openRDF.org Issue Tracker

[SES-484] Add stringValue() to org.openrdf.model.Value as a substitute for the old toString() implementation

Thu, 20 Mar 2008 20:16:33 +0100 (CET)

The behaviour of Literal.toString() and BNode.toString() was changed in beta6 to make debugging easier (see ~~SES-454~~). Although the behaviour of these methods was never specified in the RDF Model API, a lot of developers tended to use as a convenience method to retrieve a literal's label or a bnode's ID as it didn't require any casting. We should add a stringValue() method to the Value interface as a substitute for the old toString() implementation.

This suggestion originally comes from the forum: http://www.openrdf.org/forum/mvnforum/viewthread?thread=1498#5596

[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-483] DirectTypeHierarchyInferencer is triggered too often

Thu, 20 Mar 2008 20:15:29 +0100 (CET)

The DirectTypeHierarchyInferencer currently recomputes the direct-* statements upon each commit. As a simple optimization, this process can be skipped unless an rdf:type, rdfs:subClassOf or rdfs:subPropertyOf statements was updated.

[SES-485] Inline "variable assigments" in statement patterns

Thu, 20 Mar 2008 20:15:32 +0100 (CET)

The generic query optimizer should inline "variable assignments" in statement patterns to improve query evaluation performance. For example with the following SeRQL query:

select *
from {X} P {Y}
where X = <http://example.org>

To evaluate the (X, P, Y) statement pattern, it helps a lot to know that X should be equal <http://example.org> as it greatly reduces the search space for the pattern.This is a very common query pattern, therefor this optization should be implemented before 2.0-final, if possible.

For comparison, Sesame 1.x does do this optimization and performance a lot better on this type of query. See the forum for some results: http://www.openrdf.org/forum/mvnforum/viewthread?thread=1506

Care should be taken not to inline (literal) comparison. The query optimizer can, however, inline SameTerm operators. Comparison operators where one of the arguments is a URI or blank node can be converted to a SameTerm as a pre-processing step.

[SES-489] Add support for SPARQL-dataset loading

Thu, 20 Mar 2008 20:15:27 +0100 (CET)

Sesame currently supports querying of SPARQL-datasets, but it does not yet load the specified resources yet. This functionality is requried to implement SPARQL endpoints based on Sesame.

[SES-493] Sesame server fails to handle (query-) post requests that specify a charset

Thu, 20 Mar 2008 20:16:28 +0100 (CET)

Issue reported here: http://www.openrdf.org/forum/mvnforum/viewthread?thread=1521

Due to restrictions in the HTTP protocol, one can not use HTTP-GET requests to post queries containing non-ASCII characters. The best alternative is to use a POST-request and to encode the parameters in the request body. The MIME type for such requests is "application/x-www-form-urlencoded". The Sesame HTTP server currently support this mechanism, but it fails when a specific character set is specified in the Content-Type header.

[SES-491] OpenRDF Workbench fails to open when previously configured Sesame server is unavailable

Thu, 20 Mar 2008 20:15:34 +0100 (CET)

If OpenRDF Workbench was previously used on some Sesame server that is no longer available, but this server's URL is still stored in a browser's cookie, then Workbench fails to open with the stack trace shown below. As a workaround, one can remove the "server.select.url" as well as any "JSESSIONID" cookies from the browser's cache to enforce a new server selection.

HTTP Status 500 -

------------------------------------------------------------------------

*type* Exception report

*message* __

*description* _The server encountered an internal error () that
prevented it from fulfilling this request._

*exception*

org.apache.jasper.JasperException: javax.el.ELException: Error reading 'repositoryInfos' on type org.openrdf.http.webclient.server.Server
org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServletWrapper.java:541)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:435)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:320)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:247)
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1123)
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:860)
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:774)
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:460)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:415)
javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:96)
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
info.aduna.webapp.filters.ResourceRedirectFilter.doFilter(ResourceRedirectFilter.java:72)

*root cause*

javax.el.ELException: Error reading 'repositoryInfos' on type org.openrdf.http.webclient.server.Server
javax.el.BeanELResolver.getValue(BeanELResolver.java:66)
javax.el.CompositeELResolver.getValue(CompositeELResolver.java:53)
org.apache.el.parser.AstValue.getValue(AstValue.java:97)
org.apache.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)
org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:923)
org.apache.jsp.WEB_002dINF.views.server.overview_jsp._jspx_meth_c_005fforEach_005f4(overview_jsp.java:2627)
org.apache.jsp.WEB_002dINF.views.server.overview_jsp._jspService(overview_jsp.java:339)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:393)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:320)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:247)
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1123)
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:860)
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:774)
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:460)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:415)
javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:96)
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
info.aduna.webapp.filters.ResourceRedirectFilter.doFilter(ResourceRedirectFilter.java:72)

