RDAVIDWebService ERROR !!!!

didi
New Member

Posts: 1

RDAVIDWebService ERROR !!!! Nov 24, 2020 9:35:04 GMT -5

Quote

Post by didi on Nov 24, 2020 9:35:04 GMT -5

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?

?

Julia
Guest

RDAVIDWebService ERROR !!!! Nov 30, 2020 9:31:42 GMT -5

Quote

Post by Julia on Nov 30, 2020 9:31:42 GMT -5

Before you run your client script, you need make sure the server is up. For confirmation, you can try the following link by replacing the email address to your registered one and check if it returns a 'true'.
david.ncifcrf.gov/webservice/services/DAVIDWebService/authenticate?args0=YourRegisteredEmail@your.org

RDAVIDWebService package is not developed and maintained by DAVID team. Please contact Dr. Cristobal Fresno, the author of R script for help.
bioconductor.org/packages/release/bioc/html/RDAVIDWebService.html

Or you can download Java, Python or Perl client code to give it a try.
david.ncifcrf.gov/content.jsp?file=WS.html

xenia New Member Posts: 2	RDAVIDWebService ERROR !!!! Dec 17, 2020 7:09:24 GMT -5 Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by xenia on Dec 17, 2020 7:09:24 GMT -5 Didi did you manage to resolve the problem? I am having the same issue, the only thing I can think of is that I am using focal and the vignette was done on beaver..

Brad
DAVID Bioinformatics Team

Posts: 55

RDAVIDWebService ERROR !!!! Dec 17, 2020 16:39:21 GMT -5

Quote

Post by Brad on Dec 17, 2020 16:39:21 GMT -5

Hi Xenia,

Were you able to authenticate outside of your code in a browser using your registered email address in the following url?: david.ncifcrf.gov/webservice/services/DAVIDWebService/authenticate?args0=YourRegisteredEmail@your.org

Regards, Brad

xenia
New Member

Posts: 2

RDAVIDWebService ERROR !!!! Dec 18, 2020 4:54:16 GMT -5

Quote

Post by xenia on Dec 18, 2020 4:54:16 GMT -5

Hi Brad,

thank you for the quick reply, yes I was able to authenticate. I can connect via Perl but I would like to look into the R wrapper! I also followed the instructions given in stackoverflow and biocsupport with no luck. I am using the same R version (4.0.3) as in the vignette on focal and with following java version:

openjdk 11.0.9.1 2020-11-04

OpenJDK Runtime Environment (build 11.0.9.1+1-Ubuntu-0ubuntu1.20.04)
OpenJDK 64-Bit Server VM (build 11.0.9.1+1-Ubuntu-0ubuntu1.20.04, mixed mode, sharing)

Best,
Xenia

Last Edit: Dec 18, 2020 5:08:44 GMT -5 by xenia

Julia
Guest

RDAVIDWebService ERROR !!!! Dec 18, 2020 16:25:59 GMT -5

Quote

Post by Julia on Dec 18, 2020 16:25:59 GMT -5

RDAVIDWebService package is not developed and maintained by DAVID team. Please contact Dr. Cristobal Fresno, the author of R script for help.
bioconductor.org/packages/release/bioc/html/RDAVIDWebService.html

Or you can download Java, Python or Perl client code to give it a try.
david.ncifcrf.gov/content.jsp?file=WS.html

Bennie Tam Guest	RDAVIDWebService ERROR !!!! Feb 23, 2023 14:08:18 GMT -5 Quote Select Post Deselect Post Link to Post Back to Top Post by Bennie Tam on Feb 23, 2023 14:08:18 GMT -5 Hello freeforums.net administrator, Your posts are always well-cited and reliable.

Eli Brennan Guest	RDAVIDWebService ERROR !!!! Mar 11, 2023 16:46:24 GMT -5 Quote Select Post Deselect Post Link to Post Back to Top Post by Eli Brennan on Mar 11, 2023 16:46:24 GMT -5 Hello freeforums.net webmaster, Keep up the good work!

Post by didi on Nov 24, 2020 9:35:04 GMT -5

Post by Julia on Nov 30, 2020 9:31:42 GMT -5

Post by xenia on Dec 17, 2020 7:09:24 GMT -5

Post by Brad on Dec 17, 2020 16:39:21 GMT -5

Post by xenia on Dec 18, 2020 4:54:16 GMT -5

Post by Julia on Dec 18, 2020 16:25:59 GMT -5

Post by Bennie Tam on Feb 23, 2023 14:08:18 GMT -5

Post by Eli Brennan on Mar 11, 2023 16:46:24 GMT -5

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