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[bioontology-support] Error Uploading Latest Version of HHEAR Ontology

Masters, James James.Masters at mssm.edu
Mon Mar 14 11:28:11 PDT 2022


Thanks. I think I found the correct import URL anyway. I just reuploaded my ontology with the owl:imports corrected. Hopefully this one will pass.

From: John Graybeal <jgraybeal at stanford.edu>
Date: Monday, March 14, 2022 at 1:57 PM
To: Masters, James <James.Masters at mssm.edu>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu>, support at bioontology.org <support at bioontology.org>
Subject: Re: [bioontology-support] Error Uploading Latest Version of HHEAR Ontology
James,

No, I don't think so, that will land you at the summary page for the ontology.

If there is an OWL download link on that summary page, that might work—that'd be the original ontology. But the link to that will look weird, and might include an API key, and I wouldn't recommend it for those reasons.

John


On Mar 14, 2022, at 10:45 AM, Masters, James <James.Masters at mssm.edu<mailto:James.Masters at mssm.edu>> wrote:

Quick followup:

Most of the ontologies we list as imports are on Bioportal themselves. Can I use the PURL links provided by Bioportal as the target for the owl:imports ? I.e. for DOID, can I add

<owl:imports rdf:resource=”http://purl.bioontology.org/ontology/DOID<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_DOID&d=DwMGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=hQ0bGN57V39amWTBhe8j3lIW_CWY61Lm3HCA9rNEthk&s=In46_rEz48-Ml-DiIzRyhTZP_2DP5eM0XdwKu7yHDKE&e=>”>

? Will those links resolve correctly in the owl:imports processing?

Thanks,

James “Chip” Masters, PhD (he/him)
Director, Semantic Technology and HHEAR Data Repository
Scientific Computing and Data
Icahn School of Medicine at Mount Sinai
150 E 42nd St
New York, NY 10017
United States


From: Masters, James <James.Masters at mssm.edu<mailto:James.Masters at mssm.edu>>
Date: Monday, March 14, 2022 at 9:59 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>, support at bioontology.org<mailto:support at bioontology.org> <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] Error Uploading Latest Version of HHEAR Ontology
This is very helpful. Thank you for the details. I can fix the imports statements and reload.

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Date: Friday, March 11, 2022 at 8:17 PM
To: support at bioontology.org<mailto:support at bioontology.org> <support at bioontology.org<mailto:support at bioontology.org>>
Cc: Masters, James <James.Masters at mssm.edu<mailto:James.Masters at mssm.edu>>
Subject: Re: [bioontology-support] Error Uploading Latest Version of HHEAR Ontology
USE CAUTION: External Message.
Hello James,

In addition to John’s response, I can add that the system wasn’t able to load your ontology due to the owl:imports statement:

<owl:imports rdf:resource="urn:x-evn-master:dublin_core_terms_ontology"/>

This import statement occurs twice on lines 1179 and 15917.

I tried loading your ontology in the Protege ontology editing software, and noticed the same behavior:


<Screen Shot 2022-03-11 at 5.00.17 PM.png>


The Protege log file contains the following stack trace, which I though may be useful:

