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-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt.gif" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws.png" title="JABAWS:MSA" alt="JABAWS:MSA"/></td>\r
-<td class="bg"><img src="images/align.png"/></td>\r
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
-</table></div>\r
+</table>\r
+</div>\r
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<a href="man_about.html">Manual</a> \r
<a href="download.html">Download</a> \r
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-<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
+<a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
</div>\r
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<!-- panel end-->\r
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-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt.gif" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws.png" title="JABAWS:MSA" alt="JABAWS:MSA"/></td>\r
-<td class="bg"><img src="images/align.png"/></td>\r
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
-</table></div>\r
+</table>\r
+</div>\r
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-<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
+<a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
</div>\r
\r
<!-- panel end-->\r
<p> The JABAWS Server Web Application aRchive (WAR) version is for you if you want to deploy JABAWS for many users e.g. your laboratory or if you are an expert user and want to have more control on JABAWS. Typically, you will have a cluster or at least a powerful server machine which all users are willing to use. If you only have a single server then, you may use JABAWS Server Virtual Appliance instead. The server is provided as a self-contained <a href="http://en.wikipedia.org/wiki/WAR_(Sun_file_format)">Web Application\r
aRchive (WAR) </a> containing all necessary binaries. WAR file can be deployed on any\r
web application server\r
-<!-- Note - mention servlet 2.4 compliance here? -->supporting at least version 2.4 of the Java servlet specification, i.e. <a href="http://tomcat.apache.org/download-60.cgi">Tomcat 6.0</a>. </p>\r
+<!-- Note - mention servlet 2.4 compliance here? -->supporting at least version 2.4 of the Java servlet specification, i.e. <a href="http://tomcat.apache.org/download-60.cgi">Tomcat 7.0</a>. </p>\r
\r
<ul>\r
<li>A Complete Server for all platforms: <a href=\r
"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">download</a>\r
-(45M)</li>\r
+(51M)</li>\r
</ul>\r
\r
\r
<li>Command line client\r
<ul>\r
<li>binaries: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client.jar">download</a> (80 K)</li>\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client-2.0.jar">download</a> (80 K)</li>\r
<li>source: <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source.jar">download</a> (70 K)</li>\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source-2.0.jar">download</a> (70 K)</li>\r
</ul>\r
</li>\r
</ul>\r
<li>A complete Eclipse project package: <a href=\r
"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-project.zip">download</a> (82M)</li>\r
<li>JABAWS source only package: <a href=\r
-"archive/jaba-source.jar">download</a> (250K)</li>\r
+"archive/jabaws-src-2.0.jar">download</a> (250K)</li>\r
</ul>\r
\r
<!--body end -->\r
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<div id="banner">\r
<table> \r
-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt.gif" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws.png" title="JABAWS:MSA" alt="JABAWS:MSA"/></td>\r
-<td class="bg"><img src="images/align.png" alt="Multiple sequence alignment"/></td>\r
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
</div>\r
<a href="man_about.html">Manual</a> \r
<a href="download.html">Download</a> \r
<a href="contacts.html">Contact Us</a>\r
- <a href="AnnualStat">Usage stats</a>\r
+ <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
\r
<!-- panel end-->\r
<div id="content">\r
<h2 id="headtitle">JABAWS 2</h2>\r
-<p style="color:black; font-weight:normal; text-align:left;"><span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services for Multiple Sequence Alignment">JABAWS:MSA</span> is free software which provides five web services for multiple sequence alignment: <a href="http://www.clustal.org/">Clustal W</a>, <a href=\r
+<p style="color:black; font-weight:normal; text-align:left;"><span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services version 2">JABAWS<sup>2.0</sup>:Disorder</span> is free software which provides web services for prediction of protein disorder, multiple sequence alignment and amino acid conservation conveniently packaged to run on your local computer, server or cluster. Disorder prediction services are based on <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a>, <a href="http://globplot.embl.de/">GlobPlot</a>, conservation is calculated by <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>, multiple sequence alignment services are the <a href="http://www.clustal.org/">Clustal W</a>, <a href=\r
