https://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-09-16T23:39:12ZEcoinformatics RedmineKepler - Bug #5184: sanity check(s) when attempting to open owl filehttps://projects.ecoinformatics.org/ecoinfo/issues/5184?journal_id=179402010-09-16T23:39:12ZDerik Barseghianbarseghian@nceas.ucsb.edu
<ul></ul><p>As requested, stack trace:</p>
<pre><code>[run] Ran additional initialization for module reporting from class org.kepler.module.reporting.Initialize<br /> [run] Kepler Initializing...<br /> [run] getAllRspnsElement is null<br /> [run] org.semanticweb.owl.io.OWLOntologyCreationIOException: /Users/derik/dev2/kepler.modules.2.1/common-2.1/configs/ptolemy/configs/kepler/ontologies/Users/derik/KeplerData/modules/core/onto7934053400911427464.owl (No such file or directory)<br /> [run] at uk.ac.manchester.cs.owl.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:166)<br /> [run] at uk.ac.manchester.cs.owl.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:380)<br /> [run] at uk.ac.manchester.cs.owl.OWLOntologyManagerImpl.loadOntologyFromPhysicalURI(OWLOntologyManagerImpl.java:349)<br /> [run] at org.kepler.sms.NamedOntModel.initialize(NamedOntModel.java:190)<br /> [run] at org.kepler.sms.OntologyCatalog.initialize(OntologyCatalog.java:475)<br /> [run] at org.kepler.sms.OntologyCatalog.initialize(OntologyCatalog.java:450)<br /> [run] at org.kepler.sms.OntologyCatalog.&lt;init&gt;(OntologyCatalog.java:101)<br /> [run] at org.kepler.sms.OntologyCatalog.instance(OntologyCatalog.java:119)<br /> [run] at org.kepler.objectmanager.library.LibIndex.assureOntologyComponent(LibIndex.java:627)<br /> [run] at org.kepler.objectmanager.library.LibIndex.rebuild(LibIndex.java:261)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.buildLibrary(LibraryManager.java:343)<br /> [run] at org.kepler.moml.KARLibraryBuilder.buildLibrary(KARLibraryBuilder.java:78)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openLibrary(UserActorLibrary.java:202)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openUserLibrary(UserActorLibrary.java:140)<br /> [run] at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:330)<br /> [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:347)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1128)<br /> [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:477)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.&lt;init&gt;(ConfigurationApplication.java:226)<br /> [run] at ptolemy.actor.gui.MoMLApplication.&lt;init&gt;(MoMLApplication.java:81)<br /> [run] at ptolemy.vergil.VergilApplication.&lt;init&gt;(VergilApplication.java:110)<br /> [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:219)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)<br /> [run] Caused by: java.io.FileNotFoundException: /Users/derik/dev2/kepler.modules.2.1/common-2.1/configs/ptolemy/configs/kepler/ontologies/Users/derik/KeplerData/modules/core/onto7934053400911427464.owl (No such file or directory)<br /> [run] at java.io.FileInputStream.open(Native Method)<br /> [run] at java.io.FileInputStream.&lt;init&gt;(FileInputStream.java:106)<br /> [run] at java.io.FileInputStream.&lt;init&gt;(FileInputStream.java:66)<br /> [run] at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:70)<br /> [run] at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:161)<br /> [run] at org.semanticweb.owl.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:105)<br /> [run] at org.semanticweb.owl.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:128)<br /> [run] at org.coode.owl.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:85)<br /> [run] at uk.ac.manchester.cs.owl.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:154)<br /> [run] ... 28 more</code></pre> Kepler - Bug #5184: sanity check(s) when attempting to open owl filehttps://projects.ecoinformatics.org/ecoinfo/issues/5184?journal_id=179412010-09-29T20:21:39ZSean Riddleswriddle@gmail.com
<ul></ul><p>This is fixed in r25854-8. Sanity checks are present now when saving and loading the ontology_catalog.xml file to ensure that it consists of valid data.</p> Kepler - Bug #5184: sanity check(s) when attempting to open owl filehttps://projects.ecoinformatics.org/ecoinfo/issues/5184?journal_id=179422013-03-27T21:29:31ZRedmine Admin
<ul></ul><p>Original Bugzilla ID was 5184</p>