INFO  17:00:04  Imported ontology document IRI urn:x-evn-master:dublin_core_terms_ontology is malformed.
   INFO  17:12:55  Malformed URL: Unknown protocol: urn
java.net.MalformedURLException: Unknown protocol: urn
at java.net.URL.<init>(URL.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__URL.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=Ern25f5olauumpmeiFG12kZv5acN0_5G6yO0RXw6TFg&e=>:627) ~[na:1.8.0_121]
at java.net.URL.<init>(URL.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__URL.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=Ern25f5olauumpmeiFG12kZv5acN0_5G6yO0RXw6TFg&e=>:490) ~[na:1.8.0_121]
at java.net.URL.<init>(URL.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__URL.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=Ern25f5olauumpmeiFG12kZv5acN0_5G6yO0RXw6TFg&e=>:439) ~[na:1.8.0_121]
at java.net.URI.toURL(URI.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__URI.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=vkhVjHkFTxVoToVBeQEhwYrbGKWarGQhiql81wMoYSM&e=>:1089) ~[na:1.8.0_121]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.canLoad(OWLOntologyFactoryImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyFactoryImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=ANGf2aiEVFs5PszOFCJSmmaDcN46konAqrytOs2deIE&e=>:159) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyManagerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=CMsLdUZe3M6tSu7YSbpNwus_CRpuI7CxWfuydaTJSNg&e=>:1256) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyManagerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=CMsLdUZe3M6tSu7YSbpNwus_CRpuI7CxWfuydaTJSNg&e=>:1215) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyManagerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=CMsLdUZe3M6tSu7YSbpNwus_CRpuI7CxWfuydaTJSNg&e=>:1115) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyManagerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=CMsLdUZe3M6tSu7YSbpNwus_CRpuI7CxWfuydaTJSNg&e=>:1833) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyManagerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=CMsLdUZe3M6tSu7YSbpNwus_CRpuI7CxWfuydaTJSNg&e=>:1871) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__TripleHandlers.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=9FGy3I4RZa_vmpJ9DfN5ZftksMJbZTLTbA4g4Pp2Q1I&e=>:1651) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__TripleHandlers.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=9FGy3I4RZa_vmpJ9DfN5ZftksMJbZTLTbA4g4Pp2Q1I&e=>:278) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLRDFConsumer.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=KWW8YA09zzIDj5WmwFBt0unKeZHbayMtYOqkzokw5aY&e=>:1554) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__RDFParser.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=oudAxwlRUKS0PDzPIyzFPRFYKlzSYw3It6ATyyUijs4&e=>:370) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__StartRDF.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=xemKEj6J2U7kQEi837KyBRxlSVbAHxwZRFrN3kO1-g4&e=>:236) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__StartRDF.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=xemKEj6J2U7kQEi837KyBRxlSVbAHxwZRFrN3kO1-g4&e=>:658) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__RDFParser.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=oudAxwlRUKS0PDzPIyzFPRFYKlzSYw3It6ATyyUijs4&e=>:201) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__AbstractSAXParser.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=-IQvV-MqZmyR4EHbN7k1zKmn3qMSZVUjW6ekTyShiZ8&e=>:509) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__AbstractXMLDocumentParser.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=IsWIgMYGD4okeD8Z9bOgYuZj3H20C0blFi9gSq0JFag&e=>:182) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__XMLNSDocumentScannerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=WiUAMKY0MXpo834L7_9WLG9cB5AcRdXUv5BW7gKmz44&e=>:351) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__XMLDocumentFragmentScannerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=p2SYwoq9r2XKVVPI3v_b-YsmzXtTTjT6CpWeDkKWkJs&e=>:2784) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__XMLDocumentScannerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=QBWJoE4o8bH99R62oRKPzBpOpAnT5IeJKkp3A--NXW4&e=>:602) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__XMLNSDocumentScannerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=WiUAMKY0MXpo834L7_9WLG9cB5AcRdXUv5BW7gKmz44&e=>:112) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__XMLDocumentFragmentScannerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=p2SYwoq9r2XKVVPI3v_b-YsmzXtTTjT6CpWeDkKWkJs&e=>:505) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__XML11Configuration.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=F6PjkVIueMoF-_Bdl0SaOAHB43cwHcXbXzwsmOtoC0E&e=>:841) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__XML11Configuration.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=F6PjkVIueMoF-_Bdl0SaOAHB43cwHcXbXzwsmOtoC0E&e=>:770) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__XMLParser.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=UNAYWVvoznK-iUVYCIQXDC43eShw6Prm9OQsu4AZ5nA&e=>:141) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__AbstractSAXParser.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=-IQvV-MqZmyR4EHbN7k1zKmn3qMSZVUjW6ekTyShiZ8&e=>:1213) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__SAXParserImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=XDxD6gE2n8M5h0Esr2ZIFWpURsz6B0UqRWeOSf0BfEk&e=>:643) [na:1.8.0_121]
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__SAXParserImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=XDxD6gE2n8M5h0Esr2ZIFWpURsz6B0UqRWeOSf0BfEk&e=>:327) [na:1.8.0_121]
at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__RDFParser.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=oudAxwlRUKS0PDzPIyzFPRFYKlzSYw3It6ATyyUijs4&e=>:145) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__RDFXMLParser.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=sZv880vCNAIdczbeQgI4ekKAjUlb6nVowauU7VilKLg&e=>:73) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyFactoryImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=ANGf2aiEVFs5PszOFCJSmmaDcN46konAqrytOs2deIE&e=>:221) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyManagerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=CMsLdUZe3M6tSu7YSbpNwus_CRpuI7CxWfuydaTJSNg&e=>:1262) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyManagerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=CMsLdUZe3M6tSu7YSbpNwus_CRpuI7CxWfuydaTJSNg&e=>:1215) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OWLOntologyManagerImpl.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=CMsLdUZe3M6tSu7YSbpNwus_CRpuI7CxWfuydaTJSNg&e=>:1172) [owlapi-osgidistribution.jar:4.5.9.2019-02-01T07:24:44Z]
at org.protege.editor.owl.model.io.OntologyLoader.loadOntologyInternal(OntologyLoader.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OntologyLoader.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=vT7xQpq5Zk1fJMZI0PL68gZc0OOK_JdIzFeM60fH8vE&e=>:104) [protege-editor-owl.jar:na]
at org.protege.editor.owl.model.io.OntologyLoader.lambda$loadOntologyInOtherThread$0(OntologyLoader.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__OntologyLoader.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=vT7xQpq5Zk1fJMZI0PL68gZc0OOK_JdIzFeM60fH8vE&e=>:62) [protege-editor-owl.jar:na]
at java.util.concurrent.FutureTask.run(FutureTask.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__FutureTask.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=lOoJuCQcrMrG0W1ZtEYbvsSGWJDkk4yoZrkXAKnQ2ME&e=>:266) ~[na:1.8.0_121]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__ThreadPoolExecutor.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=ZEMFIWu9zVYgKrSfgY6i5eH3mCWUphE9Lv355r9DO2Q&e=>:1142) ~[na:1.8.0_121]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__ThreadPoolExecutor.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=ZEMFIWu9zVYgKrSfgY6i5eH3mCWUphE9Lv355r9DO2Q&e=>:617) ~[na:1.8.0_121]
at java.lang.Thread.run(Thread.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__Thread.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=KB34UZAEj2DRRkisxypRMsBFAXXb6oBCZO6rwKZ4WHc&e=>:745) ~[na:1.8.0_121]
Caused by: java.lang.IllegalStateException: Unknown protocol: urn
at org.apache.felix.framework.URLHandlersStreamHandlerProxy.parseURL(URLHandlersStreamHandlerProxy.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__URLHandlersStreamHandlerProxy.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=cqibaUGP3VNOne_CLffNM3UTueio8id7UQf3ZfGBa4Q&e=>:373) ~[org.apache.felix.main.jar:na]
at java.net.URL.<init>(URL.java<https://urldefense.proofpoint.com/v2/url?u=http-3A__URL.java&d=DwQGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=Ern25f5olauumpmeiFG12kZv5acN0_5G6yO0RXw6TFg&e=>:622) ~[na:1.8.0_121]



