- If on the other hand you are planning on directly hacking the jMOBY classes, the proper approach + If, on the other hand, you are planning on directly hacking the jMOBY classes, the other approach to developing services (using a code generator and the full jMOBY CVS) can be found in this document.
@@ -27,10 +28,11 @@
You need to tell Ant where your code and servlet container are located. This is done by modifying the
+ mobyService.properties file you just downloaded:
+
+# Where the project directory is located.
+project.dir=/home/gordonp/development/fastaConverter
+
+# Where the Java source directory is located.
+src.dir=${project.dir}/src
+
+# The package-qualified location of your main class (the one extending MobyServlet).
+# You could have no package, or org/bar/foo, etc. in a real service
+main.class.file=org/biomoby/service/test/ConvertAAtoFASTA_AA.java
+
+# Where all 3rd party libraries for your code are stored.
+lib.dir=${project.dir}/lib
+
+# Name of the output WAR archive to be generated (will also be the servlet name).
+my.servlet.war.file=ConvertAAtoFASTA_AA.war
+
+# The location of a test MOBY XML input data file (use as input to test your service).
+input.data.file=${project.dir}/mobyAASeq.xml
+
+# Your Java Servlet host URL
+servlet.host.url=http://moby.ucalgary.ca
+
+# Your Java Servlet port
+servlet.port=8089
+ |
MobyServlet takes care of all of the protocol
issues for you, all you need to do is override the
business logic method: processRequest
For example, the following service consumes a +
For example, the following service consumes a MOBY AminoAcidSequence object called "inseq", and returns it reformatted into a @@ -68,10 +103,22 @@ FASTA_AA object called "outseq":
+package org.biomoby.service.test; // This could be any package you want in real life...
+
import org.biomoby.shared.MobyDataType;
import org.biomoby.shared.data.*;
+import org.biomoby.service.*;
+
+ at mobyService(name="ConvertAAtoFASTA_AA",
+ type="FormatConversion",
+ provider="moby.ucalgary.ca",
+ author="gordonp at ucalgary.ca",
+ in={"inseq:AminoAcidSequence"},
+ out={"outseq:FASTA_AA"},
+ description={"Converts amino acid objects into FastA formatted records, ",
+ "primarily to increase inter-service compatibility"})
-public class ConvertAAtoFASTA_AA extends org.biomoby.service.MobyServlet{
+public class ConvertAAtoFASTA_AA extends MobyServlet{
public void processRequest(MobyDataJob request, MobyDataJob result) throws Exception{
// The input parameter for this method is registered as "inseq"
@@ -94,115 +141,54 @@
// Set the result that will be passed back to the client
result.put("outseq", fastaObject);
}
-}
- |
Save a file with the code above in a file called
+ ${src.dir}/org/biomoby/service/test/ConvertAAtoFASTA_AA.java
That's it for the coding. Really! Now compile it (remember: Java 1.5), including the MobyServlet.war
- you downloaded in the class path, e.g.:
Notice the @mobyService line. This is a Java
+ annotation used by
+ the base MobyServlet to do all the input type checking for you. If you've specified the annotation
+ correctly, you are guaranteed that processRequest will only receive syntactically
+ and semantically valid data. The same annotation is eventually used to publish your service's meta-data to
+ MOBY Central.
That's it for the coding. Really! Now compile it (Ant will automatically fetch the
+ MobyServlet.war you are extending), running the following command in the same
+ directory where you saved the build.xml file:
+javac -cp MobyServlet.war:. ConvertAAtoFASTA_AA.java
ant compile
When you go to write your own services with different data types, a quick tutorial on the data API can be found here. All of the datatypes, service types and namespaces you use must be registered - in the MOBY Ontologies.
+ in the MOBY Ontologies. Also, + when you go to create your own services, you'll put the Java code in a directory that matches a package name of your + own choosing (e.g. ${src.dir}/org/foo/bar.java, or just ${src.dir}/foo.java for no-package code)You should probably test that your business logic works! The base servlet has a built-in application test, so just type: -
+java -cp MobyServlet.war:. ConvertAAtoFASTA_AA ConvertAAtoFASTA_AA mobyAASeq.xml
and make sure the output is as you expected. - Note that the class name is given twice, - once to the JVM, and once as an argument to the application itself. + -ant test
The default MobyServlet.war business logic is to just return blank MOBY messages.
