05 January 2011

Coding a CXF web service translating a DNA to a protein. My notebook

Apache CXF is a Web Services framework. In this post, I'll will describe how I implemented a Web Service translating a DNA to a protein using the web server Apache Tomcat and the CXF libraries.

Defining the interface

First a simple java interface bio.Translate is needed to describe the service. This simple service receives a string (the dna) and returns a string (the peptide). The annotations will be used by CXF to name the parameters in the WSDL file (see later):

Implementing the service

bio.TranslateImpl implements bio.Translate. The setter/getter for ncbiString will be used by a configuration file to specify a genetic code (standard, mitochondrial) for this service. The methods initIt and cleanUp could be used to acquire and to release some resources for the service when it is created and/or disposed.

Configuring the service

CXF uses the libraries of the Spring framework (I blogged about spring here ). A XML config file beans.xml makes it easy to configure two java beans for the 'standard genetic code' and the 'mitochondrial code'. In this config file, we also tell Spring about the two methods initIt and cleanUp. Those two beans will be used by two Web Services

Defining the CXF application for Tomcat

The following web.xml file only tells tomcat, the web server, to use the CXFServlet to listen to the SOAP queries.

Compile & Deploy

Installing a CXF web service requires many libraries and at the end, the size of the deployed 'war' file was 8.5Mo(!). Currently, my structure for the current project is:
The service was compiled and deployed using the following Makefile:
mkdir -p translate/WEB-INF/lib
javac -d translate/WEB-INF/classes -sourcepath translate/WEB-INF/classes translate/WEB-INF/classes/bio/TranslateImpl.java
cp ${cxf.lib}/cxf-2.3.1.jar \
${cxf.lib}/geronimo-activation_1.1_spec-1.1.jar \
${cxf.lib}/geronimo-annotation_1.0_spec-1.1.1.jar \
${cxf.lib}/geronimo-javamail_1.4_spec-1.7.1.jar \
${cxf.lib}/geronimo-servlet_3.0_spec-1.0.jar \
${cxf.lib}/geronimo-ws-metadata_2.0_spec-1.1.3.jar \
${cxf.lib}/geronimo-jaxws_2.2_spec-1.0.jar \
${cxf.lib}/geronimo-stax-api_1.0_spec-1.0.1.jar \
${cxf.lib}/jaxb-api-2.2.1.jar \
${cxf.lib}/jaxb-impl- \
${cxf.lib}/neethi-2.0.4.jar \
${cxf.lib}/saaj-api-1.3.jar \
${cxf.lib}/saaj-impl-1.3.2.jar \
${cxf.lib}/wsdl4j-1.6.2.jar \
${cxf.lib}/XmlSchema-1.4.7.jar \
${cxf.lib}/xml-resolver-1.2.jar \
${cxf.lib}/aopalliance-1.0.jar \
${cxf.lib}/spring-core-3.0.5.RELEASE.jar \
${cxf.lib}/spring-beans-3.0.5.RELEASE.jar \
${cxf.lib}/spring-context-3.0.5.RELEASE.jar \
${cxf.lib}/spring-web-3.0.5.RELEASE.jar \
${cxf.lib}/commons-logging-1.1.1.jar \
${cxf.lib}/spring-asm-3.0.5.RELEASE.jar \
${cxf.lib}/spring-expression-3.0.5.RELEASE.jar \
${cxf.lib}/spring-aop-3.0.5.RELEASE.jar \
jar cvf translate.war -C translate .
mv translate.war path-to-tomcat/webapps

Checking the URL

We can see that the service was correctly deployed by pointing a web browser at http://localhost:8080/translate/, where we can see the two services:
Available SOAP services:
  • translate
Endpoint address: http://localhost:8080/translate/translateMit
WSDL : {http://bio/}TranslateService
Target namespace: http://bio/
  • translate
Endpoint address: http://localhost:8080/translate/translateStd
WSDL : {http://bio/}TranslateService
Target namespace: http://bio/

Here, the URLs link to the WSDL definition for the web service:

Creating a client

For creating a client consuming this service, I first used the code generated by CXF's wsdl2java but there was a bug with one of the generated classe (it is a known bug feature) so here, I'm going to use the standard ${JAVA_HOME}/bin/wsimport.
> wsimport -p generated -d client -keep "http://localhost:8080/translate/translateStd?wsdl"
parsing WSDL...
generating code...
compiling code...
I wrote a java client MyClient.java using this generated API:


> cd client
> javac MyClient.java


> java MyClient

That's it,


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