Kind regards,
Jennifer





On Mar 11, 2022, at 3:59 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Hello James,

Because we are relatively short staffed, we are unable to quickly review cases like yours ourselves. I can point you to a potentially useful resource from our OntoPortal Administration guide:
  https://ontoportal.github.io/administration/ontologies/troubleshooting_submissions/#check-the-ontology-ways-to-pre-validate-an-ontology<https://urldefense.proofpoint.com/v2/url?u=https-3A__ontoportal.github.io_administration_ontologies_troubleshooting-5Fsubmissions_-23check-2Dthe-2Dontology-2Dways-2Dto-2Dpre-2Dvalidate-2Dan-2Dontology&d=DwMGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=-vo1bVMl7D_B-t8peaSfG7UnFA8x91OQoU93ZQhHBJk&e=>

With this information, the following information from the log file may be useful. (Sorry for the ugly formatting!)  It looks like the problem may be that this is not a recognizable ontology format:
  2022-03-10T18:43:57 [main] ERROR o.s.ncbo.oapiwrapper.OntologyParser - Could not find an appropriate factory to load ontology from ontology document: <urn:x-evn-master:dublin_core_terms_ontology>

Without looking at the ontology, I might guess that there is an ontology identifier (for the Dublin Core ontology) that the parse can't find, since the identifier is a non-resolvable URN.

You can likely confirm that following one of the suggestions in the OntoPortal Administration guide link above. If not, let us know and eventually we, or someone else on the list, will find time to help.

