<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
  xmlns:dc="http://purl.org/dc/elements/1.1/"
  xml:base="http://example.com/file.rdf">
  <rdf:Description rdf:about="?qs">
    <dc:title>This should be file.rdf?qs</dc:title>
  </rdf:Description>
</rdf:RDF>

[SES-1079] RDF/XML parser should report warning on datatypes starting with 'xsd:'

Followup — Mon, 13 Aug 2012 22:44:39 +0200 (CEST)

A common mistake in (handwritten) RDF/XML is to specify the datatype of a literal using its prefixed name:

<foo:bar rdf:datatype="xsd:string">foobar</foo:bar>

However, while this is syntactically correct, it is intrepreted by the parser as meaning that the datatype URI is 'xsd:string', rather than 'http://www.w3.org/2001/XMLSchema#string'.

The correct way to specify the datatype in RDF/XML is:

<foo:bar rdf:datatype="http://www.w3.org/2001/XMLSchema#string">foobar</foo:bar>

It would be helpful if the parser, when running in VERIFY or NORMALIZE mode, would report a warning when it encounters datatype URIs that start with 'xsd'.

[SES-1080] Buffered RDF handler that groups incoming triples by context/subject/predicate

Wed, 15 Aug 2012 06:57:49 +0200 (CEST)

An RDFHandler implementation that can be used as a wrapper and which groups incoming statements together on context, subject, and predicate would be a useful new feature. This could be used in combination with any of the existing RDFWriters to produce slightly more ordered RDF documents (where all triples about the same subject are grouped together).

[SES-431] TriG parser fails to parse documents where blank nodes are used as graph names

Thu, 20 Mar 2008 20:41:24 +0100 (CET)

The TriG parser fails to parse documents such as the following:

==========
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sys: <http://www.openrdf.org/config/repository#> .

{
_:node12f9tmrtkx1 a sys:RepositoryContext .
}

_:node12f9tmrtkx1 {
_:node12f9tmrtkx2 a sys:Repository .
}
==========

This produces the following error:
org.openrdf.rio.RDFParseException: Expected '{', found '_' [line 8]

[SES-422] Lack of whitespace following bracket character results in error

Thu, 4 Oct 2007 12:06:37 +0200 (CEST)

[:foo :bar;] throws an error while [ :foo :bar;] does not:

Fatal error: Expected an RDF value here, found ';' at (file) [(line number), -1]

The error varies according to whatever the parser concludes is happening when '[' is considered part of a character sequence. The Turtle EBNF appears to specify 0-or-more whitespace characters here:

blank ::= nodeID | '[]' | '[' ws* predicateObjectList ws* ']' | collection

[SES-492] TriX parser discard leading and trailing whitespace for literals

Thu, 20 Mar 2008 20:15:01 +0100 (CET)

Issue reported at http://www.openrdf.org/forum/mvnforum/viewthread?thread=1517

The following code snippet exports a statement to TriX and reads it back in. The assertion at the end fails:

URI subj = valueFactory.createURI("http://subj");
Literal literal = valueFactory.createLiteral("text\n\n");
connection.add(subj, RDFS.LABEL, literal);

StringWriter sw = new StringWriter();
connection.export(new TriXWriter(sw));

connection.clear();
connection.add(new StringReader(sw.toString()), null, RDFFormat.TRIX);
assert literal.equals(connection.getStatements(subj, RDFS.LABEL, null, false).asList().get(0).getObject());

[SES-650] RDFXML incorrectly converts baseURI if it starts with "jar:"

Thu, 11 Dec 2008 18:25:31 +0100 (CET)

When loading RDF/XML files from a jar URL the resulting URI created for rdf:about="" is not the same URL of the file. RDF/XML converts the jar file path into the scheme. Only the RDF/XML parser does this and should be changed to respect the baseURL, even when it is not hierarchical, like the other parsers.

[SES-691] NullPointerException in error handling of TriXParser

Wed, 11 Nov 2009 09:13:16 +0100 (CET)

Some code in the TriX parser seems to assume that there will always be a nested exception. The call stack for the error is:

java.lang.NullPointerException
   at org.openrdf.rio.RDFParseException.<init>(RDFParseException.java:81)
   at org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:532)
   at org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:508)
   at org.openrdf.rio.trix.TriXParser.parse(TriXParser.java:114)
   at org.openrdf.rio.trix.TriXParser.parse(TriXParser.java:76)
<...>

Looking at this in the debugger, the value for "wrappedExc" on line 114 in TriXParser.java is null.

This is with Sesame version 2.2.2.