"http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, <a href=\r
-"http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"> TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a> conveniently packaged to run on your local computer, server or cluster. \r
+"http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"> TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. \r
<span style="color:black; font-weight:normal; text-align:left;">JABA Web Services can be accessed from the <a href="http://www.jalview.org">Jalview</a> multiple sequence alignment editor and analysis workbench to allow multiple alignment calculations limited only by your own local computing resources.</span></p>\r
\r
<div id="mainpagefeatures">\r
<div class="brick_header"><h2>For System Administrators</h2></div>\r
<div class="brick_content">\r
<p><strong>The Server: </strong><a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (45M) </p>\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (51M) </p>\r
<p>JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. Please check the quick start guide for <a href="manual_qs_war.html#qsc">installation instructions</a>.</p>\r
</div>\r
</div></td>\r
<div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>\r
<div class="brick_content">\r
<strong>The Server: </strong><a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (45M)\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (51M)\r
<br/>\r
<strong>The Client: </strong>\r
- Command Line Client <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client.jar">binary</a> | <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source.jar">source</a> \r
+ Command Line Client <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client-2.0.jar">binary</a> | <a href=\r
+"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source-2.0.jar">source</a> \r
<!-- <li><a href="http://www.jalview.org/download.html">Jalview</a> (18M)</li> -->\r
\r
\r
<div id="page">\r
<div id="banner">\r
<table> \r
-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt.gif" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws.png" title="JABAWS:MSA" alt="JABAWS:MSA"/></td>\r
-<td class="bg"><img src="images/align.png"/></td>\r
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
</div><!-- banner end-->\r
<a href="man_configuration.html" >Server<br/>\r
Configuration</a>\r
<a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
+ <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
<a href="man_dev.html" title="Accessing JABAWS from your program">Accessing<br/>\r
JABAWS</a> \r
</div>\r
<a href="download.html">Download</a>\r
<a href="contacts.html">Contact Us</a>\r
- <a href="http://www.compbio.dundee.ac.uk">Barton Group</a></div>\r
+ <a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
+\r
<!-- panel end-->\r
<div id="content">\r
\r
\r
\r
<h3><a name="wisjaba" id="wisjaba"></a>What is JABAWS?</h3>\r
-<p>JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment programs (see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.\r
- However, the scope of JABAWS is not limited to multiple sequence alignment programs. Future versions of JABAWS will incorporate protein disorder prediction, BLAST, PSIBLAST and HMMER database searches and many other tools.</p>\r
+<p>JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.\r
+ Future versions of JABAWS will incorporate many other tools.</p>\r
<h4>Getting JABAWS</h4>\r
<p>JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the JABAWS command line client is what you need. </p>\r
<h3><a name="wjaba" id="wjaba"></a>JABAWS Benefits</h3>\r
</ul>\r
<h3><a name="alprog" id="alprog"/>JABA Web Services Programs </h3>\r
<p> JABAWS currently provides access to the following programs:</p>\r
+<p>Multiple Sequence Alignement </p>\r
<ul>\r
<li><a href="http://www.clustal.org/">ClustalW</a> (version 2.0.12)</li>\r
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.713)</li>\r
- <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.7) </li>\r
- <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.14) </li>\r
+ <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>\r
+ <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>\r
+ <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
<li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
</ul>\r
\r
+<p>Protein disorder prediction</p>\r
