[MOBY-guts] biomoby commit

Andreas Groscurth groscurt at dev.open-bio.org
Fri Mar 14 14:01:01 UTC 2008

Fri Mar 14 10:01:01 EDT 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv5088/docs

Modified Files:
Added Files:
Log Message:
changes in the documentation about the integration of JMoby in Eclipse and how to solve known errors
moby-live/Java/docs ErrorsInEclipse.html,NONE,1.1 EclipseAndJMoby.html,1.8,1.9
RCS file: /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html	2008/02/21 11:44:46	1.8
+++ /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html	2008/03/14 14:01:01	1.9
@@ -123,6 +123,22 @@
 <tt>-showlocation</tt> - then the path of the current workspace is
 shown in the window title. <p>
+<h3>Integrate Maven plugin</h3>
+<p>As JMoby uses Maven we need to enable Maven in Eclipse. The Maven plugin requires two other plugins which we need to load.<br>
+<b class="step">Help -&gt; Software Updates -&gt; Find and Install -&gt; Search for new features and install</b> will open a dialog
+which shows all existing update sites your Eclipse already know.</p>
+<p>For each of the plugins please open <b class="step">New Remote Update Site</b> and add the following sites and install them 
+(make sure that you unselect optional components of the plugins if they produce errors):
+	<li>Name: Buckminster<br>URL: http://download.eclipse.org/tools/buckminster/updates</li>
+	<li>Name: Subversion<br>URL: http://subclipse.tigris.org/update_1.2.x</li>
+	<li>Name: Maven<br>URL: http://m2eclipse.sonatype.org/update/</li>
+After install the plugins please restart Eclipse to enable the Maven plugin.
 <h3>Create a new CVS repository location</h3>
 <b class="step">Window -&gt; Open Perspective -&gt; Other -&gt; CVS
@@ -162,6 +178,13 @@
 about where jMoby has things and how it uses them. But before we fix
 that let's do one more thing... <p>
+<h3>Telling Eclipse the classpath</h3>
+We need to tell Eclipse now the building structure of JMoby, so that it knows where which source files are and to where it has to compile what.<br>
+For that (and only for the first time you set up Eclipse and JMoby) rename the <tt>.classpath.template</tt> from the checkout to <tt>.classpath</tt> 
+(and by that overwrite the .classpath file generated by Eclipse) and refresh your project either by right-click on the project and selecting <b class="step">Refresh</b> or by just hitting F5.<br>
+You will now see the new source folder structure. In the case you dont have a <tt>generated/skeletons</tt> and <tt>generated/datatypes</tt> folder shown
+up as source folder please add this two folders. Eclipse will then automatically recognize them as source folders.
 <h3>Change location of Ant</h3>
@@ -184,20 +207,7 @@
 <tt>&lt;jMoby&gt;/lib/ant_home</tt>. <p>
-<h3>Gather 3rd-party libraries</h3>
-This is done only the first time (and occasionally, time to time when
-the libraries change). If you are putting into Eclipse a copy of jMoby
-that you were already been working with, you probably already have the
-libraries fetched (but it does not harm if you go through this step,
-as well). <p>
-We are doing this step now, before telling Eclipse where the libraries
-are (because we first need to have them in order to show them to
-Eclipse, don't we?). Eclipse already found some 3rd-party libraries in
-jMoby and listed them in our project. These are from the included Ant
-(they were not needed for jMoby programs until recently). <p>
+<h3>Gather 3rd-party libraries and set up JMoby</h3>
 Now it's time for our real libraries. Open an Ant view by <b
 class="step">Window -&gt; Show View -&gt; Ant</b>. Then right-click
@@ -205,7 +215,7 @@
 class="step">build.xml</b> from jMoby. You can <b class="step">Hide
 internal targets</b> by clicking on the stroke green target icon. <p>
-Double-click on <b class="step">gather</b>. It shows progress in the
+Double-click on <b class="step">install</b>. It shows progress in the
 bottom of the screen in a console window. After that you may <b
 class="step">Refresh</b> your workspace. <p>
@@ -217,15 +227,20 @@
 jMoby documentation (e.g. about <a
 href="Download.html#targets">general targets</a>, or about <a
+When the task is finished, double-click on <b class="step">initeclipse</b>, which will generate the file <tt>pom.xml</tt> 
+which the Maven plugin requires to work correctly. After the task refresh your workspace and right-click on the project 
+<b class="step">Maven -&gt; Enable Dependency Management</b>. This will now tell Eclipse to use the maven repository for the build path.<br>
+By now all your erros should be erazed and you only see several warnings (if you still got errors check <a href="ErrorsInEclipse.html">here</a>)
 Again, right-click on the project name <b class="step">(jMoby) -&gt;
 Properties -&gt; Java Build Path</b>, select again tab <b
 class="step">Libraries</b>, and <b class="step">Add External
 JARS...</b>. Select all JAR files from &lt;jMoby&gt;/lib
 directory. <p>
 <h3>Set source files</h3>
@@ -311,7 +326,7 @@
 you are an annoyed jMoby user, change warning preferences in <b
 class="step">Window -&gt; Preferences -&gt; Java -&gt; Compiler -&gt;
 Errors/Warnings</b> not to see them. <p>
 <h3>Fix <tt>javadoc</tt> location</h3>
 Ant's targets using <tt>javadoc</tt> (such as <tt>docs</tt> or

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