*root cause*

org.openrdf.repository.RepositoryException: java.io.IOException: Failed to get query result from server: /openrdf-sesame/repositories
org.openrdf.repository.manager.RemoteRepositoryManager.createRepositoryInfos(RemoteRepositoryManager.java:172)
org.openrdf.repository.manager.RepositoryManager.getRepositoryInfoMap(RepositoryManager.java:307)
org.openrdf.repository.manager.RepositoryManager.getAllRepositoryInfos(RepositoryManager.java:291)
org.openrdf.http.webclient.server.Server.getRepositoryInfos(Server.java:52)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
java.lang.reflect.Method.invoke(Unknown Source)
javax.el.BeanELResolver.getValue(BeanELResolver.java:62)
javax.el.CompositeELResolver.getValue(CompositeELResolver.java:53)
org.apache.el.parser.AstValue.getValue(AstValue.java:97)
org.apache.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)
org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:923)
org.apache.jsp.WEB_002dINF.views.server.overview_jsp._jspx_meth_c_005fforEach_005f4(overview_jsp.java:2627)
org.apache.jsp.WEB_002dINF.views.server.overview_jsp._jspService(overview_jsp.java:339)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:393)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:320)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:247)
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1123)
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:860)
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:774)
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:460)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:415)
javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:96)
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
info.aduna.webapp.filters.ResourceRedirectFilter.doFilter(ResourceRedirectFilter.java:72)

*root cause*

java.io.IOException: Failed to get query result from server: /openrdf-sesame/repositories
org.openrdf.http.client.HTTPClient.getTupleQueryResult(HTTPClient.java:1029)
org.openrdf.http.client.HTTPClient.getRepositoryList(HTTPClient.java:367)
org.openrdf.http.client.HTTPClient.getRepositoryList(HTTPClient.java:350)
org.openrdf.repository.manager.RemoteRepositoryManager.createRepositoryInfos(RemoteRepositoryManager.java:143)
org.openrdf.repository.manager.RepositoryManager.getRepositoryInfoMap(RepositoryManager.java:307)
org.openrdf.repository.manager.RepositoryManager.getAllRepositoryInfos(RepositoryManager.java:291)
org.openrdf.http.webclient.server.Server.getRepositoryInfos(Server.java:52)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
java.lang.reflect.Method.invoke(Unknown Source)
javax.el.BeanELResolver.getValue(BeanELResolver.java:62)
javax.el.CompositeELResolver.getValue(CompositeELResolver.java:53)
org.apache.el.parser.AstValue.getValue(AstValue.java:97)
org.apache.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)
org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:923)
org.apache.jsp.WEB_002dINF.views.server.overview_jsp._jspx_meth_c_005fforEach_005f4(overview_jsp.java:2627)
org.apache.jsp.WEB_002dINF.views.server.overview_jsp._jspService(overview_jsp.java:339)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:393)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:320)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:247)
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1123)
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:860)
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:774)
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:460)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:415)
javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:96)
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
info.aduna.webapp.filters.ResourceRedirectFilter.doFilter(ResourceRedirectFilter.java:72)

*note* _The full stack trace of the root cause is available in the
Apache Tomcat/6.0.13 logs._

------------------------------------------------------------------------

Apache Tomcat/6.0.13

[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-476] OutOfMemoryError from MemoryStore.startSyncTimer

Thu, 20 Mar 2008 20:15:00 +0100 (CET)

I suspect, if the store is closed short after the sync thread was started but hasn't done something, then maybe these threads live on forever? Somehow th number of threads seems to grow too large.

java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Thread.java:574)
at java.util.Timer.<init>(Timer.java:137)
at java.util.Timer.<init>(Timer.java:106)
at org.openrdf.sail.memory.MemoryStore.startSyncTimer(MemoryStore.java:723)
at org.openrdf.sail.memory.MemoryStoreConnection.commitInternal(MemoryStoreConnection.java:285)
at org.openrdf.sail.helpers.SailConnectionBase.commit(SailConnectionBase.java:255)
at org.openrdf.repository.sail.SailRepositoryConnection.commit(SailRepositoryConnection.java:83)
at org.openrdf.repository.base.RepositoryConnectionBase.autoCommit(RepositoryConnectionBase.java:211)
at org.openrdf.repository.base.RepositoryConnectionBase.remove(RepositoryConnectionBase.java:481)
at org.openrdf.rdf2go.RepositoryModel.removeStatement(RepositoryModel.java:312)
at org.ontoware.rdf2go.model.impl.AbstractModelAddRemove.removeStatement(AbstractModelAddRemove.java:83)
at org.ontoware.rdf2go.model.impl.AbstractModel.removeStatement(AbstractModel.java:399)
at org.ontoware.rdf2go.model.impl.NotifyingModelLayer.removeStatement(NotifyingModelLayer.java:242)
at org.ontoware.rdf2go.model.impl.NotifyingModelLayer.removeAll(NotifyingModelLayer.java:171)
at org.ontoware.rdfreactor.runtime.Base.removeAll_unsynchronized(Base.java:125)
at org.ontoware.rdfreactor.runtime.Base.set(Base.java:132)
at org.semanticdesktop.swecr.model.rdf.generated.Relation.setInverse(Relation.java:88)
at org.semanticdesktop.swecr.model.rdf.RelationOnCore.<init>(RelationOnCore.java:37)
at org.semanticdesktop.swecr.model.rdf.SwcmOnRDF.createRelation(SwcmOnRDF.java:1122)
at org.semanticdesktop.swecr.model.rdf.SwcmOnRDF.createRelation(SwcmOnRDF.java:1167)
at org.semanticdesktop.swecr.model.util.RepositoryUtils.addTestData_manyStatements(RepositoryUtils.java:255)