+<ul>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://iupred.enzim.hu">IUPred</a></span> (1.0) </li>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a></span> (3.1) </li>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://globplot.embl.de/">GlobPlot</a></span> (2.3) </li>\r
+ </ul>\r
+<p>Amino Acid conservation </p>\r
+<ul>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a></span> (1.0) </li>\r
+</ul>\r
<h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>\r
<p>A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web services. \r
The most basic JABAWS client is a command line Java application which can call any of the JABAWS web services methods \r
<div id="page">\r
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-<td class="bg"><img src="images/jabaws.png" title="JABAWS:MSA" alt="JABAWS:MSA"/></td>\r
-<td class="bg"><img src="images/align.png"/></td>\r
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
-</table></div><!-- banner end-->\r
+</table>\r
+</div><!-- banner end-->\r
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<a href="man_configuration.html" >Server<br/>\r
Configuration</a>\r
<a class="selected" href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
+ <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
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JABAWS</a> \r
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-<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
+<a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
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+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
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<a class="selected" href="man_configuration.html" >Server<br/>\r
Configuration</a>\r
<a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
+ <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
<a href="man_dev.html" title="Accessing JABAWS from your program">Accessing<br/>\r
JABAWS</a> \r
</div>\r
<a href="download.html">Download</a> \r
<a href="contacts.html">Contact Us</a>\r
-<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
+<a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
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\r
<!-- panel end-->\r
<li><a href="#settinglimit">Limiting the size of the job accepted by JABAWS Server </a></li>\r
<li><a href="#diffbin">Using a different version of the alignment program with JABAWS</a></li>\r
<li><a href="#mixuse">Load balancing </a></li>\r
- <li><a href="#confaccessright">Reviewing JABAWS configuration via web browser</a></li>\r
<li><a href="#testingJaba">Testing JABA Web Services</a></li>\r
<li><a href="#logs">JABAWS requests logging </a></li>\r
<li><a href="#logfiles">JABAWS internal logging </a></li>\r
- <li><a href="#execstat">Monitoring JABAWS</a></li>\r
<li><a href="#warfile">JABAWS War File Content</a></li>\r
+ <li><a href="#execstat">JABAWS Usage Statistics</a></li>\r
</ul>\r
<h3><a name="defjabaconf" id="defjabaconf"></a>JABAWS Configuration </h3>\r
<p>There are three parts of the system you can configure. The local\r
engine where to find DRMAA libraries. These variables\r
should be defined when the web application server starts up, e.g.</p>\r
\r
-<p><span class="code">SGE_ROOT=/gridware/sge<br />\r
- LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64</span></p>\r
+<p class="code">SGE_ROOT=/gridware/sge<br />\r
+ LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64</p>\r
\r
<p>Finally, do not forget to configure executables for the cluster\r
execution, they may be the same as for the local execution but may\r
<p>JABAWS supplied with binaries and source code of the executables which version it supports. So normally you would not need to install your own executables. However, if you have a different version of an executable (e.g. an alignment program) which you prefer, you could use it as long as it supports all the functions JABAWS executable supported. This could be the case with more recent executable. If the options supported by your chosen executable is different when the standard JABAWS executable, than you need to edit <em>ExecutableName</em>Paramaters.xml configuration file. </p>\r
<h3><a name="mixuse" id="mixuse"></a>Load balancing </h3>\r
<p>If your cluster is busy and have significant waiting times you can achieve a faster response by allowing the server machine to calculate small tasks and the reserve the cluster for bigger jobs. This works especially well if your server is a powerful machine with many CPUs. To do this you need to enable and configure both the cluster and the local engines. Once this is done decide on the maximum size of a task to be run on the server locally. Then, edit <span class="hightlight">"# LocalEngineExecutionLimit #" </span>preset in<span class="hightlight"> <ServiceName>Limits.xml</span> file accordingly. JABAWS server then will balance the load according to the following rule: If the task size is smaller then the maximum task size for local engine, and the local engine has idle threads, then calculate task locally otherwise submit the task to the cluster. </p>\r
