<p><a href="dm_javadoc/index.html">Data model</a> javadoc- read this if your are coding against JABA Web Services</p>\r
<p><a href="full_javadoc/index.html">Complete</a> javadoc - for developers who want to use JABAWS framework and use Engines and Executables directly</p>\r
<h4><a name="thesrc" id="thesrc"></a>The source code</h4>\r
-<p><a name="svn">Private (most up-to-date) SVN source repository:</a><a href="link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA_r1">https://svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2_r1</a></p>\r
-<p>The JABAWS public code repository containing the code for each JABAWS public release is located at https://jabaws.googlecode.com/ </p>\r
-<p> The repository contains a complete JABAWS <a href="http://www.eclipse.org">Eclipse</a> project. </p>\r
-<p>Of cause If you want to make a modification to the source code you would need to generate distributives yourself. To do that first generate JAX-WS artifacts using <span class="hightlight">build-server</span> task from <span class="hightlight">wsbuild.xml</span> ant script, than you could use build.xml tasks to generate any of the distributives you need. </p>\r
+<p><a name="svn">Publicly available Git repository:</a><a href="http://source.jalview.org/gitweb/?p=jabaws.git;a=summary">http://source.jalview.org/gitweb/?p=jabaws.git;a=summary</a></p>\r
+<p>Another publicly available JABAWS repository, containing the code for each JABAWS public release, is located at <a href="https://jabaws.googlecode.com">jabaws.googlecode.com</a></p>\r
+<p>The repositories contain a complete JABAWS <a href="http://www.eclipse.org">Eclipse</a> project. </p>\r
+<p>Of course if you want to make a modification to the source code you would need to generate distributives yourself. To do that, first generate JAX-WS artifacts using <span class="hightlight">build-server</span> task from <span class="hightlight">wsbuild.xml</span> ant script, then you could use build.xml tasks to generate any of the distributives you need. </p>\r
<h4><a name="projstruct" id="projstruct"></a>Structure of the project</h4>\r
<ul>\r
<li><span class="directory">binaries</span> contains native executables e.g. clustalw</li>\r
- <ul>\r
- <li><span class="directory">src</span> contains sources of native executables</li>\r
- <li><span class="directory">windows</span> contains pre-compiled Windows binaries</li>\r
- <li>compilebin.sh - the script to complile binaries</li>\r
- <li>setexecflag.sh - the script to set executable flag for the binaries</li>\r
- </ul>\r
+ <li style="list-style-position:inside"><span class="directory">src</span> contains sources of native executables</li>\r
+ <li style="list-style-position:inside"><span class="directory">windows</span> contains pre-compiled Windows binaries</li>\r
+ <li style="list-style-position:inside">compilebin.sh - the script to complile binaries</li>\r
+ <li style="list-style-position:inside">setexecflag.sh - the script to set executable flag for the binaries</li>\r
<li><span class="directory">conf</span> contains JABAWS configuration files </li>\r
<li><span class="directory">ExecutionStatistics</span> the database for storing collected execution statistics </li>\r
<li><span class="directory">jobsout</span> a default folder for temporary job directories </li>\r
<li><span class="directory">statpages</span> the web pages for execution statistics display</li>\r
<li><span class="directory">WEB-INF</span> default </li>\r
<li><span class="directory">website</span> contains the JABAWS web pages </li>\r
- <ul>\r
- <li><span class="directory">archive</span> contains JABAWS packages, the WAR and JAR files</li>\r
- </ul>\r
+ <li style="list-style-position:inside"><span class="directory">archive</span> contains JABAWS packages, the WAR and JAR files</li>\r
+\r
</ul>\r
<h4><a name="thecode" id="thecode"></a>The code structure</h4>\r
<ul>\r
\r
<h4><a name="runtests" id="runtests"></a>Running tests</h4>\r
<p>\r
-JABAWS uses TestNG framework for testing. The test results for the JABAWS package offered for download can be found here: \r
+JABAWS uses TestNG framework for testing. The test results for the JABAWS package offered for download can be found at: \r
<a href="http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html">Test Results</a><br/>\r
JABAWS uses <a href="http://testng.org/doc/index.html">TestNG</a> for testing. There is a TestNG plugin available for Eclipse \r
which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied \r
<p>Create a testcase suit for your wrapper in <span class="hightlight">testsrc</span> and run the test cases.</p>\r
</li><li>\r
<p>Create parser for the output files of your executable. Suggested location \r
- compbio.data.sequence.SequenceUtil </p>\r
+ compbio.data.sequence.SequenceUtil . </p>\r
</li><li>\r
- <p>Test the parser</p>\r
+ <p>Test the parser.</p>\r
</li><li>\r
<p>Decide which web services interfaces your executable is going to match. For example \r
if the executable output can be represented as SequenceAnnotation then SequenceAnnotation \r
implement a web service which confirms to it within a webservices source folder. </p>\r
</li><li> \r
<p>Register web service in <span class="hightlight">WEB-INF/web.xml</span> \r
- and <span class="hightlight">WEB-INF/sun-jaxws.xml</span></p>\r
+ and <span class="hightlight">WEB-INF/sun-jaxws.xml</span> .</p>\r
</li><li> \r
<p>Add generated wsdl to wsbuild.xml ant script to generate the stubs.</p>\r
</li><li>\r
that JAXB cannot serialize some of your new data structures. Add appropriate annotations to your data types.\r
Also check that: </p>\r
<ul>\r
- <li>you do not have interfaces to serialize, since JAXB cannot serialize them;</li>\r
- <li>you have a default no args constructor (can be private if you do not need it);</li>\r
- <li>JAXB cannot serialize Java Map class, use a custom data structure instead;</li>\r
- <li>Enum cannot be serialized as its abstract class (do not confuse with enum which is fine);</li>\r
+ <li>you do not have interfaces to serialize, since JAXB cannot serialize them</li>\r
+ <li>you have a default no args constructor (can be private if you do not need it)</li>\r
+ <li>JAXB cannot serialize Java Map class, use a custom data structure instead</li>\r
+ <li>Enum cannot be serialized as its abstract class (do not confuse with enum which is fine)</li>\r
<li> Fields serialization leaves a little more space for manoeuvre. \r
- If you do this then you may accept<br/> and return interfaces, e.g. List, Map; abstract classes etc, from your methods.\r
+ If you do this then you may accept<br/> and return interfaces, e.g. List, Map; abstract classes etc, from your methods\r
</li>\r
</ul>\r
<p>If you have the data on the server side, but nothing is coming through to the \r
</ol>\r
<p> </p>\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 30 April 2014<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
</div> <!-- page end-->\r
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git://source.jalview.org / jabaws.git / blobdiff