[MOBY-guts] biomoby commit
Martin Senger
senger at dev.open-bio.org
Thu Feb 14 06:13:35 UTC 2008
senger
Thu Feb 14 01:13:35 EST 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv22473/docs
Modified Files:
ChangeLog ChangesInBuild.html CodingGuidelines.html
ConfigureRDFAgent.html Dashboard.html
DirectoriesGuidelines.html Download.html LatestJava.html
Moses-clients.html Moses-deploy.html Moses-generators.html
Moses.html PerlMoses.html RegistryServlets.html Seahawk.html
ServiceDevelopment.html
Removed Files:
3rdPartyLibraries.html
Log Message:
Mavenization of jMoby. Many changes in build files and in the documentation.
moby-live/Java/docs ChangeLog,1.81,1.82 ChangesInBuild.html,1.1,1.2 CodingGuidelines.html,1.3,1.4 ConfigureRDFAgent.html,1.4,1.5 Dashboard.html,1.7,1.8 DirectoriesGuidelines.html,1.4,1.5 Download.html,1.8,1.9 LatestJava.html,1.3,1.4 Moses-clients.html,1.2,1.3 Moses-deploy.html,1.3,1.4 Moses-generators.html,1.4,1.5 Moses.html,1.6,1.7 PerlMoses.html,1.9,1.10 RegistryServlets.html,1.4,1.5 Seahawk.html,1.8,1.9 ServiceDevelopment.html,1.1,1.2 3rdPartyLibraries.html,1.3,NONE
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.81
retrieving revision 1.82
diff -u -r1.81 -r1.82
--- /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/31 13:42:51 1.81
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/14 06:13:34 1.82
@@ -1,3 +1,11 @@
+2008-02-14 Martin Senger <martin.senger@gmail.com>
+
+ * A new implementation of the CentralDigestCached classes fills
+ much faster local caches (used also by the Dashboard).
+
+ * The jMoby libraries and build files were all re-arranged in
+ order to take advantages of the Maven technology.
+
2007-05-31 Martin Senger <martin.senger@gmail.com>
* Added: few new constants into MobyService for async services
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangesInBuild.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/ChangesInBuild.html 2005/05/19 15:57:21 1.1
+++ /home/repository/moby/moby-live/Java/docs/ChangesInBuild.html 2008/02/14 06:13:34 1.2
@@ -26,11 +26,6 @@
Here is a list of the most common things you may want to do: <p>
-<h3>Adding sources that are compilable only with the latest Java 1.5</h3>
-
-There is a <a href="LatestJava.html">separate document</a> how to do
-it.
-
<h3>API documentation</h3>
The Ant's target <tt>docs</tt> creates <a href="API/index.html">API
@@ -60,15 +55,15 @@
<h3>Adding the third-party libraries</h3>
-There is a <a href="3rdPartyLibraries.html">separate document</a> how
-to do it.
+Edit <tt>xmls/project.pom</tt> and then type <tt>ant clean
+compile</tt>. <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 15:26:54 2005
+Last modified: Thu Feb 14 15:09:35 2008
<!-- hhmts end -->
</div>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/CodingGuidelines.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/docs/CodingGuidelines.html 2005/05/25 10:09:16 1.3
+++ /home/repository/moby/moby-live/Java/docs/CodingGuidelines.html 2008/02/14 06:13:34 1.4
@@ -74,8 +74,7 @@
<tt>xmls/libraries</tt> that is used by <tt>build.xml</tt>). <p>
All third parties come to your CVS local copy when you execute
-<tt>gather</tt> Ant target, or when you use <tt>./build.sh</tt>
-script.
+<tt>ant install</tt> (from various Maven repositories). <p>
</blockquote>
@@ -103,7 +102,7 @@
<div align=right class="address">
<address><A HREF="mailto:edward.kawas at gmail.com">Eddie Kawas</A><BR></address>
<!-- hhmts start -->
-Last modified: Wed May 25 10:50:58 2005
+Last modified: Thu Feb 14 15:05:58 2008
<!-- hhmts end -->
</div>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2007/09/11 16:48:27 1.4
+++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2008/02/14 06:13:34 1.5
@@ -48,20 +48,10 @@
<br>
</li>
<li class="dcount"> You can build the latest RDFAgent from the cvs.
