openRDF.org Issue Tracker

[RIO-28] RDF/XML parser removes leading and trailing spaces from literals

Tue, 20 Sep 2005 13:39:59 +0200 (CEST)

While parsing literals, the RDF/XML parser removes leading and trailing white space characters from literal values. The RDF/XML spec seems to suggest that this should not be done by default, but only if the whitespace facet of the literal's datatype dictates this. All of XML's built-in datatypes except for xs:string and its decendents specify a whiteSpace facet value of 'collapse'.

[RIO-30] predicate names starting with non-NCNAME chars can not be serialized.

Fri, 23 Sep 2005 15:02:25 +0200 (CEST)

A URI like http://www.pfif.org/1.1name , when used as a predicate, can currently not be serialized in RDF/XML, because the namespace/localname split results in a local name that starts with a non-NCNAME char.

Instead, the Rio writer should split the URI differently, splitting after the last non-NCNAME char, to result in:

<name xmlns="http://www.pfif.org/1.1">

[RIO-49] Turtle parser breaks on extra semicolon

Wed, 2 Aug 2006 18:04:38 +0200 (CEST)

I could not parse the following file:
https://sommer.dev.java.net/atom/2006-06-06/examples/example-1.atom.turtle

@prefix : <http://bblfish.net/work/atom-owl/2006-06-06/#> .
@prefix iana: <http://www.iana.org/assignments/relation/>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .

[ a :Feed;
:title [ :text "Example Feed" ];
:link [ a :Link;
           :rel iana:alternate ;
           :to [ :src <http://example.org/>;]
           ];
:updated "2003-12-13T18:30:02Z"^^xsd:dateTime;
:author [ a :Person;
           owl:sameAs _:author1;
            :name [ :text "John Doe" ];
          ];
:id "urn:uuid:60a76c80-d399-11d9-b93C-0003939e0af6"^^xsd:anyUri;
:entry [ a :Entry;
           :author _:author1;
           :title [ :text "Atom-Powered Robots Run Amok" ];
           :link [ a :Link;
                   :rel iana:alternate ;
                   :to [ :src <http://example.org/2003/12/13/atom03>;]
                   ];
           :id "urn:uuid:1225c695-cfb8-4ebb-aaaa-80da344efa6a"^^xsd:anyUri;
           :updated "2003-12-13T18:30:02Z"^^xsd:dateTime;
           :summary [ :text "Some text." ];
           ];
] .

If I remove the semicolon just before the last line, it works.

[RIO-63] beatiful Turtle writer

Wed, 4 Jun 2008 14:17:21 +0200 (CEST)

I am writing a foaf editor/explorer [1] and I need it to create foaf files that are somewhat humanly readable at least, so that developers can help debug things.
to publish a foaf I create a SPARQL CONSTRUCT query [2] and write the triples to a special temporary context. Using a (set of) CONSTRUCT query should makes it easy to fine tune the triples that one wishes to make public in one's foaf file. I then serialise that foaf file to a (local or remote) file.

It would be nice if the serialiser could group the statements together by subject more. Currently there are a lot of statements about me in the output.
Also relations with the same predicate should be linked together by ","

I will attach the current output of my SPARQL query.

[1] http://blogs.sun.com/bblfish/entry/bof_5911_building_a_web
[2] https://sommer.dev.java.net/source/browse/sommer/trunk/misc/AddressBook/src/net/java/sommer/addressbook/resources/publishfoaf.sparql?rev=384&view=markup
[3] https://sommer.dev.java.net/source/browse/sommer/trunk/misc/AddressBook/src/net/java/sommer/addressbook/FoafPublisher.java?rev=384&view=markup

[RIO-62] TriG writer does not group statements

Wed, 4 Jun 2008 14:17:08 +0200 (CEST)

When I serialise all the contexts of Sesame statements that appear in one graph don't get clustered together.
I find things like

<urn:a> { :me foaf:name "Henry" ... }

...

<urn:a> { :me a foaf:Person ... }

See http://www.openrdf.org/forum/mvnforum/viewthread?thread=1699

This is not a serious problem, but it makes it more difficult to debug the code. It should be easy to fix right? Just select all the graphs, then iterate through the statements in the graph...

[RIO-64] When loading big file with most of it commented, loading is very slow.