-<h3><a name="confaccessright" id="confaccessright"></a>Reviewing JABAWS configuration via web browser</h3>\r
-<p>Access to configuration files is prohibited to any unauthorized users by means of security constrain defined in web application descriptor file. There is a special user role called <span class="hightlight">admin</span> who can access these files. This comes handy if you would like to keep an eye on any of the task outputs stored in jobsout, or would like to view the configuration files. To access the configuration files add admin user into your application server. The way you do it depends on where you would like the user passwords to come from and your web application server. If you use Tomcat, then the simplest way is to use Tomcat Memory Realm which is linked to a plain text configuration file. To define the user in Tomcat server add an entry in <span class="hightlight">conf/tomcat-user.xml</span> file. <span class="code"><role rolename="admin"/><br />\r
- <user username="admin" password="your password here " roles="admin"/></span></p>\r
-<p>Once this is done make sure the servlet that returns the web application directory listings is enabled. Look in the <span class="hightlight"><tomcatroot>/conf/web.xml</span> file for the following <span class="code"><param-name>listings</param-name><br />\r
- <param-value>true</param-value></span></p>\r
-<p>The whole section that defines default listing servlet is below</p>\r
-<p class="code"> <servlet><br />\r
- <servlet-name>default</servlet-name><br />\r
- <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class><br />\r
- <init-param><br />\r
- <param-name>debug</param-name><br />\r
- <param-value>0</param-value><br />\r
- </init-param><br />\r
- <init-param><br />\r
- <param-name>listings</param-name><br />\r
- <param-value>true</param-value><br />\r
- </init-param><br />\r
- <load-on-startup>1</load-on-startup><br />\r
- </servlet><br />\r
-</p>\r
-<p>These listings are read only by default.</p>\r
<h3><a name="testingJaba" id="testingJaba"></a>Testing JABA Web Services</h3>\r
<p>You can use a command line client (part of the client only\r
package) to test your JABAWS installation as described <a href="man_client.html">here</a>. If you downloaded a JABAWS\r
<p>If you would like to know who is using your services, you might\r
want to <a href="#logs">enable Tomcat request\r
logging</a>.</p>\r
-<h3><a name="execstat" id="execstat"></a>Monitoring JABAWS</h3>\r
-<p>JABAWS stores cluster task ids for all tasks which were run on the cluster. Using cluster ids the detailed statistics can be extracted from cluster accounting system. Due to the fact that each cluster supported by JABAWS have different accounting system it was not possible to provide ready to use statistics. <br />\r
- For the local execution the starting and finishing time in nano seconds can be found in STARTED and FINISHED files respectively. In time we will provide the tools to extract execution time statistics, so keep the content of your working directory ready!</p>\r
<h3><a name="warfile" id="warfile"></a>JABAWS War File Content</h3>\r
<table width="100%">\r
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+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
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+<!-- panel end-->\r
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+\r
+ <h4>JABAWS Javadoc</h4>\r
+ <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>Starting up from the source code</h4>\r
+<p><a name="svn">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/JABA_r1</a><br/>\r
+The repository contains a complete JABAWS <a href="http://www.eclipse.org">Eclipse</a> project. To use Eclipse with this repository you need to install Eclipse SVN plugin which could be found here: http://subclipse.tigris.org/servlets/ProjectProcess?pageID=p4wYuA. Eclipse update web site address is <a href="http://subclipse.tigris.org/update_1.4.x">http://subclipse.tigris.org/update_1.4.x</a> Take care to install 1.4.x version of the plugin, as SVN repository will not work with more recent clients. it would help to install TestNG plugin as well which could be downloaded from <a href="http://testng.org/doc/download.html">http://testng.org/doc/download.html</a>. Please note however that no generated code is stored in the repository. That is to say that if you like to obtain client or server packages it is better to download them from the download section of this web site. 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>Structure of the project</h4>\r