- <ol>
- <li> on a unix box, </li>
- <blockquote>
- <p>/moby-live/Java/build.sh bindist_rdfagent </p>
- </blockquote>
- </ol>
+ <blockquote>
+ <p>ant bindist-rdfagent </p>
+ </blockquote>
</li>
- <ol>
- <li>on a windows box
- <blockquote>
- <p>/moby-live/Java/build.bat bindist_rdfagent </p>
- </blockquote>
- </li>
- </ol>
<blockquote>
<p>The newly created archive will be placed at <b class="step">/moby-live/Java/docs/dist/</b>, with the filename <b class="step">'rdfagent-yyyy-mm-dd.zip'</b> or <b class="step">'rdfagent-yyyy-mm-dd.tar.gz'</b><br>
<br>
@@ -493,8 +483,8 @@
<A HREF="mailto:ekawas at mrl.ubc.ca">Edward Kawas</A><BR>
</address>
<!-- hhmts start -->
- Last modified: Tue May 17 15:49:04 2005
- <!-- hhmts end -->
+Last modified: Thu Feb 14 15:07:15 2008
+<!-- hhmts end -->
<p>$Date$</p>
</div>
</body>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Dashboard.html,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/docs/Dashboard.html 2006/10/02 21:12:45 1.7
+++ /home/repository/moby/moby-live/Java/docs/Dashboard.html 2008/02/14 06:13:34 1.8
@@ -51,7 +51,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh dashboard
+ant dashboard
</pre>
</blockquote>
@@ -69,7 +69,7 @@
<blockquote>
<pre class=script>
-build-dev.bat dashboard
+ant dashboard
</pre>
</blockquote>
@@ -118,7 +118,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh docs
+ant docs
</pre>
</blockquote>
@@ -303,7 +303,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh dashboard
+ant dashboard
</pre>
</blockquote>
@@ -352,7 +352,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Mon Oct 2 22:09:01 2006
+Last modified: Thu Feb 14 15:02:09 2008
<!-- hhmts end -->
</div>
</body> </html>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/DirectoriesGuidelines.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/docs/DirectoriesGuidelines.html 2005/08/29 17:08:01 1.4
+++ /home/repository/moby/moby-live/Java/docs/DirectoriesGuidelines.html 2008/02/14 06:13:35 1.5
@@ -75,12 +75,6 @@
<dd>Here are files and templates that are used when the servlets
<tt>war</tt> files are being created.
- <dt><tt>lib</tt>
- <dd>A place for the third-party libraries (that are not part of the
-jMoby CVS). If you need to add a library here, you need to follow
-instructions in the <a href="3rdPartyLibraries.html">Third-party
-libraries Guidelines</a>.
