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- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
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<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
<h4><a name="projstruct" id="projstruct"></a>Structure of the project</h4>\r
<ul>\r
- <li>\r
- <span class="directory">binaries</span> contains native executables e.g. clustalw</li>\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
+ <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><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">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
- </ul>\r
+ <ul>\r
+ <li><span class="directory">archive</span> contains JABAWS packages, the WAR and JAR files</li>\r
+ </ul>\r
+</ul>\r
<h4><a name="thecode" id="thecode"></a>The code structure</h4>\r
<ul>\r
<li><span class="directory">datamodel</span> contains the JABAWS datamodel </li>\r
<p>A client package contains only classes from data model layer and a simple web services client. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Framework exclude the web services layer. Server package contains all the code.</p>\r
\r
<h4><a name="runtests" id="runtests"></a>Running tests</h4>\r
-<p>JABAWS uses TestNG framework for testing. The test results for the JABAWS package offered for download can be found here: <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 which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied with JABAWS together with an ant tasks to run the test cases. </p>\r
+<p>\r
+JABAWS uses TestNG framework for testing. The test results for the JABAWS package offered for download can be found here: \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
+with JABAWS together with an ant tasks to run the test cases. </p>\r
<p>The best way to ensure that JABAWS framework is completely functional on your system is to run all test cases. \r
-Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding those that depends on the cluster.\r
-Several testing groups are supported: \r
-<p>All tests (Test)</p>\r
-<p>Cluster tests (Run_cluster_dependent_test)</p>\r
-<p>Cluster independent tests () </p>\r
-<p>Windows only tests (All_cluster_independent_windows_only_tests) </p>\r
-<p>Performance and stability tests (Long_tests) </p>\r
-<p>Re-run failed tests (Rerun_failed_tests) </p>\r
-<p>Run custom test (CustomTest) </p>\r
+Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support \r
+of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding \r
+those that depends on the cluster.</p>\r
+<p>Several testing groups are supported:</p>\r
+<ul>\r
+<li>All tests (Test)</li>\r
+<li>Cluster tests (Run_cluster_dependent_test)</li>\r
+<li>Cluster independent tests () </li>\r
+<li>Windows only tests (All_cluster_independent_windows_only_tests) </li>\r
+<li>Performance and stability tests (Long_tests) </li>\r
+<li>Re-run failed tests (Rerun_failed_tests) </li>\r
+<li>Run custom test (CustomTest) </li>\r
+</ul>\r
<p>To run the tests you need to download all sources from <a href="#svn">repository</a>. Once you have done that, enter into the command line mode, change directory to the project directory and type: \r
<span class="code">ant -f build.xml <test group name></span> </p>\r
- <p>. Make sure you have <a href="http://ant.apache.org/">Apache Ant</a> \r
+ <p>Make sure you have <a href="http://ant.apache.org/">Apache Ant</a> \r
installed and path to ant executable is defined in your path environmental variable. \r
Replace test group name with the one of the names given in the list above to run required group of tests e.g for running cluster only tests \r
use the following \r
command: <span class="code">ant -f build.xml Run_cluster_dependent_test</span>\r
- If you work under Linux you could use a simple script from the root folder of repository called <span class="hightlight">runtests.sh</span> This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, which you can define once for your system and then reuse. </p>\r
- </p>\r
- <p>A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in <span class="hightlight">test-output/testng-failed.xml</span>. and is used in the ant task called <span class="hightlight">Rerun_failed_tests</span>. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: <span class="code">ant -f build.xml Rerun_failed_tests</span> CustomTest runs the test defined in the project root directory file called <span class="hightlight">temp-testng-customsuite.xml</span>. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure. </p>\r
+ If you work under Linux you could use a simple script from the root folder of repository called <span class="hightlight">runtests.sh</span> \r
+ This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, \r
+ which you can define once for your system and then reuse.</p>\r
+ <p>\r
+ A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in \r
+ <span class="hightlight">test-output/testng-failed.xml</span>. and is used in the ant task called \r
+ <span class="hightlight">Rerun_failed_tests</span>. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: <span class="code">ant -f build.xml Rerun_failed_tests</span> CustomTest runs the test defined in the project root directory file called <span class="hightlight">temp-testng-customsuite.xml</span>. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure. </p>\r
<p class="hightlight">For cluster execution make sure that the property LD_LIBRARY_PATH defined in build.xml points to cluster engine LD libraries directory in your local system.</p>\r
\r
<h4><a name="prepexec" id="prepexec"></a>Preparing distributive's</h4>\r
- <p>There are a number of ant tasks aimed for preparing distributives for download.\r
- Currently a few types of JABAWS packages are offered \r