- You've got to customize it for your service with the following:
MobyServlet.war to ConvertAAtoFASTA_AA.warWEB-INF/web.xml to tell it about your class
- (a WAR is just a JAR with a particular directory structure):
--# Extract the existing web.xml from the WAR -jar xvf ConvertAAtoFASTA_AA.war WEB-INF/web.xml -# Edit the file with your favorite editor (see the table below) -vi WEB-INF/web.xml -
For our example converter, it should minimally look like this, with the required changes to the default web.xml shown in bold:
-
--<?xml version="1.0" encoding="ISO-8859-1"?> -<!DOCTYPE web-app - PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" - "http://java.sun.com/dtd/web-app_2_3.dtd"> - -<web-app> - <display-name>BioMOBY Web Service: Convert AA -> FASTA_AA</display-name> - <servlet> - <servlet-name>ConvertAAtoFASTA_AA</servlet-name> - <servlet-class>ConvertAAtoFASTA_AA</servlet-class> - - </servlet> - <servlet-mapping> - <servlet-name>ConvertAAtoFASTA_AA</servlet-name> - <url-pattern>/</url-pattern> - </servlet-mapping> - - <context-param> - <param-name>mobyServiceDescription</param-name> - <param-value>Converts amino acid objects into FastA formatted records, - primarily to increase inter-service compatibility</param-value> - </context-param> - - <context-param> - <param-name>mobyInput</param-name> - <param-value>inseq:AminoAcidSequence</param-value> - </context-param> - - <context-param> - <param-name>mobyOutput</param-name> - <param-value>outseq:FASTA_AA</param-value> - </context-param> - - <context-param> - <param-name>mobyServiceType</param-name> - <param-value>FormatConversion</param-value> - </context-param> - - <context-param> - <param-name>mobyProviderURI</param-name> - <param-value>your.domain.name</param-value> - </context-param> - - <context-param> - <param-name>mobyAuthorContact</param-name> - <param-value>yourname at email.com</param-value> - </context-param> - -</web-app> |
-mkdir WEB-INF/classes -cp ConvertAAtoFASTA_AA.class WEB-INF/classes -jar uvf ConvertAAtoFASTA_AA.war WEB-INF -
The web.xml file is used by the Servlet container (e.g. Tomcat), and by the base MobyServlet
-to do all the input type checking for you. If you've specified this file correctly, you are guaranteed that
-processRequest will only receive syntactically valid data.
+ +ant war
The resulting ConvertAAtoFASTA_AA.war is in the build directory you specified in Step 1.
-
ConvertAAtoFASTA_AA.war now contains your Web Service, and is ready to be deployed
+
ConvertAAtoFASTA_AA.war now contains your MOBY-S Web Service, and is ready to be deployed
in the Servlet container. How you do this depends on the container. For Tomcat, the easiest way is to use
the management Web interface (e.g. http://your.servlet.host:8080/manager/html, but change 8080 appropriately
if you had to follow Step 0) and upload the WAR.
@@ -228,14 +214,15 @@
You should test your service to make sure it works in the servlet environment. - A testing client program is automagically included in your WAR, so type (with - the fully qualified host name, and change 8080 appropriately if you had follow - Step 0): -
+ A testing client program is automagically included in your WAR, so type: + +java -jar ConvertAAtoFASTA_AA.war http://your.servlet.host:8080/ConvertAAtoFASTA_AA mobyAASeq.xml
+ +ant testService
If the service fails, a useful error message should be printed to help you diagnose the problem.
- This would usually be an incorrect web.xml, or the data type you return isn't what you declared
+ This would usually be because the data type you return isn't what you declared
(this is the first occasion your output is thoroughly checked).
If you get a java.lang.NoClassDefFoundError, please see the notes below. If that doesn't help,
let me know (gordonp
-Last modified: Tue Nov 21 13:16:31 MST 2006
+Last modified: Wed Dec 6 08:39:50 MST 2006