-
<dt><tt>docs</tt>
<dd>A place for the public documentation. The contents of this
sub-directory - once committed - is visible from the main BioMoby page
@@ -187,7 +181,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Tue Aug 30 02:02:17 2005
+Last modified: Thu Feb 14 15:10:15 2008
<!-- hhmts end -->
</div>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Download.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/docs/Download.html 2006/08/18 22:32:55 1.8
+++ /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/14 06:13:35 1.9
@@ -12,26 +12,40 @@
<dl>
<dt> <a href="#cvs">Using jMoby from CVS</a>
+
<dd> The jMoby software is part of the <a
href="http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=biomoby">Moby
CVS repository</a> - look for a subdirectory
-<em>moby-live/Java</em>. The CVS is the best way to get the latest
-fixes and features (but sometimes also the latest bugs). The active
-developers should use this option (even if they do not commit their
-changes back). <p>
-
- <dt> <a href="#binary">Using jMoby binary distributions</a>
- <dd> This is an option for those wanting just to start some clients,
-to browse registries from a command line, or to call some BioMoby
-services. The main difference from the <a href="#cvs">CVS option</a>
-is that the binary distribution already contains all compiled Java
-classes, so you do not need to build them - and you can start to use
-it at once. <p>
+<em>moby-live/Java</em>. <p>
+
+
+ <dt> <a href="#binary">Using binary distributions</a>
- Another - and significant - difference is that nobody
-recently updated jMoby binary distribution. So it is quite old... <p>
+ <dd> There are several binary distributions, each of them focusing on
+some specific features. (Remember, however, that you can always get
+everything in one go from the <a href="#cvs">CVS repository</a>.) <p>
+ <dt> <a href="#maven">Using jMoby for Maven</a>
+
+ <dd> This is an option for those wanting to use jMoby libraries in
+their own Java projects. <p>
+
+ The only thing you need to know is how to refer to the jMoby
+library in a Maven repository (you need to find the latest version
+number by browsing the given Maven repository):
+
+<pre class="sscript">
+<groupId>org.biomoby</groupId>
+<artifactId>jmoby</artifactId>
+<version>1.0.0</version>
+
+<repository>
+ <id>bio.maven.repository</id>
+ <url>http://repo1.maven.org/maven2/</url>
+</repository>
+</pre>
+
</dl>
<p>
@@ -52,12 +66,42 @@
are in this directory. <p>
<blockquote>
+<a href="#req">Requirements</a><br>
<a href="#build">How to build it</a><br>
<a href="#targets">What are the build targets</a><br>
<a href="DirectoriesGuidelines.html">Where to put things</a><br>
<a href="#use">How to use it</a><br>
</blockquote>
+<a name="reqs"></a>
+<h3>Requirements</h3>
+
+
+<ul>
+
+ <li> <span class="bb">Java</span><p>
+
+ Install <a
+href="http://java.sun.com/javase/downloads/index.jsp">JDK Java 1.5 or
+later</a>. <p>
+
+ <li> <span class="bb">Apache Tomcat</span> (or a similar servlet container)<p>
+
+ BioMoby is about Web Services - and Web Services are web
+applications run in a servlet container. The development of BioMoby
+services was mostly done by using the <a
+href="http://tomcat.apache.org/download-55.cgi">Apache Tomcat
+5</a>. But other container should work, as well. <p>
+
+ <li> <span class="bb">Apache Ant</span><p>
+
+ The Ant is a Java tool for building, executing and playing with
+Java (and perhaps other, as well) programs. jMoby, as most of any
+Java projects, uses it a lot. <p>
+
+</ul>
+
+
<a name="build"></a>
<h3>How to build it</h3>
@@ -65,56 +109,26 @@
Just type:
<pre>
- ./build.sh
-</pre>
-
-or, on Windows platform.
-<pre>
- build.bat
+ ant install
</pre>
-You <b>can</b> use <tt>build.sh</tt> (or <tt>build.bat</tt>) script to compile everything
-anytime, but you <b>must</b> use it the first time (because it gathers all
-third-party libraries needed for compilation). Otherwise you <b>may</b>
-use <tt>build-dev.sh</tt> (or <tt>build-dev.bat</tt>) which is slightly faster
-because it does not attemp to fetch libraries.<p>
-
-Therefore, when re-building, you would normally type:
-<pre>
- ./build-dev.sh
-</pre>
-or, on Windows platform.
+or, if you have already installed it before, type:
<pre>
- build-dev.bat
+ ant clean compile
</pre>
In order to find what tasks are available, type:
<pre>
- ./build-dev.sh -projecthelp
-</pre>
-or
-<pre>
- build-dev.bat -projecthelp
+ ant -projecthelp
</pre>
-The available task can be specified on the command line of the
-building scripts. For example:
+The available task can be specified on the command line when invoking
+the Ant. For example:
<pre>
- ./build-dev.sh all
+ ant all
</pre>
-Default task is <em>compile</em>.
-
-The building scripts can make use of the following environment
-variables:
-
-<dl>
- <dt><tt>JAVA_HOME</tt>
- <dd> Pointing to a directory with your Java JDK. If not set the
-script tries to find it anyway (but not for the Windows platform - I
-do not know how to do it there :-)).
