I don't know of one. The package maintainer needs to change the package to use the new (https) URL. However, I think there are also issues on the server side as the SSL certificate appears to be misconfigured, and the site appears to go down frequently (or at least DNS at my location cannot resolve its name). So both of those issues will have to be fixed before the package can work. I will ping the maintainer of the package so that at least he can get started on the first problem.

Apparently you can specify the url as an argument to new(), but this doesn't get very far (except in the length of Java error generated)

> DAVIDWebService$new(email="...", url="https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/")
[INFO] Unable to sendViaPost to url[https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/]
org.apache.axis2.AxisFault: Connection has been shutdown: javax.net.ssl.SSLHandshakeException: Remote host closed connection during handshake
    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 has been shutdown: javax.net.ssl.SSLHandshakeException: Remote host closed connection during handshake
    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: javax.net.ssl.SSLException: Connection has been shutdown: javax.net.ssl.SSLHandshakeException: Remote host closed connection during handshake
    at sun.security.ssl.SSLSocketImpl.checkEOF(SSLSocketImpl.java:1496)
    at sun.security.ssl.SSLSocketImpl.checkWrite(SSLSocketImpl.java:1508)
    at sun.security.ssl.AppOutputStream.write(AppOutputStream.java:70)
    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
Caused by: javax.net.ssl.SSLHandshakeException: Remote host closed connection during handshake
    at sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:953)
    at sun.security.ssl.SSLSocketImpl.performInitialHandshake(SSLSocketImpl.java:1332)
    at sun.security.ssl.SSLSocketImpl.writeRecord(SSLSocketImpl.java:709)
    at sun.security.ssl.AppOutputStream.write(AppOutputStream.java:122)
    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.BaseStreamWriter.flush(BaseStreamWriter.java:311)
    at org.apache.axiom.util.stax.wrapper.XMLStreamWriterWrapper.flush(XMLStreamWriterWrapper.java:50)
    at org.apache.axiom.om.impl.MTOMXMLStreamWriter.flush(MTOMXMLStreamWriter.java:184)
    at org.apache.axis2.databinding.utils.writer.MTOMAwareXMLSerializer.flush(MTOMAwareXMLSerializer.java:79)
    at org.apache.axis2.databinding.ADBDataSource.serialize(ADBDataSource.java:94)
    at org.apache.axiom.om.impl.llom.OMSourcedElementImpl.internalSerialize(OMSourcedElementImpl.java:691)
    at org.apache.axiom.om.impl.llom.OMElementImpl.internalSerialize(OMElementImpl.java:965)
    at org.apache.axiom.soap.impl.llom.SOAPEnvelopeImpl.serializeInternally(SOAPEnvelopeImpl.java:283)
    at org.apache.axiom.soap.impl.llom.SOAPEnvelopeImpl.internalSerialize(SOAPEnvelopeImpl.java:245)
    at org.apache.axiom.om.impl.llom.OMSerializableImpl.serializeAndConsume(OMSerializableImpl.java:193)
    ... 19 more
Caused by: java.io.EOFException: SSL peer shut down incorrectly
    at sun.security.ssl.InputRecord.read(InputRecord.java:482)
    at sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:934)
    ... 37 more
Error in .jcall(stub, "S", "authenticate", email) : 
  org.apache.axis2.AxisFault: Connection has been shutdown: javax.net.ssl.SSLHandshakeException: Remote host closed connection during handshake

There does seem to be something wrong with the site's SSL configuration, e.g.,

/tmp$ wget https://david.ncifcrf.gov/webservice/sample_clients/JavaClient-1.1.zip
--2015-07-30 17:26:06--  https://david.ncifcrf.gov/webservice/sample_clients/JavaClient-1.1.zip
Resolving david.ncifcrf.gov (david.ncifcrf.gov)... 129.43.40.120
Connecting to david.ncifcrf.gov (david.ncifcrf.gov)|129.43.40.120|:443... connected.
ERROR: cannot verify david.ncifcrf.gov's certificate, issued by ‘/C=US/ST=Arizona/L=Scottsdale/O=GoDaddy.com, Inc./OU=http://certs.godaddy.com/repository//CN=Go Daddy Secure Certificate Authority - G2’:
  Unable to locally verify the issuer's authority.
To connect to david.ncifcrf.gov insecurely, use `--no-check-certificate'.

Xiaoli Jiao from the DAVID team was mentioned in another part of this post so might be someone who can help us.

 

Greetings,

Thank you for your interest in RDAVIDWebService package. Please follow the instructions below with the update for MAC users.

Please let me know if the problem is solved.

Regards,

Cristóbal Fresno.

Work around for the new DAVID Web service configuration V 2.0

1) First of all the HTTPS certificate needs Java 8 in order to run. 

Previous versions will not run due to prime size. The maximum size that Java accepts is 1024 bits. This is a known issue (see JDK-6521495). 

1.1) Check your java version 

java -version

java version "1.8.0_60"

Java(TM) SE Runtime Environment (build 1.8.0_60-b27)

Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)

 

If the version is 1.7.XX or earlier then you need to install Java 8. If not, go to step 2.