John

# Logfile created on 2022-03-10 18:43:40 -0800 by logger.rb/v1.5.0
I, [2022-03-10T18:43:40.327999 #20987]  INFO -- : ["Starting to processhttp://data.bioontology.org/ontologies/HHEAR/submissions/9<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_ontologies_HHEAR_submissions_9&d=DwMGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=WF9x69cBa7A-Na7eYriK3qjYfwtAhq3yiqogMNbH2-4&e=>"]
I, [2022-03-10T18:43:40.767469 #20987]  INFO -- : ["Starting to process HHEAR/submissions/9"]
I, [2022-03-10T18:43:41.445991 #20987]  INFO -- : ["Java call [java -DentityExpansionLimit=2500000 -Xmx10240M -jar /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/bin/owlapi-wrapper-1.3.8.jar -m /srv/ncbo/repository/HHEAR/9/hhear-ontology-1.6.rdf -o /srv/ncbo/repository/HHEAR/9 -r true]"]
I, [2022-03-10T18:43:57.183604 #20987]  INFO -- : ["2022-03-10T18:43:41 [main] INFO  o.s.n.o.OntologyParserCommand - Parsing invocation with values: ParserInvocation [inputRepositoryFolder=null, outputRepositoryFolder=/srv/ncbo/repository/HHEAR/9, masterFileName=/srv/ncbo/repository/HHEAR/9/hhear-ontology-1.6.rdf, invocationId=0, parserLog=, userReasoner= true]\n\n2022-03-10T18:43:41 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - executor ...\n\n2022-03-10T18:43:42 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Input repository folder is null. Unique file being parsed.\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.binary.BinaryRDFParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.n3.N3ParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.nquads.NQuadsParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.ntriples.NTriplesParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.rdfjson.RDFJSONParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.jsonld.JSONLDParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.rdfxml.RDFXMLParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.trix.TriXParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.turtle.TurtleParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.trig.TriGParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.XMLSchemaDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.RDFDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.DBPediaDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.VirtuosoGeometryDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.GeoSPARQLDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.LanguageHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.languages.RFC3066LanguageHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.LanguageHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.languages.BCP47LanguageHandler\n\n2022-03-10T18:43:57 [main] ERROR o.s.ncbo.oapiwrapper.OntologyParser - Could not find an appropriate factory to load ontology from ontology document: <urn:x-evn-master:dublin_core_terms_ontology>\n\n2022-03-10T18:43:57 [main] INFO  o.s.n.o.OntologyParserCommand - Parse result: false\n\n2022-03-10T18:43:57 [main] INFO  o.s.n.o.OntologyParserCommand - Output triples in: {}/srv/ncbo/repository/HHEAR/9/owlapi.xrdf\n\n2022-03-10T18:43:57 [main] INFO  o.s.n.o.OntologyParserCommand - Finished parsing!\n"]
I, [2022-03-10T18:43:57.184029 #20987]  INFO -- : ["OWLAPI Java command: parsing finished successfully."]
E, [2022-03-10T18:43:57.184321 #20987] ERROR -- : ["LinkedData::Parser::OWLAPIParserException: OWLAPI java command exited with  0. Output file /srv/ncbo/repository/HHEAR/9/owlapi.xrdf cannot be found.\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/parser/owlapi.rb:125:in `block in call_owlapi_java_command'\n\t/usr/local/rbenv/versions/2.6.8/lib/ruby/2.6.0/open3.rb:219:in `popen_run'\n\t/usr/local/rbenv/versions/2.6.8/lib/ruby/2.6.0/open3.rb:101:in `popen3'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/parser/owlapi.rb:76:in `call_owlapi_java_command'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/parser/owlapi.rb:153:in `parse'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/models/ontology_submission.rb:462:in `generate_rdf'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/models/ontology_submission.rb:973:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:47:in `block in process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `each'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/bin/ncbo_cron:246:in `block (3 levels) in <main>'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:65:in `block (3 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `fork'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `block (2 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:43:in `lock'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:234:in `lock'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:50:in `block in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:230:in `trigger_block'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:204:in `block in trigger'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/scheduler.rb:430:in `block in trigger_job'"]




On Mar 11, 2022, at 2:00 PM, Masters, James <James.Masters at mssm.edu<mailto:James.Masters at mssm.edu>> wrote:

Hello,

I am the primary curator of the HHEAR ontology, and I tried to upload our latest release (1.6) to Bioportal yesterday. I see on the Submissions list that this submission failed with an error:

1.6 (Uploaded, Error Rdf)
03/10/2022
03/10/2022
OWL<https://urldefense.proofpoint.com/v2/url?u=https-3A__data.bioontology.org_ontologies_HHEAR_submissions_9_download-3Fapikey-3D840ae862-2D3a0a-2D4a6d-2D8118-2D2304b98e1e29&d=DwMGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=jy5ac9DuztO_E6WgMyR7LB7ayTTItMNFMU4huVZZ8k8&e=>


However, I do not know or see how to inspect the error that was found in order to fix it and resubmit. Can you please provide me with an error log or details of how I can retrieve the error from the website, if possible?

Thank you,

James “Chip” Masters, PhD (he/him)
Director, Semantic Technology and HHEAR Data Repository
Scientific Computing and Data
Icahn School of Medicine at Mount Sinai
150 E 42nd St
New York, NY 10017
United States

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https://mailman.stanford.edu/mailman/listinfo/bioontology-support<https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwMGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=fIwESIDp7U2K1yOk3kUEQrRVG-Pg3qAl1WYb5BfzGcs&m=1d7-gqpk1CzetsG_8WOyTiO-hl6H19tZvXJQtqJjsGA&s=XvATjxudmpppxZJ37duojl4zfEsV5_OsuH2uemkHN4E&e=>

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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