+<img style="padding:0 1em;" align="left" src="images/ws-structure.png" alt="JABAWS layers" />\r
+<p>Layers in the source code are defined in a different source folders which are: \r
+<br/><span class="hightlight">/webservices<br />\r
+ /runner<br />\r
+ /engine<br />\r
+ /datamodel</span></p>\r
+<p style="clear:both">JABAWS project is split into 4 layers. From bottom-up the first layer consists from the value classes used by all other layers of the hierarchy, in particular web services. So, to be able to use JABAWS one needs to have these classes. At the same time classes on this layer does not have any dependencies on the layers above.</p>\r
+<p>The second layer contains code for execution of the wrappers, which are the abstraction describing native executables. The code on this level code engine. JABAWS can execute tasks locally that is on the same machine as JVM and on the cluster. Thus currently code on this layer contain two engines. This layer depends on the layer underneath, the data model layer, but is completely independent from the code above.</p>\r
+<p>The third layer consists of the wrappers for the native executables and classes to handle their configuration. It depends on the engines and the data model, but know nothing about the web services.</p>\r
+<p>Finally, the upper layer contains the web services, that depend on all the layers below.</p>\r
+<p>The layer isolation is archived though specially designed compilation task which is executed sequentially in several stages so that the first layer compiles before any other layers, second layer compiles after that and process continies before all the code is compiled. Any violation of the layer boundaries results in the compilation failure. Use Ant "Compile" or "Complile_with_debug" tasks to perform the staged compilation.</p>\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>Running tests</h4>\r
+<p>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>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
+<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
+ 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.\r
+ </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
+ <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>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
+ <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>JABA Web Services without JAXWS libraries ( a the runtime dependency) </li>\r
+ <li>JABAWS without binaries</li>\r
+ <li>JABAWS without binaries and jax-ws </li>\r
+ <li>JABAWS framework </li>\r
+ </ol>\r
+ </p>\r
+ Corresponding build task names are: \r
+ <ol>\r
+ <li>min-jaba-client</li>\r
+ <li>jaba-windows, jaba-complete</li>\r
+ <li>jaba-without-jaxws</li>\r
+ <li>jaba-no-binaries</li>\r
+ <li>jaba-no-jaxws-no-binaries</li>\r
+ <li>full-jaba-client</li>\r
+ </ol>\r
+\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
+ <h4>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. However, if you would like to generate portable artifacts using wsimport based on the generated WSDL files then, <span class="code"><soap:address location="REPLACE_WITH_ACTUAL_URL"/></span></p>\r
+\r
+<p>must be replaced with an actual server URL including the web services context path. For example: </p>\r
+<p class="code">http://www.compbio.ac.uk:8080/ws</p>\r
+<p>JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible. </p>\r
+</div>\r
+<!-- content end--> \r
+<div id="copyright">Last update: 19 August 2010<br/>Peter Troshin, The Barton Group, University of Dundee, UK</div>\r
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+<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
+</div>\r
+\r
+<!-- panel end-->\r
+<div id="content">\r
+<h2 id="headtitle">JABAWS MANUAL</h2>\r
+\r
+<h2><a name="usingcclient" id="usingcclient"></a>JABAWS Usage Statistics </h2>\r
+<ul>\r
+ <li><a href="#usage_sum">Summary of Usage</a></li>\r
+ <li><a href="#detailed_usage">Detailed Usage Statistic </a></li>\r
+ <li><a href="#job_list">Job List</a></li>\r
+ <li><a href="#job_dir">Single Job Directory Content </a></li>\r
+ <li><a href="#conf_tomcat_user">Configuring a privileged access for Tomcat web application server</a></li>\r
+ <li><a href="#exec_stat_conf">Configuring JABAWS execution statistics</a></li>\r
+</ul>\r
+<h3><a name="usage_sum"></a>Summary of Usage </h3>\r
+<p>JABAWS comes with a web application for visualizing usage statistics. The screenshot below shows the main page of this application. Each month is a link to the detailed usage statistics for this month described later. Please note however, that the links to the detailed monthly statistics are only available for authenticated users in the role <span class="hightlight">admin</span>. There is a link at the bottom of the page that would let you login, if you have not done so. </p>\r
