[MOBY-guts] biomoby commit

[Martin Senger]

senger
Tue Jul 19 08:39:58 EDT 2005
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv19358/docs

Modified Files:
	3rdPartyLibraries.html ChangeLog Download.html 
Added Files:
	CVS.html 
Log Message:


moby-live/Java/docs CVS.html,NONE,1.1 3rdPartyLibraries.html,1.2,1.3 ChangeLog,1.30,1.31 Download.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/3rdPartyLibraries.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/docs/3rdPartyLibraries.html	2005/05/19 20:25:40	1.2
+++ /home/repository/moby/moby-live/Java/docs/3rdPartyLibraries.html	2005/07/19 12:39:58	1.3
@@ -10,20 +10,47 @@
 <h1>Third-party Libraries Guidelines</h1>
 </center>
 
-<em>Comming soon..</em>
-<p>
+The third-party libraries are (mostly) <tt>.jar</tt> files whose
+source code is not included in the jMoby CVS repository. <p>
 
-For now, just look into <tt>xmls/libraries.xml</tt> - and it's almost
-self-explanatory...
+Neither their binary code (classes themselves). That's why the jMoby's
+Ant tasks need to get it first from some remote repository. The
+question is where is such remote repository and how to update it (if
+needed). This document explains that. <p>
+
+The third-party <tt>jar</tt> files are retrievable by HTTP protocol
+from the place that is defined in the Ant property <tt>remote.dir</tt>
+in the <tt>xmls/libraries</tt> file. In the same file, there is also a
+full list of the third-party libraries needed in jMoby. If you need to
+add a library, put it there (the name must appear in three places in
+that file, actually). <p>
+
+However, to put the new name there, it is not enough. You need also to
+add such new <tt>jar</tt> file into the remote repository (or to
+update there one if you wish jMoby to use a newer version). In order
+to do that, you need to check-out and update/commit to the CVS module
+<tt>jars-archive</tt> (note that you <em>do not need</em> to do this
+if you are just using jMoby, or developing with jMoby). The module is
+located together with other Biomoby CVS modules - so follow the normal
+way:
+
+<pre>
+export CVS_RSH=ssh
+cvs -d :ext:your-user-name at pub.open-bio.org:/home/repository/moby co -P jars-archive
+</pre>
+
+Once you have committed there a new library, or a new version of an
+existing library, you need to wait until it is propagated to the place
+indicated by the <tt>remote.dir</tt>. This is done by a cron job that
+runs at 20 past the hour every other hour. <p>
 
-<p>
        
 
 <hr>
 <div align=right class="address">
 <address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
 <!-- hhmts start -->
-Last modified: Thu May 19 20:35:23 2005
+Last modified: Tue Jul 19 14:16:23 2005
 <!-- hhmts end -->
 </div>
 

===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2005/05/19 20:18:53	1.30
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2005/07/19 12:39:58	1.31
@@ -1,3 +1,16 @@
+2005-07-19  Martin Senger  <senger at ebi.ac.uk>
+
+	* Changed the remote repository for the third-party jar files.
+
+	* Added a new option -la to the MobyCmdLineClient to list services
+	by authorities.
+
+	* Added new method getServiceNamesByAuthority() to the
+	Central.java interface. getServiceNames() deprecated.
+
+	* Default location and namespace of the Moby Central has been
+	changed (in CentralImpl.java).
+
 2005-05-19  Martin Senger  <senger at ebi.ac.uk>
 
 	* Updated build.xml; also separate some fragments into xmls

===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Download.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/docs/Download.html	2005/05/19 20:18:53	1.4
+++ /home/repository/moby/moby-live/Java/docs/Download.html	2005/07/19 12:39:58	1.5
@@ -42,9 +42,10 @@
 <a name="cvs"></a>
 <h2>Using jMoby from CVS</h2>
 
-Once you checked out your local CVS copy, go to the
-<tt>moby-live/Java</tt> subdirectory. All directory and files names
-used below assume that you are in this directory. <p>
+Once you checked out your local CVS copy (here is <a
+href="CVS.html">how to do it</a>), go to the <tt>moby-live/Java</tt>
+subdirectory. All directory and files names used below assume that you
+are in this directory. <p>
 
 <blockquote>
 <a href="#build">How to build it</a><br>
@@ -367,7 +368,7 @@
 <div align=right class="address">
 <address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
 <!-- hhmts start -->
-Last modified: Thu May 19 19:07:17 2005
+Last modified: Tue Jul 19 11:34:08 2005
 <!-- hhmts end -->
 </div>
 </body> </html>