- <p>
-</dl>
+Default task is <em>compile</em>.<p>
It also uses file <tt>build.properties</tt> (if such file exists
either in this directory or in your home directory) - where you can
@@ -122,39 +136,20 @@
set there - are described in more details in
<tt>build.properties.template</tt>). <p>
-A note for developers:
- If you want to commit your changes back consider to copy file(s)
-<tt>.cvsignore.template</tt> into <tt>.cvsignore</tt> (they may be in
-several directories). This will save you from warning messages about
-local files which you do not want to commit (e.g. generated
-<tt>build</tt> directory). <p>
-
-Yet another note for developers: Developers are encouraged to add
-their code to the jMoby CVS and share it with others. There are only
-few, more or less organizational, rules suggested in <a
-href="CodingGuidelines.html">The Twelve Commandments for jMoby
-developers</a>. <p>
<a name="targets"></a>
<h3>What are the build targets</h3>
-The build scripts (as usual for building with Ant) are based on file
-<tt>build.xml</tt>. There you can find all details what can be build,
-and what properties are used. Here are just main targets explained in
-more details.<p>
+The build Ant's targets are based on file <tt>build.xml</tt>. There
+you can find all details what can be build, and what properties are
+used. Here are just main targets explained in more details.<p>
There is also a <a href="images/ant-snapshot.png">graphical
snapshot</a> of our Ant tagrets (<span class="smaller">and <a
href="vizant.txt">here</a> you can find how it was
created</span>). <p>
-Note that a target name is used as the command-line parameter of a
-build script. For example a target <em>docs</em> is invoked by typing:
-<pre>
- ./build-dev.sh docs
-</pre>
-
Here are the common targets:
<dl>
@@ -167,16 +162,14 @@
<tt>src</tt> and all jar files from the <tt>lib</tt> directory).
<p>
- <a href="LatestJava.html">Here</a> are some notes how to use Java 1.5.<p>
-
<dt><tt>clean</tt>
<dd> It removes all generated files, including all compiled classes
(but it does not remove third-party libraries from the <tt>lib</tt>
directory). It is always good idea to make sure that all your changes
are really compilable before you commit, by typing:
- <pre>
- ./build-dev.sh clean compile
- </pre>
+<pre>
+ant clean compile
+</pre>
<dt><tt>docs</tt>
<dd> It generates API documentation (into <tt>docs/API</tt>) for all
@@ -185,13 +178,12 @@
<tt>excluded.documented.files</tt>.
<p>
- <dt><tt>jar</tt>
- <dd> It creates a jar file (<tt>build/lib/jmoby.jar</tt>) with all
-classes from <tt>src</tt> (so it does not include the third-party
-classes from <tt>lib</tt>).
+ <dt><tt>jars</tt>
+ <dd> It creates several jar files (<tt>build/lib/*.jar</tt>) with
+all classes from <tt>src</tt>.
<p>
- <dt><tt>jar_rdfagent</tt>
+ <dt><tt>jar-rdfagent</tt>
<dd> It creates a jar file (<tt>build/lib/RDFagent.jar</tt>) with
classes for <em>RDF Agent</em> sub-project.
<p>
@@ -207,36 +199,15 @@
target.
<p>
- <dt>Targets for binary distributions are <tt>bindist</tt>,
-<tt>bindist_rdfagent</tt>, and <tt>wardist</tt>
- <dd> These targets creates tarred and zipped files with binary
-distributions in <tt>docs/dist</tt>.
- <p>
-
<dt><tt>all</tt>
<dd> It calls many other targets to clean, compile, generate API and
to build all binary distributions.
<p>
- <dt><tt>gather</tt>
- <dd> This is a special target fetching all out-of-dated third-party
-libraries from a remote location (the location can be changed by
-property <tt>remote.dir</tt>) using HTTP protocol.
- <p>
- The target must be called before you build the first time. This
-is done by script <tt>./build.sh</tt> that guarantees to call this
-target before doing anything else. But normally, you would call this
-target only time to time just to make sure that you have really the
-latest versions of the third-party libraries.