[SES-693] TriXParser throws NullPointerException on use

Tue, 15 Dec 2009 19:32:39 +0100 (CET)

The following code will throw a null pointer exception:

RDFParser parser = Rio.createParser(RDFFormat.TRIX);
parser.parse(new ByteArrayInputStream(("<trix>" + "<graph><triple>"
+ "<uri>http://example.org/Bob</uri>" + "<uri>http://example.org/wife</uri>"
+ "<uri>http://example.org/Mary</uri>" + "</triple></graph>" + "</trix>")
.getBytes()), "");

Don't know whether this is somehow related to the fix for ~~SES-691~~, but just in case it is, the following test case should also work:

public void testTrixParserErrorHandling() throws Exception {
RDFParser parser = Rio.createParser(RDFFormat.TRIX);
try {
parser.parse(new ByteArrayInputStream("rubbish".getBytes()), "");
fail("Parse should not succeed.");
} catch(RDFParseException e) {
//Expected
}
}

[SES-635] Allow specification of base URI (xml:base) in RDFXMLWriter

Thu, 27 Jan 2011 01:54:29 +0100 (CET)

Currently, you can not specify a base URI for the RDFXMLWriter, however, there are cases when this would be useful.

As an example, I am trying to export an RDF/XML file containing owl:Ontology metadata. In RDF/XML, this is supposed to look like this:

<owl:Ontology rdf:about="baseURI">
<owl:imports ....

where "baseURI" is the actual base URI of the current file (or the empty string).

However, since the RDF statement (X, RDF.TYPE, OWL.ONTOLOGY) can not be inserted into the repository through the API if X is an empty string, I need to be able to specify an actual URI that is the base URI of the exported file. This in turn requires that I can set an xml:base directive to specify that same base URI.

Especially when combining Sesame output with ontology editors like TopBraid this is essential, since such tools often inspect the ontology metadata to look for imports and such. Currently I can not export an ontology from Sesame that can be easily read by TopBraid, because of this.

[SES-756] Sesame RDF/XML writer can blow up if default namespace is same as a defined namespace

Mon, 4 Apr 2011 11:40:22 +0200 (CEST)

Turtle like this:

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

<http://www.w3.org/1999/02/22-rdf-syntax-ns#> a :Foo .

can be parsed fine, but if then rendered as RDF/XML, will cause:

java.lang.RuntimeException: No prefix has been declared for the namespace used in this attribute: http://www.w3.org/1999/02/22-rdf-syntax-ns#
at org.openrdf.rio.rdfxml.RDFXMLWriter.writeAttribute(RDFXMLWriter.java:391)
at org.openrdf.rio.rdfxml.RDFXMLWriter.handleStatement(RDFXMLWriter.java:244)
at org.openrdf.repository.sail.SailRepositoryConnection.exportStatements(SailRepositoryConnection.java:210)
at org.openrdf.repository.base.RepositoryConnectionBase.export(RepositoryConnectionBase.java:159)
at com.ontologypartners.sesame.test.SesameTest.testRdfXmlWriterHandlesDefaultNamespace(SesameTest.java:237)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at junit.framework.TestCase.runTest(TestCase.java:164)
at junit.framework.TestCase.runBare(TestCase.java:130)
at junit.framework.TestResult$1.protect(TestResult.java:106)
at junit.framework.TestResult.runProtected(TestResult.java:124)
at junit.framework.TestResult.run(TestResult.java:109)
at junit.framework.TestCase.run(TestCase.java:120)
at org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestReference.run(JUnit3TestReference.java:130)
at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:467)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:683)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:390)
at org.eclipse.pde.internal.junit.runtime.RemotePluginTestRunner.main(RemotePluginTestRunner.java:62)
at org.eclipse.pde.internal.junit.runtime.CoreTestApplication.run(CoreTestApplication.java:23)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:574)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:368)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:559)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:514)
at org.eclipse.equinox.launcher.Main.run(Main.java:1311)
at org.eclipse.equinox.launcher.Main.main(Main.java:1287)

Test case:

    public void testRdfXmlWriterHandlesDefaultNamespace() throws Exception {
        Repository repository = new SailRepository(new MemoryStore());
        repository.initialize();
        try {
            RepositoryConnection connection = repository.getConnection();
            try {
                connection.setNamespace("", RDF.NAMESPACE);
                connection.setNamespace("rdf", RDF.NAMESPACE);
                connection.add(connection.getValueFactory().createURI(RDF.NAMESPACE), RDF.TYPE,
                        OWL.ONTOLOGY);

                RDFWriter writer = Rio.createWriter(RDFFormat.RDFXML, new ByteArrayOutputStream());

                //Just don't explode...
                connection.export(writer);
            } finally {
                connection.close();
            }
        } finally {
            repository.shutDown();
        }
    }