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11 <c:param name="title">Documentation</c:param>
14 <ol class="breadcrumb">
15 <li><a href="${pageContext.request.contextPath}/index.jsp">Home</a></li>
16 <li><a href="man_docs.jsp">Documentation</a></li>
17 <li class="active"><a href="man_server_dev.jsp">Developing JABAWS</a></li>
20 <div class="col-md-12">
21 <div class="panel panel-default">
22 <div class="panel panel-heading">
23 <h1 class="panel-title">For JABAWS Developers</h1>
25 <div class="panel-body">
26 <!--<h4>JABAWS Server Virtual Appliance</h4>-->
28 <li><a href="#api">The API</a></li>
29 <li><a href="#thesrc">The source code</a></li>
30 <li><a href="#projstruct">Structure of the project</a></li>
31 <li><a href="#thecode">The code structure</a></li>
32 <li><a href="#runtests">Running tests</a></li>
33 <li><a href="#prepexec">Preparing distributive's</a></li>
34 <li><a href="#buildstubs">Building web services artifacts</a></li>
35 <li><a href="#addnewws">Adding a new web service (rough guide)</a></li>
37 <!--<p class="justify">-->
43 <div class="row" id="api">
44 <div class="col-md-12">
45 <div class="panel panel-default">
46 <div class="panel panel-heading">
47 <h1 class="panel-title">The API</h1>
49 <div class="panel-body">
50 <p>This page is for anyone who wants to add a new webservice into the JABAWS framework.</p>
51 <p><a href="${pageContext.request.contextPath}/dm_javadoc/index.html">Data Model JavaDoc</a> - read this if your are coding
52 against JABA Web Services
54 <p><a href="${pageContext.request.contextPath}/full_javadoc/index.html">Complete JavaDoc</a> - for developers who want to
55 use JABAWS framework and use Engines and Executables directly
57 <p class="text-right">
58 <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
64 <div class="row" id="thesrc">
65 <div class="col-md-12">
66 <div class="panel panel-default">
67 <div class="panel panel-heading">
68 <h1 class="panel-title">The source code</h1>
70 <div class="panel-body">
71 <p><strong>Publicly available Git repository:</strong>
72 <a href="http://source.jalview.org/gitweb/?p=jabaws.git;a=summary">
73 http://source.jalview.org/gitweb/?p=jabaws.git;a=summary</a></p>
74 <p>Another publicly available JABAWS repository, containing the code for each
75 JABAWS public release, is located at
76 <a href="https://jabaws.googlecode.com">jabaws.googlecode.com</a></p>
77 <p>The repositories contain a complete JABAWS
78 <a href="http://www.eclipse.org">Eclipse</a> project. </p>
79 <p>Of course if you want to make a modification to the source code you would need to
80 generate distributives yourself. To do that, first generate JAX-WS artifacts using
81 <em2>build-server</em2> task from <em2>wsbuild.xml</em2>
82 ant script, then you could use build.xml tasks to generate any of the distributives you need.
