RDAVIDWebService Connection or outbound has closed
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Entering edit mode
Didi ▴ 10
@didi-10905
Last seen 7 months ago
Spain

Hi,

I'm trying to run RDAVIDWebService:

library("RDAVIDWebService")
e_mail <- myemail.org
david<-DAVIDWebService$new(email = e_mail,
                           url =  'https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/' )

and I'm getting this error

[INFO] Unable to sendViaPost to url[https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/] org.apache.axis2.AxisFault: Connection or outbound has closed at org.apache.axis2.AxisFault.makeFault(AxisFault.java:430) at org.apache.axis2.transport.http.SOAPMessageFormatter.writeTo(SOAPMessageFormatter.java:83) at org.apache.axis2.transport.http.AxisRequestEntity.writeRequest(AxisRequestEntity.java:84) at org.apache.commons.httpclient.methods.EntityEnclosingMethod.writeRequestBody(EntityEnclosingMethod.java:499) at org.apache.commons.httpclient.HttpMethodBase.writeRequest(HttpMethodBase.java:2114) at org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:1096) at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:398) at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346) at org.apache.axis2.transport.http.AbstractHTTPSender.executeMethod(AbstractHTTPSender.java:560) at org.apache.axis2.transport.http.HTTPSender.sendViaPost(HTTPSender.java:199) at org.apache.axis2.transport.http.HTTPSender.send(HTTPSender.java:76) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:400) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:225) at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:435) at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:402) at org.apache.axis2.description.OutInAxisOperationClient.executeImpl(OutInAxisOperation.java:229) at org.apache.axis2.client.OperationClient.execute(OperationClient.java:165) at sample.session.client.stub.DAVIDWebServiceStub.authenticate(DAVIDWebServiceStub.java:2288) Caused by: com.ctc.wstx.exc.WstxIOException: Connection or outbound has closed at com.ctc.wstx.sw.BaseStreamWriter.finishDocument(BaseStreamWriter.java:1692) at com.ctc.wstx.sw.BaseStreamWriter.close(BaseStreamWriter.java:288) at org.apache.axiom.util.stax.wrapper.XMLStreamWriterWrapper.close(XMLStreamWriterWrapper.java:46) at org.apache.axiom.om.impl.MTOMXMLStreamWriter.close(MTOMXMLStreamWriter.java:174) at org.apache.axiom.om.impl.llom.OMSerializableImpl.serializeAndConsume(OMSerializableImpl.java:197) at org.apache.axis2.transport.http.SOAPMessageFormatter.writeTo(SOAPMessageFormatter.java:79) ... 18 more Caused by: java.net.SocketException: Connection or outbound has closed at sun.security.ssl.SSLSocketImpl$AppOutputStream.write(SSLSocketImpl.java:967) at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82) at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140) at org.apache.commons.httpclient.ChunkedOutputStream.flush(ChunkedOutputStream.java:191) at com.ctc.wstx.io.UTF8Writer.flush(UTF8Writer.java:99) at com.ctc.wstx.sw.BufferingXmlWriter.flush(BufferingXmlWriter.java:214) at com.ctc.wstx.sw.BufferingXmlWriter.close(BufferingXmlWriter.java:194) at com.ctc.wstx.sw.BaseStreamWriter.finishDocument(BaseStreamWriter.java:1690) ... 23 more Error in .jcall(stub, "S", "authenticate", email) : org.apache.axis2.AxisFault: Connection or outbound has closed

I followed the inscructions given in stackoverflow and biocsupport but still getting the same error.

When I type java -version in my terminal I get this:

openjdk version "1.8.0_272"
OpenJDK Runtime Environment (build 1.8.0_272-8u272-b10-0ubuntu1~20.04-b10)
OpenJDK 64-Bit Server VM (build 25.272-b10, mixed mode)

And this in R:

> library(rJava)
> .jinit()
[1] 0
> .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
[1] "1.8.0_272-8u272-b10-0ubuntu1~20.04-b10"

Am I doing something wrong?

Bioconductor RDAVIDWebService • 1.9k views
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I had a similar problem months ago when I also tried to use RDavid, the difference was that the default URL argument was outdated and would produce a 301 Error: Moved Permanently. I eventually took to their forum to ask this question and got a good response from the person who maintains it. I would recommend contacting them for more information, either by posting on the forum or by reaching out to them by email (I would post on the forum first).

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