- <p>
-
- <dt>Target to deploy things to your local Tomcat are <tt>deploy</tt>
-and <tt>deploy-servlets</tt> (or <tt>deploy</tt> that calls the other two)
- <dd> These targets definitely needs to create some properties in
-<tt>build.properties</tt> to reflect where your Tomcat is
-located. Check <tt>build.properties.template</tt> to see what
-properties are expected.
- <p>
+ <dt><tt>bootstrap</tt>
+ <dd> This is a special target fetching the Maven library (that is
+needed to fetch all jMoby dependencies). It is called automatically
+when you call <tt>ant install</tt>. <p>
</dl>
@@ -259,8 +230,8 @@
or, on Windows platforms:
<pre>
- build/run/run-cmdline-client.bat -help
- build/run/run-testing-central.bat
+ build\run\run-cmdline-client.bat -help
+ build\run\run-testing-central.bat
</pre>
More details what individual clients actually do can be found in <a
@@ -272,10 +243,6 @@
<a name="binary"></a>
<h2>Using jMoby from binary distributions</h2>
-There are actually several binary distributions, each of them focusing on
-some specific features. (Remember, however, that you can always get
-everything in one go from the <a href="#cvs">CVS repository</a>.) <p>
-
The binary distributions are available from the main <a
href="dist/">jMoby site</a> (located on the same place as the main
BioMoby pages). <p>
@@ -283,7 +250,6 @@
<blockquote>
<a href="#easyservlet">Servlet for host MOBY services</a><br>
<a href="#guiclient">Graphical end-user client</a><br>
-<a href="#cmdline">Command-line clients exploring BioMoby</a><br>
<a href="#servlets">Servlets producing BioMoby graphs</a><br>
<a href="#rdfagent">RDF Agent</a><br>
</blockquote>
@@ -303,37 +269,6 @@
client that can be used as a <a href="Seahawk.html">standalone
browser</a>, or it can be easily <a href="Seahawk.html#component">embedded in another Java application</a>.
-<a name="cmdline"></a>
-<h3>Command-line clients exploring BioMoby</h3>
-
-This distribution contains several main jMoby clients, ready to be
-used and to communicate with a real Moby registry. The file is named
-<em>jMoby-<date>.[zip|tar.gz]</em>, take the latest version
-(pick up either <tt>.tar.gz</tt> or <tt>.zip</tt> - both are
-equivalent). <p>
-
-Unpack it. It creates a directory named <tt>jMoby</tt>, go there,
-check the <tt>README</tt> file, and start using it. For example, type:
-
-<pre>
- sh run-testing-central
- sh run-cmdline-client -help
-</pre>
-
-or on the Windows platform:
-<pre>
- run-testing-central.bat
- run-cmdline-client.bat -help
-</pre>
-
-
-More details what individual clients actually do can be found in <a
-href="CmdLineClients.html">a separate document</a>.
-<p>
-
-Please report all problems, or submit features and wishes about these clients to
-<span class="address"><a href="mailto:martin.senger at gmail.com">Martin Senger</a></span>.