 

1.2) In windows, download and install jre or jdk 8 from oracle site 

1.3) In linux follow the instructions in http://www.webupd8.org/2014/03/how-to-install-oracle-java-8-in-debian.html 

Briefly, you need to add webupd8team repository and install the package:

su -

echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" | tee /etc/apt/sources.list.d/webupd8team-java.list

echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list

apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886

apt-get update

apt-get install oracle-java8-installer

exit

 

1.4) In MAC (tested in Yosemite), there are some things to take into account:

• Download JDK 8 for MAC from oracle.
• However, there is a reported bug for Java 8 which searches for JRE 6 installed in your system, in order to work (JDK-7131356).  Ironically, you have to install 1.6 from Apple then Oracle Java 1.8 will start working.
• Check that your working version is the 1.8

java -version

java version "1.8.0_60"

Java(TM) SE Runtime Environment (build 1.8.0_60-b27)

Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)

 

2) The actual certificate used by DAVID is not signed by a recognized authority in Java brunch. Then, it must be incorporated to "cacerts" files to properly use it.

 

2.1) In Windows:

Download  cygwin and follow linux instructions. Usually for JRE should be installed in C:\Program Files\Java\jre1.8.0_51\lib\security or C:\Program Files\Java\jdk1.8.0_51\jre\lib\security for JDK. Reboot the computer if necessary.

 

2.2) In Linux:

Get the certificate:

echo -n | openssl s_client -connect david.ncifcrf.gov:443 | sed -ne '/-BEGIN CERTIFICATE-/,/-END CERTIFICATE-/p' > ncifcrf.cert

 

Check if it was properly downloaded:

openssl x509 -in ncifcrf.cert -text

 

Backup the cacerts file. In my case it is located in /etc/ssl/certs/java directory

sudo cp /etc/ssl/certs/java/cacerts .

sudo cp /etc/ssl/certs/java/cacerts cacerts.org

sudo keytool -import -trustcacerts -keystore cacerts -storepass changeit -noprompt -alias david -file ncifcrf.cert

 

The certificate should be added to the keystore. Now, copy the new cacerts version to the original position

sudo cp cacerts /etc/ssl/certs/java/

 

2.3) In MAC (tested in Yosemite) the certificate will not work for the present stable openssl version 0.9.8.

2.3.1) Check your openssl version

openssl version

OpenSSL 0.9.8

If it is >= 1.0.2.d then go to step 2.3.3)

2.3.2) Update your openssl, i.e., download, compile and install it

Download the official release from OpenSSL >= 1.0.2.d

tar -xzvf openssl-1.0.2d.tar.gz

cd openssl-1.0.2d

#Compile it with 64 bits support

./Configure darwin64-x86_64-cc   
make
make test
sudo make install

 

Now you may need to reflect the change in your system if openssl version keeps pointing to the old version.

cd /usr/bin

mv sudo openssl openssl098
sudo ln -s /usr/local/ssl/bin/openssl openssl

 

2.3.3)  Get DAVID's certificate and install it into cacerts

Get the certificate:

cd

echo -n | openssl s_client -connect david.ncifcrf.gov:443 | sed -ne '/-BEGIN CERTIFICATE-/,/-END CERTIFICATE-/p' > ncifcrf.cert

 

Check if it was properly downloaded:
openssl x509 -in ncifcrf.cert -text

 

Backup the cacerts file. In my case the 1.8.0_60 jdk version is located in /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/jre/lib/security/ directory

sudo find / -name cacerts
/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/security/cacerts
/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/security/cacerts
/Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/jre/lib/security/cacerts
/System/Library/Java/Support/CoreDeploy.bundle/Contents/Home/lib/security/cacerts
/System/Library/Java/Support/Deploy.bundle/Contents/Home/lib/security/cacerts

 

sudo cp /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/jre/lib/security/cacerts .

sudo cp /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/jre/lib/security/cacerts cacerts.org
sudo keytool -import -trustcacerts -keystore cacerts -storepass changeit -noprompt -alias david -file ncifcrf.cert
Certificate was added to keystore

 

The certificate should be added to the keystore. Now, copy the new cacerts version to the original position

sudo cp cacerts /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/jre/lib/security/cacerts

 

3) Update Java configuration in R. The output may slightly change from windows, linux or mac. 

R CMD javareconf

 

Java interpreter : /usr/bin/java

Java version     : 1.8.0_60

Java home path   : /usr/lib/jvm/java-8-oracle/jre

Java compiler    : /usr/bin/javac

Java headers gen.: /usr/bin/javah

Java archive tool: /usr/bin/jar

 

Please check that both Java version and path are appropriate. In addition JNI support should also be available. 

 

4) Check that rJava R library works as supposed to.

R

library(rJava)

.jinit()

.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")

[1] "1.8.0_20-b26"

 

In Mac the rJava that downloads is tied to 1.6 java version. If it is the case, you should install it from the source.

 

install.packages('rJava', type='source’)

library(rJava)

.jinit()

.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")

[1] "1.8.0_20-b26"

 

5)Finally, use the new DAVID web service URL in RDAVIDWebService

library("RDAVIDWebService")

david<-DAVIDWebService(email="user@email", url="https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/")

david

DAVIDWebService object to access DAVID's website. 

User email:  user@email 

Available Gene List/s: not submitted yet. 

Hi Ben,

Great news!!! I'll include your suggestion in the next vignette. Also I'm working on a SOAP client for DAVID to avoid Java issues.

Best,

Cristobal