RDAVIDWebService Connection or outbound has closed
0
0
Entering edit mode
Didi ▴ 10
@didi-10905
Last seen 2.7 years 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 • 3.1k views
ADD COMMENT
0
Entering edit mode

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).

ADD REPLY

Login before adding your answer.

Traffic: 673 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6