84 <p class="text-right">
85 <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
91 <div class="row" id="projstruct">
92 <div class="col-md-12">
93 <div class="panel panel-default">
94 <div class="panel panel-heading">
95 <h1 class="panel-title">Structure of the project</h1>
97 <div class="panel-body">
99 <li><i class="fa fa-folder-o" aria-hidden="true"></i> <span class="directory">binaries</span> contains native executables e.g. clustalw</li>
100 <li style="list-style-position:inside"><i class="fa fa-folder-o" aria-hidden="true"></i> <span class="directory">src</span> contains sources of native executables</li>
101 <li style="list-style-position:inside"><i class="fa fa-folder-o" aria-hidden="true"></i> <span class="directory">windows</span> contains pre-compiled Windows binaries</li>
102 <li style="list-style-position:inside"><i class="fa fa-folder-o" aria-hidden="true"></i> compilebin.sh - the script to complile binaries</li>
103 <li style="list-style-position:inside"><i class="fa fa-folder-o" aria-hidden="true"></i> setexecflag.sh - the script to set executable flag for the binaries</li>
104 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> conf</span> contains JABAWS configuration files </li>
105 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> ExecutionStatistics</span> the database for storing collected execution statistics </li>
106 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> jobsout</span> a default folder for temporary job directories </li>
107 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> statpages</span> the web pages for execution statistics display</li>
108 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> WEB-INF</span> default </li>
109 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> website</span> contains the JABAWS web pages </li>
110 <li style="list-style-position:inside"><i class="fa fa-folder-o" aria-hidden="true"></i> <span class="directory">archive</span> contains JABAWS packages, the WAR and JAR files</li>
112 <p class="text-right">
113 <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
119 <div class="row" id="thecode">
120 <div class="col-md-12">
121 <div class="panel panel-default">
122 <div class="panel panel-heading">
123 <h1 class="panel-title">The code structure</h1>
125 <div class="panel-body">
126 <img src="../static/img/ws-structure.png" alt="JABAWS Code Structure"
127 width="260" height="300" align="left" style="padding-right: 2em;" />
129 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> datamodel</span> contains the JABAWS datamodel </li>
130 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> engine</span> contains the JABAWS engine - the code that abstract the execution environment and executes native binaries</li>
131 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> runner</span> contains the JABAWS runners - thin wrappers for native binaries </li>
132 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> webservices</span> contains the JABAWS SOAP web services </li>
133 <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> testsrc</span> contains the JABAWS unit tests</li>
136 Each source folder depends on the upper folders for compilation. For example, the datamodel
137 is the top level folder so it has no other dependencies on other JABAWS code.
138 The Engine level depends on the datamodel to compile etc. The web services folder is the
139 bottom layer and depends on all the other source code.
142 So the JABAWS project is split into 4 layers. From bottom-up the first layer
143 consists from the value classes used by all other layers of the hierarchy, in
144 particular web services. So, to be able to use JABAWS one needs to have these
145 classes. At the same time classes on this layer does not have any dependencies
149 The second layer contains code for execution of the wrappers, which are the
150 abstraction describing native executables. JABAWS can execute tasks locally
151 that is on the same machine as JVM and on the cluster. Thus currently code on
152 this layer contain two engines. This layer depends on the layer underneath, the
153 data model layer, but is completely independent from the code above.
156 The third layer consists of the wrappers for the native executables and classes to
157 handle their configuration. It depends on the engines and the data model, but know
158 nothing about the web services.
161 Finally, the upper layer contains the web services, that depend on all the layers below.
164 The layer isolation is archived though specially designed compilation task which is
165 executed sequentially in several stages so that the first layer compiles before
166 any other layers, second layer compiles after that and process continies before
167 all the code is compiled. Any violation of the layer boundaries results in the
168 compilation failure. Use Ant "Compile" or "Complile_with_debug"
169 tasks to perform the staged compilation.
172 A client package contains only classes from data model layer and a simple web
173 services client. Framework package is for anyone who want to use JABAWS framework
174 for controlling native executables in local or cluster environments. Framework exclude
175 the web services layer. Server package contains all the code.
177 <p class="text-right">
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184 <div class="row" id="runtests">
185 <div class="col-md-12">
186 <div class="panel panel-default">
187 <div class="panel panel-heading">
188 <h1 class="panel-title">Running tests</h1>
190 <div class="panel-body">
192 JABAWS uses TestNG framework for testing. The test results for the JABAWS
193 package offered for download can be found at:
194 <a href="http://www.compbio.dundee.ac.uk/user/www-jws2/tests/index.html">
195 Test Results</a><br/>
196 JABAWS uses <a href="http://testng.org/doc/index.html">TestNG</a>
197 for testing. There is a TestNG plugin available for Eclipse
198 which has functionality similar to JUnit. However, no plugins are
199 necessary to run the test cases, as testng jar is supplied
200 with JABAWS together with an ant tasks to run the test cases.
203 The best way to ensure that JABAWS framework is completely functional on your
204 system is to run all test cases.
205 Test cases tests all aspects of JABAWS functionality. Consequently, one need
206 to have non windows operation system and support
207 of the cluster to be able to run all tests. If your system does not support
208 cluster, then you could run all test excluding those that depends on the cluster.