- <p>Client only (contains classes required to access JABA Web Services)</p>\r
- <p>Platform specific JABAWS (windows and other)</p>\r
- <p>JABAWS without binaries</p>\r
- <p>JABAWS framework </p>\r
- </p>\r
- Corresponding build task names are: \r
- <p>min-jaba-client</p>\r
- <p>jaba-windows, jaba-complete</p>\r
- <p>jaba-no-binaries</p>\r
- <p>full-jaba-client</p>\r
- <p>The easiest way to build all distributives is to call <span class="hightlight">build-all </span>ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory. </p>\r
- <p class="hightlight">If you made any changes to the data model and would like to generate a complete JABAWS distro make sure you have rebuilt jaxws artifact as described below. </p>\r
+ <p>There are a number of ant tasks aimed for preparing distributives for download. Currently a few types of JABAWS packages are offered:</p> \r
+ <ol>\r
+ <li>Client only (contains classes required to access JABA Web Services)</li>\r
+ <li>Platform specific JABAWS (windows and other)</li>\r
+ <li>JABAWS without binaries</li>\r
+ <li>JABAWS framework </li>\r
+ </ol>\r
+ <p>Corresponding build task names are:</p> \r
+ <ol>\r
+ <li>min-jaba-client</li>\r
+ <li>jaba-windows, jaba-complete</li>\r
+ <li>jaba-no-binaries</li>\r
+ <li>full-jaba-client</li>\r
+ </ol>\r
+ <p>The easiest way to build all distributives is to call <span class="hightlight">build-all </span>ant task. \r
+ There are more tasks defined in build.xml than described here. They are mostly self explanatory.</p>\r
+ <p class="hightlight">If you made any changes to the data model and would like to generate a complete JABAWS \r
+ distro make sure you have rebuilt jaxws artifact as described below.</p>\r
<h4><a name="buildstubs" id="buildstubs"></a>Building web services artifacts</h4>\r
-<p>Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in <span class="hightlight">webservices/compbio/ws/server/resource</span> directory. It is not necessary to edit them if any of the JABAWS clients are used. JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible. </p>\r
+<p>Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. \r
+ To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in \r
+ <span class="hightlight">webservices/compbio/ws/server/resource</span> directory. It is not necessary to \r
+ edit them if any of the JABAWS clients are used. JABAWS are the standard JAX-WS web services, which are \r
+ WS-I basic profile compatible. </p>\r
<h4><a name="addnewws" id="addnewws"></a>Rough guide - adding a new web service</h4>\r
<ol>\r
-<li> Add a new executable which you'd like to wrap as a JABAWS web service to the binaries folder. If it has the source code and can be \r
- recompiled for different platforms include it under binaries/src.\r
- Edit binaries/src setexecutableflag.sh and compilebin.sh scripts accordingly. </li>\r
-<li> Make sure that all the dependencies of the software being installed are satisfied. \r
- If there are other binaries they should be included as well. Keep the dependent \r
- binaries in subfolder for the main executable. Update compilebin and setexecflag </li>\r
- scripts accordingly.<li> Make sure that the new executable </li>\r
- does not have any hard links to its dependencies, e.g. is able to run from \r
- any installation folder and does not contain any hard coded paths. \r
- <li> Describe executable in conf/Exectuable.properties file. The lowercase name of the \r
- wrapper should be included in the name of the property for example Clustal \r
- properties all include clustal as a part of the name e.g. local.clustalw.bin.\r
- The same property for Mafft will be called local.mafft.bin. For more help please refer to the Executable.properties file. </li>\r
- <li> Describe the executable supported parameters in the <ExecutableName>Parameters.xml, presets in the <ExecutableName>Presets.xml and the execution limits in the <ExecutableName>Limit.xml. By convention these files are stored in conf/settings. All of these are optional. If the \r
- executable does not support parameters you do not have to mention the \r
- XXXParameter.xml file in the Executable.properties file at all. The same is true for \r
- Presets and Limits. </li>\r
-<li> Create a Java wrapper class for your executable. Create it within runner \r
- source directory. Examples of other wrappers can be found in compbio.runner.msa \r
- or compbio.runner.disorder packages. Wrapper should extend SkeletalExecutable<T> \r
- implements PipedExecutable<T> if you need to pass the input or collect the \r
- results from the standard in/out. Please see Mafft code as example. Wrapper \r
- should expend SkeletalExecutable<T> if input/output can be set as a parameter \r
- for an executable. Please see ClustalW code as example. </li>\r
-<li> Create a testcase suit for your wrapper and run the test cases. </li>\r
-<li> Create parser for the output files of your executable. Suggested location \r
- compbio.data.sequence.SequenceUtil </li>\r
-<li> Test the parser</li>\r
-<li> Decide which web services interfaces your executable is going to match. \r
- For example if the executable output can be represented as <br />\r
- SequenceAnnotation then SequenceAnnotation interface might be appropriate. \r
- For multiple sequence alignment an Msa interface should be used. </li>\r
-<li> If you find a web interface that matches your returning data type, then \r
- implement a web service which confirms to it within a webservices source folder. </li>\r
-<li> Register web service in WEB-INF/ web.xml and sun-jaxws.xml</li>\r
-<li> Add generated wsdl to wsbuild.xml ant script to generate the stubs.</li>\r
-<li> Run build-server task in wsbuild file. Watch for errors. If the task fails <br />\r