Tue, 23 Sep 2008 17:20:48 +0200 (CEST)

loading the data with this statement
    repository.getConnection().add(new FileInputStream(file), baseUri, RDFFormat.RDFXML);

if I comment out (with ) most of the data i have this result:
  loaded statements: 280
  time to load: +7minutes

if nothing is commented out:
  loaded statements: 37002
  time to load: about 1 second

[RIO-67] Relative jar: URIs broken by SES-650 fix

Thu, 12 Mar 2009 02:01:42 +0100 (CET)

The fix for ~~SES-650~~ ('RDFXML incorrectly converts baseURI if it starts with "jar:"') removes the fix for ~~RIO-4~~ ("Should support relative URIs based on 'jar:'").

Ideally, the relative URI support would be returned without breaking ~~SES-650~~.

[RIO-68] Blank nodes merged in TriG

Thu, 2 Apr 2009 03:50:07 +0200 (CEST)

The _:a nodes are merged when uploading the following TriG data. However, since they are in different graphs they name different resources and should be kept as separate blank nodes.

Uploaded data (from http://www4.wiwiss.fu-berlin.de/bizer/TriG/):
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
{
         <http://example.org/bob> dc:publisher "Bob" .
         <http://example.org/alice> dc:publisher "Alice" .
}
<http://example.org/bob> {
          _:a foaf:name "Bob" .
          _:a foaf:mbox <mailto:bob@oldcorp.example.org> .
}
<http://example.org/alice> {
          _:a foaf:name "Alice" .
          _:a foaf:mbox <mailto:alice@work.example.org> .
}

Exported RDF (context nodes removed):
<http://example.org/bob> dc:publisher "Bob" .
<http://example.org/alice> dc:publisher "Alice" .
_:node13vksu2l4x1 foaf:name "Bob" .
_:node13vksu2l4x1 foaf:mbox <mailto:bob@oldcorp.example.org> .
_:node13vksu2l4x1 foaf:name "Alice"
_:node13vksu2l4x1 foaf:mbox <mailto:alice@work.example.org> .

[RIO-65] rio.rdfxml.util.RDFXMLPrettyWriter generates invalid xml for some URIs

Mon, 31 Aug 2009 09:11:52 +0200 (CEST)

The following is a test case for a situation where the resulting RDF/XML is invalid when using the RDFXMLPrettyWriter but valid when printed using the default RDF/XML safe printer. The URI used for the type is a perfectly valid URI and should not interfere with a pretty printer.

//--------------------------------

String testString = "<rdf:Description xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" rdf:about=\"http://bio2rdf.org/uniprot:Q64VS5\"><rdf:type rdf:resource=\"http://bio2rdf.org/uniprot:Protein\"/></rdf:Description>";

Repository myRepository = new SailRepository(new MemoryStore());

myRepository.initialize();

RepositoryConnection myRepositoryConnection = myRepository.getConnection();

myRepositoryConnection.add(new java.io.StringReader(testString), "http://localhost/error-sesame-output", RDFFormat.RDFXML);

java.io.StringWriter stBuff = new java.io.StringWriter();

/****
// The following works
try
{
myRepositoryConnection.export(Rio.createWriter(RDFFormat.RDFXML, stBuff));
}
catch(RepositoryException e)
{
log.error(e.toString());
}
catch(RDFHandlerException e)
{
log.error(e.toString());
}
***/

// The following does not work
try
{
myRepositoryConnection.export(new RDFXMLPrettyWriter(stBuff));
}
catch(RepositoryException e)
{
log.error(e.toString());
}
catch(RDFHandlerException e)
{
log.error(e.toString());
}

String actualRdfXml = stBuff.toString();

//--------------------------------

[RIO-73] Turtle Files with a UTF-8 BOM fail to parse

Tue, 22 Feb 2011 15:35:55 +0100 (CET)

If a Turtle file starts with a UTF-8 BOM then it will fail to parse. The UTF-8 BOM is not required by the Unicode specifications but is not disallowed by it so the parser should accept such files.

A sample file ttl-with-bom.ttl is attached to this issue

[RIO-17] Allow production of relative URIs

Dependency — Fri, 29 Apr 2005 13:08:11 +0200 (CEST)

Currently Rio's parsers automatically resolve relative URIs against the supplied base URI. For some use case it is useful however to delay resolving URIs to serialization time rather than at deserialization time; for example when working with data where the location of a file (specified by a relative URI) is changed between parsing time and writing time.

See also forum thread at http://www.openrdf.org/forum/mvnforum/viewthread?thread=296

[RIO-78] RDFFormat.register(RDFFormat) is not thread-safe

Mon, 27 Feb 2012 16:36:18 +0100 (CET)

This is obvious by inspection.