+<p>If you are using JABAWS VA (Virtual Appliance) then the username is <span class="hightlight">jabaws</span> and password is not defined, e.g. empty. </p>\r
+<p>If you have deployed a JABAWS WAR file, then please see the <a href="#conf_tomcat_user">configuring privileged access for Tomcat web application server</a> section for further details. </p>\r
+<p><img src="images/usage_statistics_main.gif" alt="JABAWS usage statistics" width="608" height="318"></p>\r
+<p>The table contains the number of jobs processed by JABAWS per month, for the whole period when the statistics was collected</p>\r
+<p>For each month the table contains the following information.</p>\r
+<ul>\r
+ <li>Month - the period of time for which statistics is displayed. For example Jan 2011 means period of time from the first of January to the first of February.</li>\r
+ <li>Total - the total number of jobs accepted by JABAWS</li>\r
+ <li>Incomplete - the number of jobs for which the result file was not found or was empty excluding cancelled</li>\r
+ <li>Cancelled - the number of jobs cancelled by the user</li>\r
+ <li>Abandoned - the number of jobs which result(s) were not collected</li>\r
+</ul>\r
+<p>The summary for each column is displayed in the last row of the table.</p>\r
+<h3><a name="detailed_usage"></a>Detailed Usage Statistic </h3>\r
+<p>Detailed execution statistics for each month is available for authenticated users only. </p>\r
+<p><img src="images/usage_statistics_month.gif" alt="JABAWS one month usage statistics" width="670" height="902"></p>\r
+<p>Each table contains the number of jobs processed by JABAWS during the period of time specified in the title.</p>\r
+<ul>\r
+ <li>The "All Jobs" table contains the summary of all jobs.</li>\r
+ <li>"Local Jobs" table - contains the summary of the jobs calculated by the local engine.</li>\r
+ <li>"Cluster Jobs" table - contains the summary of the jobs calculated by the cluster.</li>\r
+</ul>\r
+Each table contains the following information for each web service\r
+<ul>\r
+ <li>Total - the total number of jobs accepted by a particular JABA service</li>\r
+ <li>Incomplete - the number of jobs for which the result file was not found or was empty excluding cancelled</li>\r
+ <li>Cancelled - the number of jobs cancelled by the user</li>\r
+ <li>Abandoned - the number of jobs which result(s) were not collected</li>\r
+</ul>\r
+<h3><a name="job_list"></a>Job List </h3>\r
+<p>Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view the application server may need to be configured. Please see <a href="#exec_stat_conf">Configuring JABAWS execution statistics</a> section for further details. </p>\r
+<p><img src="images/usage_statistics_details.gif" alt="JABAWS - job list" width="917" height="198"> </p>\r
+<p>Columns </p>\r
+<ul>\r
+ <li>JobID - the JABAWS job id, unique for every job</li>\r
+ <li>Cluster JobID - cluster job id</li>\r
+ <li>InputSize - input size in bytes</li>\r
+ <li>ResultSize - result size in bytes</li>\r
+ <li>Runtime (s) - job's runtime in seconds</li>\r
+ <li>Start time (s)- job's start time and date</li>\r
+ <li>Finish time (s)- job's finish time and date</li>\r
+ <li>isCancelled - whether the job was cancelled</li>\r
+ <li>isCollected - whether the job was collected. False for the jobs that has been initiated but which results has never been retrieved</li>\r
+ <li>isFinished - whether the job has finished. This does not necessarily mean that the job has produced the result. The job can sometime finish in failure.</li>\r
+</ul>\r
+<h3><a name="job_dir"></a>JABAWS Job Directory Content </h3>\r
+<p><img src="images/usage_statistics_job_details.gif" alt="JABAWS- job details" width="716" height="420"></p>\r
+<p>STARTED and FINISHED files contain Unix timestamp - when the job was started and completed respectively. STARTED is replaced by SUBMITTED if the job has been submitted to the cluster, as opposed to executed locally, on the server. </p>\r
+<p>COLLECTED file is empty and indicates that the job results were collected by the user. Due to asynchronous nature of the job it is possible that the job was started and finished, but the results has never been requested. </p>\r
+<p>RunnerConfig.xml file contains a complete description of the job and JABAWS can restart the job based on this description. </p>\r
+<p>procError.txt and procOutput.txt files contains the content of the standard out and standard error streams of the process. </p>\r
+<p>result.txt file contains the results. </p>\r
+<p>input.txt file contains input into the process. </p>\r
+<p>There are maybe other files depending on the nature of the job, but the one described above will present in most cases. In this example, stat.log file stories the execution statistics generated by the process (clustal executable in this example).</p>\r