- that means that JAXB cannot serialize some of your new data structures. Add <br />\r
- appropriate annotations to your data types.\r
- Also check that <br />\r
- - you do not have interfaces to serialize. JAXB cannot serialize them.<br />\r
- - you have a default no args constructor (can be private if you do not need it)<br />\r
- - JAXB cannot serialize a Map, use custom data structure instead!<br />\r
- - Enum cannot be serialized as its abstract class (do not confuse with enum <br />\r
- which is fine)<br />\r
- - Fields serialization leave a little more space for manoeuvre, so use it. If <br />\r
- you do then you can accept and return interfaces, e.g. List, Map; abstract <br />\r
- classes etc, from your methods. <br />\r
- <br />\r
- If you have the data on the server side, but nothing is coming through to the <br />\r
- client, this is a JAXB serialization problem. They tend to be very silent and <br />\r
- thus hard to debug. Check your data structure can be serialized! </li>\r
-<li>Modify the client to work with your new web service. Update Services \r
- enumeration to include new service and ensure that all the methods of this \r
- enumeration take into account the new service. Update the client help text \r
- (client_help.txt) and insert it into the Constraints class. </li>\r
-<li> Test the web service with the client </li>\r
-<li> Test on the cluster.</li>\r
+ <li> \r
+ <p>Add a new executable which you'd like to wrap as a JABAWS web service to the binaries folder. \r
+ If it has the source code and can be recompiled for different platforms include it under \r
+ <span class="hightlight">binaries/src</span>. Edit <span class="hightlight">setexecutableflag.sh</span> \r
+ and <span class="hightlight">compilebin.sh</span> scripts in <span class="hightlight">binaries/src</span> \r
+ accordingly.</p>\r
+ </li><li>\r
+ <p>Make sure that all the dependencies of the software being installed are satisfied. \r
+ If there are other binaries they should be included as well. Keep the dependent \r
+ binaries in a subfolder for the main executable. Update \r
+ <span class="hightlight">compilebin.sh</span> and <span class="hightlight">setexecflag.sh</span> scripts accordingly.</p>\r
+ </li><li>\r
+ <p>Make sure that the new executable does not have any hard links to its dependencies, e.g. is able to run from \r
+ any installation folder and does not contain any hard coded paths.</p>\r
+ </li><li>\r
+ <p>Describe executable in <span class="hightlight">conf/Exectuable.properties</span> file. The lowercase name of the wrapper should be included \r
+ in the name of the property for example Clustal properties all include clustal as a part of the name e.g. local.clustalw.bin.\r
+ The same property for MAFFT will be called local.mafft.bin. For more help please refer to the Executable.properties file.</p>\r
+ </li><li>\r
+ <p>Describe the executable supported parameters in the \r
+ <span class="hightlight"><ExecutableName>Parameters.xml</span>, presets in the \r
+ <span class="hightlight"><ExecutableName>Presets.xml</span> and the execution limits in the \r
+ <span class="hightlight"><ExecutableName>Limit.xml</span>. By convention these files are stored \r
+ in <span class="hightlight">conf/settings</span>. All of these are optional. If the executable \r
+ does not support parameters you do not have to mention the <span class="hightlight">XXXParameter.xml</span> file \r
+ in the <span class="hightlight">Executable.properties</span> file at all. The same is true for \r
+ Presets and Limits.</p>\r
+ </li><li>\r
+ <p>Create a Java wrapper class for your executable. Create it within <span class="hightlight">runner</span> source directory. \r
+ Examples of other wrappers can be found in <span class="hightlight">compbio.runner.msa</span> or \r
+ in other <span class="hightlight">compbio.runner.*</span> packages. Wrapper should extend \r
+ <span class="hightlight">SkeletalExecutable<T></span> and implement \r
+ <span class="hightlight">PipedExecutable<T></span> \r
+ if you need to pass the input or collect the results from the standard in/out. Please see Mafft \r
+ code as example. Wrapper should expend <span class="hightlight">SkeletalExecutable<T></span> \r
+ if input/output can be set as a parameter for an executable. Please see the ClustalW code as example.</p>\r
+ </li><li>\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
+ </li><li>\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
+ interface might be appropriate. For multiple sequence alignment an Msa interface should be used.</p>\r
+ </li><li>\r
+ <p>If you find a web interface that matches your returning data type, then \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
+ </li><li> \r
+ <p>Add generated wsdl to wsbuild.xml ant script to generate the stubs.</p>\r
+ </li><li>\r
+ <p>Run build-server task in wsbuild file. Watch for errors. If the task fails that means \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> 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
+ </li>\r
+ </ul>\r
+ <p>If you have the data on the server side, but nothing is coming through to the \r
+ client, this is a JAXB serialization problem. They tend to be very silent and \r
+ thus hard to debug. Check your data structure can be serialized!</p>\r
+ </li><li>\r
+ <p>Modify the client to work with your new web service. Update Services \r
+ enumeration to include new service and ensure that all the methods of this \r
+ enumeration take into account the new service. Update the client help text \r
+ (client_help.txt) and insert it into the Constraints class.</p>\r
+ </li><li>\r
+ <p>Test the web service with the client.</p>\r
+ </li><li> \r
+ <p>Test on the cluster.</p>\r
+ </li>\r
</ol>\r
<p> </p>\r
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