211 <p>Several testing groups are supported:</p>
213 <li>All tests ('Test')</li>
214 <li>Cluster tests ('Run_cluster_dependent_test')</li>
215 <li>Cluster independent tests ('All_cluster_independent_tests') </li>
216 <li>Windows only tests ('All_cluster_independent_windows_only_tests') </li>
217 <li>Performance and stability tests ('Long_tests') </li>
218 <li>Re-run failed tests ('Rerun_failed_tests') </li>
219 <li>Run custom test ('CustomTest') </li>
223 To run the tests you need to download all sources from <a href="#thesrc">repository</a>.
224 Once you have done that, enter into the command line mode, change directory to the
225 project directory and type:
227 <pre><code class="bash">ant -f build.xml <test group name></code></pre>
229 Make sure you have <a href="http://ant.apache.org/">Apache Ant</a>
230 installed and path to ant executable is defined in your path environmental variable.
231 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
234 <pre><code class="bash">ant -f build.xml Run_cluster_dependent_test</code></pre>
236 If you work under Linux you could use a simple script from the root folder of repository called <em2>runtests.sh</em2>
237 This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable,
238 which you can define once for your system and then reuse.
241 A handy feature of TestNG is its ability to re-run failed tests. Failed test
242 ant file is stored in
243 <em2>test-output/testng-failed.xml</em2>. and is used in the ant task called
244 <em2>Rerun_failed_tests</em2>. So re-running failed tests requires no more
245 work than running any other test group and could be accomplished with the command:
247 <pre><code class="bash">ant -f build.xml Rerun_failed_tests</code></pre>
249 CustomTest runs the test defined in the project root directory file called
250 <em2>temp-testng-customsuite.xml</em2>. This
251 file is generated by TestNG plugin every time you run the test from Eclipse.
252 Thus an easy way to run a test in a different environment is to run it from
253 Eclipse first and then from ant using a custom test procedure.
256 For cluster execution make sure that the property
257 LD_LIBRARY_PATH defined in build.xml points to cluster engine LD
258 libraries directory in your local system.
260 <p class="text-right">
261 <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
267 <div class="row" id="prepexec">
268 <div class="col-md-12">
269 <div class="panel panel-default">
270 <div class="panel panel-heading">
271 <h1 class="panel-title">Preparing distributives</h1>
273 <div class="panel-body">
275 There are a number of ant tasks aimed for preparing distributives for download.
276 Currently a few types of JABAWS packages are offered:
279 <li>Client only (contains classes required to access JABA Web Services)</li>
280 <li>Platform specific JABAWS (windows and other)</li>
281 <li>JABAWS without binaries</li>
282 <li>JABAWS framework </li>
284 <p>Corresponding build task names are:</p>
286 <li>min-jaba-client</li>
287 <li>jaba-windows, jaba-complete</li>
288 <li>jaba-no-binaries</li>
289 <li>full-jaba-client</li>
292 The easiest way to build all distributives is to call
293 <em2>build-all</em2> ant task.
294 There are more tasks defined in build.xml than described here.
295 They are mostly self explanatory.
298 If you made any changes to the data model and
299 would like to generate a complete JABAWS
300 distro make sure you have rebuilt jaxws artifact as described below.
302 <p class="text-right">
303 <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
309 <div class="row" id="buildstubs">
310 <div class="col-md-12">
311 <div class="panel panel-default">
312 <div class="panel panel-heading">
313 <h1 class="panel-title">Building web services artifacts</h1>
315 <div class="panel-body">
317 Server side artifacts should be rebuild whenever the data model, meta model or MSA
318 interface were changed.
319 To do that run build-server task from wsbuild.xml ant build file. WSDL files will
321 <em2>webservices/compbio/ws/server/resource</em2> directory. It is not necessary to
322 edit them if any of the JABAWS clients are used. JABAWS are the standard JAX-WS web
323 services, which are WS-I basic profile compatible.
325 <p class="text-right">
326 <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
332 <div class="row" id="addnewws">
333 <div class="col-md-12">
334 <div class="panel panel-default">
335 <div class="panel panel-heading">
336 <h1 class="panel-title">Adding a new web service (rough guide)</h1>
338 <div class="panel-body">
341 <p>Add a new executable which you'd like to wrap as a JABAWS web service to the binaries folder.