-
<a name="servlets"></a>
<h3>Servlets producing BioMoby graphs</h3>
@@ -386,7 +321,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Thu Apr 27 23:33:24 2006
+Last modified: Thu Feb 14 14:56:18 2008
<!-- hhmts end -->
</div>
</body> </html>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/LatestJava.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/docs/LatestJava.html 2006/06/28 16:28:30 1.3
+++ /home/repository/moby/moby-live/Java/docs/LatestJava.html 2008/02/14 06:13:35 1.4
@@ -70,7 +70,7 @@
in your <tt>build.property</tt> file, or use it on the Ant's command line:
<pre>
- ./build-dev.sh -Djava.latest.version=false compile
+ ant -Djava.latest.version=false compile
</pre>
</div>
@@ -80,7 +80,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Wed Jun 28 17:22:10 2006
+Last modified: Thu Feb 14 15:01:34 2008
<!-- hhmts end -->
</div>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Moses-clients.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/docs/Moses-clients.html 2006/02/12 18:47:38 1.2
+++ /home/repository/moby/moby-live/Java/docs/Moses-clients.html 2008/02/14 06:13:35 1.3
@@ -196,7 +196,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh samples-compile
+ant samples-compile
</pre>
</blockquote>
@@ -1053,7 +1053,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Thu Feb 9 12:46:38 2006
+Last modified: Thu Feb 14 15:01:16 2008
<!-- hhmts end -->
</div>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Moses-deploy.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/docs/Moses-deploy.html 2005/11/21 17:17:27 1.3
+++ /home/repository/moby/moby-live/Java/docs/Moses-deploy.html 2008/02/14 06:13:35 1.4
@@ -65,7 +65,7 @@
<blockquote>
<pre class="script">
-./build-dev.sh -Dusers.lib.dir=/home/services/jars deploy-services
+ant -Dusers.lib.dir=/home/services/jars deploy-services
</pre>
</blockquote>
@@ -296,7 +296,7 @@
<blockquote>
<pre class="script">
-./build-dev.sh deploy-services
+ant deploy-services
</pre>
</blockquote>
@@ -306,7 +306,7 @@
<blockquote>
<pre class="script">
-./build-dev.sh undeploy-services
+ant undeploy-services
</pre>
</blockquote>
@@ -359,7 +359,7 @@
<blockquote>
<pre class="script">
-./build-dev.sh deploy-remote
+ant deploy-remote
</pre>
</blockquote>
@@ -419,7 +419,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Mon Nov 21 23:55:46 2005
+Last modified: Thu Feb 14 15:01:03 2008
<!-- hhmts end -->
</div>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Moses-generators.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/docs/Moses-generators.html 2006/01/14 02:12:19 1.4
+++ /home/repository/moby/moby-live/Java/docs/Moses-generators.html 2008/02/14 06:13:35 1.5
@@ -304,8 +304,8 @@
<blockquote>
<pre class=script>
-./build-dev.sh <b>moses-datatypes</b>
-./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache <b>moses-datatypes</b>
+ant <b>moses-datatypes</b>
+ant -Dregistry.cache.dir=/tmp/biomobycache <b>moses-datatypes</b>
</pre>
</blockquote>
@@ -313,9 +313,9 @@
<blockquote>
<pre class=script>
-./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache <b>generate-datatypes</b>
-./build-dev.sh <b>moses-compile</b>
-./build-dev.sh <b>moses-docs</b>
+ant -Dregistry.cache.dir=/tmp/biomobycache <b>generate-datatypes</b>
+ant <b>moses-compile</b>
+ant <b>moses-docs</b>
</pre>
</blockquote>
@@ -327,7 +327,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.nogener=true <b>generate-datatypes</b>
+ant -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.nogener=true <b>generate-datatypes</b>
</pre>
</blockquote>
@@ -338,8 +338,8 @@
<blockquote>
<pre class=script>
-./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.filter.dt=sequence <b>generate-datatypes</b>
-./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache '-Dmoses.filter.dt=(?i)sequence' <b>generate-datatypes</b>
+ant -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.filter.dt=sequence <b>generate-datatypes</b>
+ant -Dregistry.cache.dir=/tmp/biomobycache '-Dmoses.filter.dt=(?i)sequence' <b>generate-datatypes</b>
</pre>
</blockquote>
<p>
@@ -429,8 +429,8 @@
Class 'org.biomoby.shared.datatypes.MapDataTypes' was not found.
It may indicate that you have not generated all Biomoby data types from a Biomoby registry.
See http://www.biomoby.org/moby-live/Java/docs/Moses.html for details.
-If you are a jMoby developer just type: ./build-dev.sh moses-datatypes.
-Or perhaps, they just need to be compiled: ./build-dev.sh moses-compile.
+If you are a jMoby developer just type: ant moses-datatypes.
+Or perhaps, they just need to be compiled: ant moses-compile.
