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?
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 a301 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).