CytoKEGG

[Ignatius Pang]

Hi,

I'm using the CytoKEGG app latest version in Cytoscape version 3.7.1. I have used the 'Apps -> CytoKEGG -> Search Pathways' tool. I selected a organism (human hsa) and searched for the relevant pathway (e.g. Fatty Acid Biosynthesis). Once I have chosen the pathway, I clicked open. Then I've got the following errors from the Cytoscape karaf OSGi command line environment (see below), and no KEGG network was being downloaded. Please note that doing the same with an older version of Cytoscape v3.6.1, the app still works properly without problems. I'm currently using Java(TM) SE Runtime Environment (build 1.8.0_201-b09). Would you please let me know if it is an error that I could fix on my end (other than using the older versin of Cytoscape or rather it requires an update to fixt this?

Debug: KGML URL name = http://rest.kegg.jp/get/path:hsa00061/kgml

javax.xml.bind.UnmarshalException

 - with linked exception:

[org.xml.sax.SAXParseException; lineNumber: 2; columnNumber: 73; External DTD: Failed to read external DTD 'KGML_v0.7.2_.dtd', because 'http' access is not allowed due to restriction set by the accessExternalDTD property.]

at javax.xml.bind.helpers.AbstractUnmarshallerImpl.createUnmarshalException(AbstractUnmarshallerImpl.java:335)

at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.createUnmarshalException(UnmarshallerImpl.java:563)

at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:249)

at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(UnmarshallerImpl.java:214)

at javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:157)

at javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:204)

at de.mpg.biochem.cytokegg.internal.task.NetworkCreationTask.run(NetworkCreationTask.java:115)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

Caused by: org.xml.sax.SAXParseException; lineNumber: 2; columnNumber: 73; External DTD: Failed to read external DTD 'KGML_v0.7.2_.dtd', because 'http' access is not allowed due to restriction set by the accessExternalDTD property.

at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)

at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)

at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)

at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)

at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1472)

at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1157)

at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1045)

at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:959)

at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)

at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)

at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)

at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)

at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)

at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)

at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)

at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643)

at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:243)

... 11 more

Kind Regards,

Igy

[Scooter Morris]

Hi Igy,

   I'm forwarding this off to the author of the app.  I've never used the search capability of CytoKEGG...

-- scooter

[Keiichiro Ono]

Recently, we released Cytoscape 3.7 compatible version of KEGGScape:

http://apps.cytoscape.org/apps/keggscape

I think this done does not have the problem you have now.

Kei

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--
===================================
Keiichiro Ono
https://viz2k.com/
===================================

[Alex Pico]

Posted here: https://github.com/jmvillaveces/cytokegg/issues/4

Hopefully there will be a response.

- Alex

On Tuesday, February 5, 2019 at 8:15:07 PM UTC-8, Ignatius Pang wrote:

[Ignatius Pang]

Dear Kei,

Thank you for the information. I'll give this a try as soon as possible and let you know if this worked. 

Kind Regards,

Igy

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