===========
</pre>
</blockquote>
@@ -439,8 +439,7 @@
generating service skeletons. But - because the slice of bread always
falls down on the buttered site - very often you have generated them
but either forgot to compile them, or (it happens to me all the time)
-you removed the compiled classes by calling <tt>./build-dev.sh
-clean</tt>. <p>
+you removed the compiled classes by calling <tt>ant clean</tt>. <p>
Now we can go back to the options and Ant's properties: <p>
@@ -525,9 +524,9 @@
<blockquote>
<pre class=script>
-./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache <b>generate-services</b>
-./build-dev.sh <b>moses-compile</b>
-./build-dev.sh <b>moses-docs</b>
+ant -Dregistry.cache.dir=/tmp/biomobycache <b>generate-services</b>
+ant <b>moses-compile</b>
+ant <b>moses-docs</b>
</pre>
</blockquote>
@@ -535,7 +534,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache <b>moses-services</b>
+ant -Dregistry.cache.dir=/tmp/biomobycache <b>moses-services</b>
</pre>
</blockquote>
@@ -792,7 +791,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Sat Jan 14 09:26:59 2006
+Last modified: Thu Feb 14 15:00:35 2008
<!-- hhmts end -->
</div>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Moses.html,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/docs/Moses.html 2005/09/22 08:54:40 1.6
+++ /home/repository/moby/moby-live/Java/docs/Moses.html 2008/02/14 06:13:35 1.7
@@ -183,7 +183,7 @@
Details and explanation follow in the next sections. The examples of
typing assumes that you have a CVS copy of jMoby and you have already
compiled all classes (which is easy to do just by typing
-<tt>./build.sh</tt>. <p>
+<tt>ant install</tt>. <p>
<ol>
@@ -202,7 +202,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh moses-datatypes
+ant moses-datatypes
</pre>
</blockquote>
@@ -211,7 +211,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh -Dmoses.service=TheService moses-services
+ant -Dmoses.service=TheService moses-services
</pre>
</blockquote>
@@ -225,7 +225,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh
+ant
</pre>
</blockquote>
@@ -235,7 +235,7 @@
<blockquote>
<pre class=script>
-./build-dev.sh -Dservice.name=TheService deploy-services
+ant -Dservice.name=TheService deploy-services
</pre>
</blockquote>
@@ -305,7 +305,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Thu Sep 22 08:42:37 2005
+Last modified: Thu Feb 14 15:05:21 2008
<!-- hhmts end -->
</div>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/PerlMoses.html,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/docs/PerlMoses.html 2006/10/14 20:46:55 1.9
+++ /home/repository/moby/moby-live/Java/docs/PerlMoses.html 2008/02/14 06:13:35 1.10
@@ -97,7 +97,7 @@
cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login
cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live/Java
cd <somewhere>/moby-live/Java
-./build.sh</pre>
+ant install</pre>
Under Windows, the last command is <tt>build.bat</tt> (and some
slashes become backslashes). More about building jMoby can be found <a
@@ -400,7 +400,7 @@
<pre class="script">
cd moby-live/Java
-./build.sh
+ant
</pre>
@@ -2505,7 +2505,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Sat Oct 14 21:42:54 2006
+Last modified: Thu Feb 14 15:04:56 2008
<!-- hhmts end -->
</div>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/RegistryServlets.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/docs/RegistryServlets.html 2006/11/16 21:57:41 1.4
+++ /home/repository/moby/moby-live/Java/docs/RegistryServlets.html 2008/02/14 06:13:35 1.5
@@ -68,10 +68,7 @@
<br>
</li>
<li class="dcount">From the command line, enter the following command from a *nix box <br/>
- <pre class="script">./build.sh bindist_registry</pre>
- <p>Or the following on a windows machine:</p>
