[MOBY-guts] biomoby commit

senger@ebi.ac.uk senger at pub.open-bio.org
Sun Dec 5 22:28:02 UTC 2004

Sun Dec  5 17:28:02 EST 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv14933/docs

Modified Files:
	ChangeLog index.html 
Added Files:
	CmdLineClients.html Download.html 
	MOBYSHoundGetGenBankff-result.xml.txt RDFAgent.html 
	SimpleClient.html TavernaGuide.html Testing_service.rdf 
Log Message:
a lot of changes in docs; but also in code

moby-live/Java/docs CmdLineClients.html,NONE,1.1 Download.html,NONE,1.1 MOBYSHoundGetGenBankff-result.xml.txt,NONE,1.1 RDFAgent.html,NONE,1.1 SimpleClient.html,NONE,1.1 TavernaGuide.html,NONE,1.1 Testing_service.rdf,NONE,1.1 ToDo.html,NONE,1.1 ChangeLog,1.26,1.27 index.html,1.5,1.6
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/11/14 16:43:49	1.26
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/12/05 22:28:02	1.27
@@ -1,3 +1,13 @@
+2004-12-05  Martin Senger  <senger at ebi.ac.uk>
+	* Updated documentation (significantly, but not yet finished).
+2004-11-30  Martin Senger  <senger at ebi.ac.uk>
+	* Fixed CentralImpl dealing now better with
+	<expandObjects>1</expandObjects> and
+	<expandservices>1</expandServices>.
 2004-11-14  Martin Senger  <senger at ebi.ac.uk>
 	* Added MobyDigestClient for retrieving cummulative (digested)

RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/docs/index.html	2004/11/14 17:33:57	1.5
+++ /home/repository/moby/moby-live/Java/docs/index.html	2004/12/05 22:28:02	1.6
@@ -3,83 +3,72 @@
 <link rel="shortcut icon" href="images/whale.gif">
+<body LINK="#0000FF" TEXT="#000000" BGCOLOR="#FFFFCD" VLINK="#0099FF">
 <img src="images/moby-java.gif">
-<h1>BioMoby in Java</h1>
+<h1>jMoby - BioMoby in Java</h1>
-This is a sub-project of the <a href="http://biomoby.org/" target="_top">BioMoby</a> project.
-It aims to develop an access to the Moby registry using pure Java, and later perhaps to
-develop a stand-alone Java Moby server. It will also provide Java support for providers
-of the Moby-compliant services.
-This is the overview of the current Moby java clients, and their
-relationship to the whole BioMoby project.
-<img src="images/moby-overview.jpg" width=790>
-<a name="api">
-<h2>Java API</h2>
-The detailed documentation of the involved classes and interfaces
-is <a href="API/index.html">available</a>
+This is a sub-project of the <a href="http://biomoby.org/"
+target="_top">BioMoby</a> project.  It aims to develop tools <b>in Java</b>
+in order:
+  <li> to access BioMoby registries, allowing all features provided by
+such registries, including but not limited to registering and
+deregistering of the BioMoby services and their parts, discovering
+them, and understanding their data in various formats (such as RDF),
-<a name="clients-download">
-<h2>Moby Java Clients - download and use</h2>
+  <li> to create Java implementations of BioMoby services, especially
+to help service providers with creating BioMoby data containers (input
+and output data) without exposing providers to the complexity of the
+XML required and produced by BioMoby services, and finally <p>
-The Moby Java clients are part of the
-<a href="http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/?cvsroot=biomoby">Moby CVS repository</a>
-but for convenience they can be downloaded also separately from
-<a href="http://industry.ebi.ac.uk/~senger/jMoby/dist/">http://industry.ebi.ac.uk/~senger/jMoby/dist/</a>
-(take the latest version, pick up either <tt>.tar.gz</tt> or <tt>.zip</tt> - both are equivalent).
+  <li> to provide support for those writing Java clients accessing
+both BioMoby registries and BioMoby services. <p>
-After downloading, unpack it, check the README file and start using it:
-  <li> <tt>sh run-testing-central</tt>
-  <li> <tt>sh run-cmdline-client -help</tt>
-or on the Windows platform:
-  <li> <tt>run-testing-central.bat</tt>
-  <li> <tt>run-cmdline-client.bat -help</tt>
-Latest changes are available either as a
-<a href="ChangeLog">summary</a> or in details from the
-<a href="http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/Java/?cvsroot=biomoby">CVS repository</a>.
+<h2>Where to go now</h2>
-Please report all problems, or submit features and wishes to
-<a href="mailto:senger at ebi.ac.uk">Martin Senger</a>.
+  <dt><img src="images/whale.gif" border=0 align=left/> <a href="Download.html">How to get jMoby</a>
+       <p>
+  <dt><img src="images/whale.gif" border=0 align=left/> How to use jMoby
+       <dl>
+	 <dt><a href="CmdLineClients.html">Command-line clients</a>
+	 <dt><a href="TavernaGuide.html">Integration with Taverna</a>
+	 <dt><a href="RDFAgent.html">RDF Agent</a>
+       </dl>
+       <p>
+  <dt><img src="images/whale.gif" border=0 align=left/> How to develop with jMoby
+       <dl>
+	 <dt><a href="API/index.html">Available APIs</a> (<em>more explanation coming...</em>)
+	 <dt><a href="SimpleClient.html">How to develop a client talking to a BioMoby service</a>
+	 <dt>How to develop a BioMoby service (<em>coming...</em>)
+       </dl>
+       <p>
+  <dt><img src="images/whale.gif" border=0 align=left/> <a href="ToDo.html">Next plans</a>
-<a name="todo">
-<h2>Next steps</h2>
-The future plans and steps in this sub-project may or should include
-  <li> Design and implement Java interfaces that can be used for the providers
-       of the Moby-compliant services
-  <li> Start to work on a pure Java Moby server (talk to Brian Gilman who had already started to work on it)
-<a name="ackno">
-The work on BioMoby Java sub-project is supported by
+The work on BioMoby Java sub-project is partly supported by
 <a href="http://www.mygrid.org.uk" target="_top">myGrid</a>,
 a multi-organisational project developing the infrastructural
 middleware for an <em>e-Biologist's</em> workbench,
 funded by <a href="http://www.epsrc.ac.uk/website/index.aspx" target="_top">EPSRC</a>.
+Other parts of jMoby are funded from the same sources as the BioMoby
@@ -87,7 +76,7 @@
 <div align=right><font size=-2>
 <address><A HREF="mailto:senger at ebi.ac.uk">Martin Senger</A><BR></address>
 <!-- hhmts start -->
-Last modified: Sun Nov 14 17:29:05 2004
+Last modified: Sun Dec  5 21:32:23 2004
 <!-- hhmts end -->
 </body> </html>

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