342 If it has the source code and can be recompiled for different platforms include it under
343 <em2>binaries/src</em2>. Edit <em2>setexecutableflag.sh</em2>
344 and <em2>compilebin.sh</em2> scripts in <em2>binaries/src</em2>
347 <p>Make sure that all the dependencies of the software being installed are satisfied.
348 If there are other binaries they should be included as well. Keep the dependent
349 binaries in a subfolder for the main executable. Update
350 <em2>compilebin.sh</em2> and <em2>setexecflag.sh</em2> scripts accordingly.</p>
352 <p>Make sure that the new executable does not have any hard links to its dependencies, e.g. is able to run from
353 any installation folder and does not contain any hard coded paths.</p>
355 <p>Describe executable in <em2>conf/Exectuable.properties</em2> file. The lowercase name of
356 the wrapper should be included
357 in the name of the property for example Clustal properties all include clustal as a
358 part of the name e.g. local.clustalw.bin.
359 The same property for MAFFT will be called local.mafft.bin. For more help please refer
360 to the Executable.properties file.
363 <p>Describe the executable supported parameters in the
364 <em2><ExecutableName>Parameters.xml</em2>, presets in the
365 <em2><ExecutableName>Presets.xml</em2> and the execution limits in the
366 <em2><ExecutableName>Limit.xml</em2>. By convention these files are stored
367 in <em2>conf/settings</em2>. All of these are optional. If the executable
368 does not support parameters you do not have to mention the <em2>XXXParameter.xml</em2> file
369 in the <em2>Executable.properties</em2> file at all. The same is true for
370 Presets and Limits.</p>
372 <p>Create a Java wrapper class for your executable. Create it within <em2>runner</em2> source directory.
373 Examples of other wrappers can be found in <em2>compbio.runner.msa</em2> or
374 in other <em2>compbio.runner.*</em2> packages. Wrapper should extend
375 <em2>SkeletalExecutable<T></em2> and implement
376 <em2>PipedExecutable<T></em2>
377 if you need to pass the input or collect the results from the standard in/out. Please see Mafft
378 code as example. Wrapper should expend <em2>SkeletalExecutable<T></em2>
379 if input/output can be set as a parameter for an executable. Please see the ClustalW code as example.</p>
381 <p>Create a testcase suit for your wrapper in <em2>testsrc</em2> and run the test cases.</p>
383 <p>Create parser for the output files of your executable. Suggested location
384 compbio.data.sequence.SequenceUtil . </p>
386 <p>Test the parser.</p>
388 <p>Decide which web services interfaces your executable is going to match. For example
389 if the executable output can be represented as SequenceAnnotation then SequenceAnnotation
390 interface might be appropriate. For multiple sequence alignment an Msa interface should be used.</p>
392 <p>If you find a web interface that matches your returning data type, then
393 implement a web service which confirms to it within a webservices source folder. </p>
395 <p>Register web service in <em2>WEB-INF/web.xml</em2>
396 and <em2>WEB-INF/sun-jaxws.xml</em2>.</p>
398 <p>Add generated wsdl to wsbuild.xml ant script to generate the stubs.</p>
400 <p>Run build-server task in wsbuild file. Watch for errors. If the task fails that means
401 that JAXB cannot serialize some of your new data structures. Add appropriate annotations to your data types.
402 Also check that: </p>
404 <li>you do not have interfaces to serialize, since JAXB cannot serialize them</li>
405 <li>you have a default no args constructor (can be private if you do not need it)</li>
406 <li>JAXB cannot serialize Java Map class, use a custom data structure instead</li>
407 <li>Enum cannot be serialized as its abstract class (do not confuse with enum which is fine)</li>
408 <li> Fields serialization leaves a little more space for manoeuvre.
409 If you do this then you may accept<br/> and return interfaces, e.g. List, Map; abstract classes etc, from your methods
412 <p>If you have the data on the server side, but nothing is coming through to the
413 client, this is a JAXB serialization problem. They tend to be very silent and
414 thus hard to debug. Check your data structure can be serialized!</p>
416 <p>Modify the client to work with your new web service. Update Services
417 enumeration to include new service and ensure that all the methods of this
418 enumeration take into account the new service. Update the client help text
419 (client_help.txt) and insert it into the Constraints class.</p>
421 <p>Test the web service with the client.</p>
423 <p>Test on the cluster.</p>
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