- <br>
- <pre class="script">build.bat bindist_registry</pre>
+ <pre class="script">ant bindist-registry</pre>
</li>
<li class="dcount">Once the build is complete, a zip file will be located at <b class="step">/moby-live/Java/build/registry_servlets</b> called authority.zip. Unzip this file into the webapps directory of Tomcat or other J2EE container.<br>
<br>
@@ -296,7 +293,8 @@
<A HREF="mailto:ekawas at mrl.ubc.ca" class="mail">Edward A Kawas</A><BR>
</address>
<!-- hhmts start -->
- <!-- hhmts end -->
+Last modified: Thu Feb 14 15:03:17 2008
+<!-- hhmts end -->
</div>
</body>
</html>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Seahawk.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/docs/Seahawk.html 2007/06/30 22:21:56 1.8
+++ /home/repository/moby/moby-live/Java/docs/Seahawk.html 2008/02/14 06:13:35 1.9
@@ -55,7 +55,7 @@
<a name="launch"></a>
<h2>How do I launch it?</h2>
- <p>The applet can be launched from the following Web site: <a href="http://moby.ucalgary.ca/seahawk/">http://moby.ucalgary.ca/seahawk/</a>. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: <tt>./build.sh seahawk</tt></p>
+ <p>The applet can be launched from the following Web site: <a href="http://moby.ucalgary.ca/seahawk/">http://moby.ucalgary.ca/seahawk/</a>. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: <tt>ant seahawk</tt></p>
<a name="classes"></a>
@@ -127,7 +127,7 @@
<address><a href="mailto:gordonp at ucalgary.ca">Paul Gordon</a></address>
<!-- Created: Wed Jul 20 11:44:30 MDT 2005 -->
<!-- hhmts start -->
-Last modified: Sun Mar 25 08:20:27 MDT 2007
+Last modified: Thu Feb 14 15:02:47 2008
<!-- hhmts end -->
</body>
</html>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ServiceDevelopment.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/ServiceDevelopment.html 2006/04/28 14:52:47 1.1
+++ /home/repository/moby/moby-live/Java/docs/ServiceDevelopment.html 2008/02/14 06:13:35 1.2
@@ -70,16 +70,15 @@
cd moby-live/Java
</pre>
- <li> Build jMoby (and create jar file with jMby libraries)
+ <li> Build jMoby (and create a jar file with jMoby libraries)
<pre class="script2">
-./build.sh
-./build-dev jar
+ant jars
</pre>
<li> Start <a href="Dashboard.html">BioMoby Dashboard</a> in order
to fill local cache with BioMoby entities (this may take a
while when it runs the first time):
<pre class="script2">
-./build-dev.sh dashboard
+ant dashboard
</pre>
</ul>
<p>
@@ -152,7 +151,7 @@
<pre class="script2">
cd moby-live/Java
-./build-dev.sh dashboard
+ant dashboard
Setting<b> -> </b>Panel selection<b> -> </b>Registration<b> -> </b>Service Registration
</pre>
@@ -169,7 +168,7 @@
<pre class="script2">
cd moby-live/Java
-./build-dev.sh dashboard
+ant dashboard
Setting<b> -> </b>Panel selection<b> -> </b>MoSeS Generator
<b>Select service...:</b> <em>your-service-name</em>
@@ -250,7 +249,7 @@
<pre class="script2">
cd moby-live/Java
-./build-dev.sh dashboard
+ant dashboard
Setting<b> -> </b>Panel selection<b> -> </b>Simple Client
<b>Select service...:</b> <em>your-service-name</em>
<em>add your input data on the right</em>
@@ -306,7 +305,7 @@
<pre class="script2">
cd moby-live/Java
-./build-dev.sh dashboard
+ant dashboard
Setting<b> -> </b>Panel selection<b> -> </b>MoSeS Generator
<b>Pattern for implementation class names:</b> <em>your-package-name</em>.{SERVICE}Impl
@@ -344,7 +343,7 @@
<div align=right class="address">
<address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
<!-- hhmts start -->
-Last modified: Fri Apr 28 15:49:39 2006
+Last modified: Thu Feb 14 14:58:25 2008
<!-- hhmts end -->
</div>
rcsdiff: /home/repository/moby/moby-live/Java/docs/RCS/3rdPartyLibraries.html,v: No such file or directory
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