[SES-479] ORDER BY modifier does not always produce expected/correct results

Thu, 20 Mar 2008 20:14:56 +0100 (CET)

Running the query:

   select ?o { ?s ?p ?o } order by ?o

on this set of triples:

   <foo:bar1> <foo:prop3> "4"@en .
   <foo:bar2> <foo:prop2> "10"^^<http://www.w3.org/2001/XMLSchema#int> .
   <foo:bar3> <foo:prop1> "9"^^<http://www.w3.org/2001/XMLSchema#int> .

produces the following result:

   "10"^^<http://www.w3.org/2001/XMLSchema#int>
   "4"@en
   "9"^^<http://www.w3.org/2001/XMLSchema#int>

While the individual consecutive value pairs are ordered correctly (the order of literals with language tags and datatyped literals is not defined), the total result is not: "9"^^xsd:int should come before "10"^^xsd:int.

FWIW: running this test through ARQ (tested with v2.1) produces the exact same (erroneous) result.

[SES-480] NativeStore doesn't correctly report removed statements to SailConnectionListener's

Thu, 20 Mar 2008 20:14:51 +0100 (CET)

NativeStore doesn't correctly report removed statements to SailConnectionListener's

[SES-481] DirectTypeHierarchyInferencer doesn't initialize newly created repositories

Thu, 20 Mar 2008 20:14:24 +0100 (CET)

Newly created repositories that use the DirectTypeHierarchyInferencer do not initially contain the direct* properties. The DirectTypeHierarchyInferencer forgets to add these statements upon the first initialization of the repository.

[SES-487] MemoryStore.getContextIDs() sometimes returns IDs of cleared contexts

Thu, 20 Mar 2008 20:14:35 +0100 (CET)

Issue reported on the forum: http://www.openrdf.org/forum/mvnforum/viewthread?thread=1503

"I've just moved to 2.0-rc1 and I'm seeing some strange synchronisation issues. Specifically:

Create a repository containing statements with contexts (about 150 statements in this case)
Create a connection, clear(), commit(), close().
Open a new connection (in the same thread) and get the list of contexts.

If this is done with no yeald or sleep I still see the old contexts that should have been cleared. If i sleep or single step in the debugger I see no contexts remaining."

...

"Also calling clear() after the add but before the first commit doesn't seem to remove the contexts at all."

[SES-486] NativeStore doesn't properly handle transaction with combined add & remove operations

Thu, 20 Mar 2008 20:14:53 +0100 (CET)

The following JUnit test for the RepositoryConnectionTest class fails on the NativeStore:

public void testAddRemove()
throws Exception
{
URI FOAF_PERSON = vf.createURI("http://xmlns.com/foaf/0.1/Person");
final Statement stmt = vf.createStatement(bob, name, nameBob);

testCon.add(bob, RDF.TYPE, FOAF_PERSON);

testCon.setAutoCommit(false);
testCon.add(stmt);
testCon.remove(stmt);
testCon.commit();

testCon.exportStatements(null, null, null, false, new RDFHandlerBase() {

@Override
public void handleStatement(Statement st)
throws RDFHandlerException
{
assertTrue(!stmt.equals(st));
}
});
}

[SES-488] MemoryStore doesn't process "statements neutral" transactions correctly

Related — Mon, 30 Jun 2008 17:06:09 +0200 (CEST)

The MemoryStore doesn't correctly process transactions that do not affect the set of stored statements. Examples of this are transactions where a statement is added and removed in the same transaction, and transactions where an inferred statement is substituted by an explicit one (or vice versa). In those cases, MemoryStore doesn't increase the snapshot number for the store and it also doesn't schedule a snapshot cleanup.

[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-490] MemoryStore's leaves a running file sync thread after being shut down

Thu, 20 Mar 2008 20:14:31 +0100 (CET)

The MemoryStore uses a separate thread for delayed file synchronization if such behaviour is specified using the syncDelay parameter. This thread, however, keeps running even after the store has been shut down. This running thread prevents a normal exit of the JVM.

This problem was likely introduced while fixing ~~SES-476~~.

[SES-478] Inferred statements not visible to connection during transaction

Thu, 20 Mar 2008 20:14:26 +0100 (CET)

The current inferencing Sails (only) apply their inferencing when commit is called. As a result of this, the (updated) inferred statements are not available during a transactions. For example, consider this code fragment:

  con.setAutoCommit(false);
  con.add(....);
  con.remove(...);
  con.getStatements(..., true);
  con.setAutoCommit(true);

The results returned by getStatements(...) are based on the data that was available before the transaction started, and are thus out of date, at least as far as this connection is concerned.