+<p> If you have deployed JABAWS WAR file or made changes to JABAWS configuration you may need to make a few changes to the Tomcat configuration to be able to see the content of the job directory. Please see <a href="#exec_stat_conf">Configuring JABAWS execution statistics</a> section for further details. </p>\r
+<h3><a name="exec_stat_conf"></a>Configuring JABAWS execution statistics</h3>\r
+<p>JABAWS execution statistics is a multi-component system. First is a crawler which job is to collect and preprocess the statistics from the job temporary directories and record the collected statistics into the database. The second part of the system is a web application which job is to visualise the statistics from the database. </p>\r
+<p>It is possible to enable/disable the statistics collector by changing the following properties in the conf/Cluster.engine.properties and conf/Local.engine.properties files. </p>\r
+<p class="box"># Enable/disable cluster statistics collector true = enable, false = disable <br>\r
+ cluster.stat.collector.enable=false\r
+ <br/>\r
+ # Maximum amount of time the job is considered be running in hours. Optional defaults to 7 days (168h) <br>\r
+ cluster.stat.maxruntime=24</p>\r
+<p class="box"># Enable/disable cluster statistics collector true = enable, false = disable <br>\r
+ local.stat.collector.enable=true\r
+ <br/>\r
+ # Maximum amount of time the job is considered to be running in hours. Optional defaults to 24 hours<br>\r
+ local.stat.maxruntime=6</p>\r
+<p>If the statistics collector is enabled then the crawler starts automatically soon after (10 minutes for local engine, and 60 minutes for cluster engine) the JABAWS web application and will be collecting the execution statistics every 24 hours after the start. </p>\r
+<p>The details of the job are only available if the job temporary directory is located within a JABAWS web application. If not, the system administrator can create a symbolic link pointing to the temporary job directories outside of a web application and configure the application server to allow navigation to the links. For the Tomcat application server the context configuration file should be created and copied to the <TOMCAT_ROOT>/conf/Catalina/localhost directory. The name of the file should be the same as the web application context name, for example "<span class="hightlight">jabaws.xml</span>" for jabaws. Where the TOMCAT_ROOT is the location of the Tomcat web application server. Here is an example of such a file: </p>\r
+<p><span class="code"><?xml version="1.0" encoding="UTF-8"?><br>\r
+<Context antiResourceLocking="false" privileged="true" allowLinking="true"/></span></p>\r
+<p>The key option here is this: <span class="hightlight">allowLinking="true"</span>. Please also make sure that you have defined the user in role "<span class="hightlight">admin</span>" as described <a href="#conf_tomcat_user">below</a>.</p>\r
+<h3><a name="conf_tomcat_user" id="conf_tomcat_user"></a>Configuring a privileged access for Tomcat web application server</h3>\r
+<p>Access to configuration files, detailed job execution statistics and job directories are allowed only for authenticated users in role "<span class="hightlight">admin</span>". </p>\r
+<p>If you use Tomcat, then the simplest way to set up privileged access is to use a plain text configuration file <span class="hightlight">conf/tomcat-user.xml</span>. Here is an example of such configuration file defining user "<span class="hightlight">peter</span>" in role "<span class="hightlight">admin</span>". <span class="code"><tomcat-users><br/>\r
+ <role rolename="admin"/><br />\r
+ <user username="peter" password="your password here " roles="admin"/><br/>\r
+ </tomcat-users></span></p>\r
+<p>For more information on users and roles please consult Apache-Tomcat help pages. </p>\r
+<p><br>\r
+</p>\r
+</div>\r
+\r
+<!-- content end-->\r
+<div id="copyright">Last update: 1 April 2011<br />\r
+ Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
+Dundee, UK</div>\r
+</div>\r
+\r
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+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
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+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
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+ <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
+\r
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+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
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+ <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
+\r
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git://source.jalview.org / jabaws.git / commitdiff