The backing data structure is an array list. That list is not wrapped with a Collections.synchronizedList().

private static List<RDFFormat> RDF_FORMATS = new ArrayList<RDFFormat>(8);

The register() method also does not use any synchronization.

public static void register(RDFFormat rdfFormat) {
RDF_FORMATS.add(rdfFormat);
}

As a consequence, concurrent modification exceptions are possible with this API.

[RIO-79] SPARQL 1.1 Service Description requires unique uris for RDF and SPARQL interchange formats.

Fri, 2 Mar 2012 18:21:19 +0100 (CET)

SPARQL 1.1 Service Description requires unique uris for RDF and SPARQL interchange formats. Those URIs should be published for the openrdf RDFFormat.BINARY and TupleQueryResultFormat.BINARY. The "unique" URIs are currently being documented at http://www.w3.org/ns/formats/.

This issue really applies to both RIO and Sesame as it spans RDF data interchange and SPARQL result set interchange.

It would be nice if the "unique" URI was part of the RDFFormat and TupleQueryResultFormat data structures. That would make it possible to generate SPARQL 1.1 Service Descriptions in a more declarative manner.

See http://www.w3.org/TR/sparql11-service-description/
See http://www.w3.org/ns/formats/

[RIO-80] TurtleParser does not support bare unlabelled blank node from latest Turtle Working Draft

Dependency — Tue, 23 Oct 2012 02:47:10 +0200 (CEST)

I am having some difficulty parsing turtle files generated by OWLAPI, and from looking at the Turtle TeamSubmission document it seems like the Turtle file syntax is valid.

The offending file samples have lines similar to the following sets of lines, where the turtle parser baulks at each one of them with the same stack trace:

@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
[<urn:P> "007"^^xsd:int] .
[<urn:P> "007"^^<http://www.w3.org/2001/XMLSchema#int>] .
[<urn:P> "007"^^<http://www.w3.org/2001/XMLSchema#integer>] .
[<urn:P> "7"^^<http://www.w3.org/2001/XMLSchema#integer>] .
[<urn:P> 7 ] .
[<urn:P> "7" ].
[<urn:P> "not a number" ].
[ <urn:P> "language literal"@fr ].
[ <urn:P> <urn:Q> ] .

The following file, which is similar, parses fine however:
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
[] <urn:P> "007"^^xsd:int .
[] <urn:P> "007"^^<http://www.w3.org/2001/XMLSchema#int> .
[] <urn:P> "007"^^<http://www.w3.org/2001/XMLSchema#integer> .
[] <urn:P> "7"^^<http://www.w3.org/2001/XMLSchema#integer> .
[] <urn:P> 7 .
[] <urn:P> "7" .
[] <urn:P> "not a number" .
[] <urn:P> "language literal"@fr .
[] <urn:P> <urn:Q> .

The stack trace in each case is as follows, although the samples do not all contain numbers. I focused on testing numbers as the initial broken file had numbers and the break appeared to come from parseNumber, but it breaks in the same way for plain non-numeric literals and URIs:

org.openrdf.rio.RDFParseException: Object for statement missing [line 3]
at org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:525)
at org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1109)
at org.openrdf.rio.turtle.TurtleParser.parseNumber(TurtleParser.java:759)
at org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:541)
at org.openrdf.rio.turtle.TurtleParser.parsePredicate(TurtleParser.java:391)
at org.openrdf.rio.turtle.TurtleParser.parsePredicateObjectList(TurtleParser.java:311)
at org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:301)
at org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:208)
at org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:186)
at org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:131)

[RIO-5] character check in NTriplesParser

Wed, 2 Mar 2005 11:15:43 +0100 (CET)

The NTriplesParser does not check that the parsed characters are legal N-Triples characters. I.e. characters like ä or ô are accepted without warning but they are not legal N-Triples characters.

[RIO-1] XML Literal normalization

Wed, 2 Mar 2005 11:15:14 +0100 (CET)

XML literal normalization is not implemented yet.

[RIO-29] blank node handling in parsers doesn't scale

Wed, 21 Sep 2005 12:54:57 +0200 (CEST)

The processing of blank nodes in Rio's parsers doesn't scale for documents with huge amount of named blank nodes in it. The reason for this is that the parsers keep track of all encountered named blank nodes as they may be referenced again later in the document. As blank node names scope to the entire document, the same blank node name must map to the same blank node objects. Possibly the best way to solve this is to do the mapping in an external handler. One such handler might use a database or the file system to store mapping information instead of keeping this information in main memory.

[RIO-47] Reduce memory requirements for verifying uniqueness of rdf:ID attributes

Wed, 14 Jun 2006 12:24:04 +0200 (CEST)

Source: http://www.openrdf.org/forum/mvnforum/viewthread?thread=967

The RDF/XML specification requires the values of rdf:ID attributes combined with the applicable base URI to be unique within a single RDF/XML document[1]. The RDF/XML parser currently stores these ID-base URI-combinations as URIs in a HashMap. As a result, a considerable amount of memory is needed to be able to parse documents that contain large amounts of rdf:ID attributes, such as the Uniprot benchmark files[2]. As the number of base URIs normally is much smaller than the number of IDs it is possible to reduce the memory requirements by storing the IDs per base URI so that the base URI only needs to be stored once.

[1] http://www.w3.org/TR/2004/REC-rdf-syntax-grammar-20040210/#section-constraints-id
[2] http://expasy3.isb-sib.ch/~ejain//rdf/data-for-benchmarks/

[RIO-53] Turtle Parser does not update location

Fri, 3 Nov 2006 06:10:20 +0100 (CET)

The Turtle Parser only updates the line location at the beginning of the file and when skipping lines.

[RIO-59] Add a stylesheet to the RDF/XML serialized data

Mon, 30 Jul 2007 15:18:10 +0200 (CEST)

RDF/XML is sometimes unreadable for human beings, so we developped an XSL that render it nicely. We had to extends the RDFXML writer to incorporate it to the data. Might be cleaner and useful to other rio user to integrate it into the RDFXMLWriter.

[RIO-43] N3Parser

Mon, 13 Apr 2009 06:34:08 +0200 (CEST)

Is a N3Parser planned?
It would be nice, since we can write n3 files!

[RIO-69] N3 and Turtle media types need updating

Tue, 7 Jul 2009 19:00:29 +0200 (CEST)

The MIME / media / content types for N3 and Turtle are currently defined as text/rdf+n3 and application/x-turtle respectively: http://repo.aduna-software.org/svn/org.openrdf/sesame/trunk/core/rio/api/src/main/java/org/openrdf/rio/RDFFormat.java .

They need to be updated to text/n3 and text/turtle. For Turtle see the latest specification at http://www.w3.org/TeamSubmission/turtle/#sec-mediaReg . The N3 specification is a bit buggy with regard to that, it switches between text/rdf+n3 and text/n3: http://www.w3.org/TeamSubmission/n3/ . However see also http://www.w3.org/blog/SW/2008/01/15/w3c_team_submission_on_n3_and_turtle , http://chatlogs.planetrdf.com/swig/2009-04-01.html#T14-00-16 and some more discussion on http://lists.w3.org/Archives/Public/semantic-web/2009May/0021.html .

Since RDFFormat accepts a collection of MIME types perhaps it would be even better to add the old ones as well so that the right parser can be selected for data served with the old types. For Turtle the type application/turtle could be added to such a collection as well, as it was the primary type mentioned on http://www.dajobe.org/2004/01/turtle/2007-11-20/#sec-mime .

[RIO-72] There is no way to specify "preserveBNodeIDs" property when doing RDF import

Tue, 1 Dec 2009 18:35:05 +0100 (CET)

* There is now way to pass pre-created to RepositoryConnection.add(Reader|InputStream|File) method with this option enabled.
* Both RDFParserBase and RDFInserter have preserveBNodeIDs property. In the first class it is false by default, in the second is true by default. There should be a single place for this functionality.

Nice to have feature:
- renumerateBNodeIDs property for RDFWriter, which should re-number nodes like "n1", "n2", "n3" ([see forum|http://sourceforge.net/mailarchive/forum.php?thread_name=4B139FB4.5080809%40mail.ru&forum_name=sesame-general])

[RIO-54] RDFXMLPrettyWriter needs cleanup

Mon, 26 Feb 2007 14:59:59 +0100 (CET)

Only private method should start with an '_'
The method flushStatements should be renamed and should not throw IOException.

[RIO-71] RDFXMLWriter does not make the XML declaration optional

Mon, 23 Nov 2009 02:24:17 +0100 (CET)

In RDFXMLWriter there is a hardcoded line:

writer.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");

If this line could be configurable it would be great, so I can use the resulting RDF as part of an existing XML document without manually stripping these characters off.