-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"\r
+<?xml version="1.0" encoding="UTF-8"?>\r
+<!DOCTYPE html PUBLIC "XHTML 1.0 Strict"\r
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
<head>\r
-<meta name="Last-modified" content="Mon, 11 Dec 2010 01:03:33 GMT"/>\r
+<meta name="Last-modified" content="Mon, 4 Apr 2011 12:00:00 GMT"/>\r
<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Configuration manual</title>\r
<link href="ws.css" rel="stylesheet" type="text/css" media=\r
"screen, projection, handheld, tv" />\r
<div id="page">\r
<div id="banner">\r
<table> \r
-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><h1><span class="headeru">JA</span>va <span class=\r
-"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
-class="headeru">S</span>ervices</h1></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" title="Java Bioinformatics Analysis Web Services version 2.0"/></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
\r
<div id="wrapper">\r
<div id="panel"><a href="index.html">Home</a> \r
- <a class="selected" href="manual.html">Manual</a> \r
+ <a href="quick_start.html">Getting Started</a> \r
+ <a class="selected" href="man_about.html">Manual</a> \r
<div id="submenu">\r
- <a href="manual.html">Quick Start Guide</a>\r
<a href="man_about.html">About</a>\r
<a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
+ <a href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
<a href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
<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
+ <a href="man_server_dev.html" >JABAWS Development</a>\r
</div>\r
-<a href="download.html">Download</a> \r
-<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
+<a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
+<a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+ <a href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
+<a href="contacts.html">Contact Us</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
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
-<h2>JABAWS Configuration </h2>\r
+<h2>JABAWS Server Configuration </h2>\r
<ul>\r
<li><a href="#defjabaconf">JABAWS Configuration </a></li>\r
<li><a href="#locEngConf">Local Engine Configuration</a></li>\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="#ga">JABAWS and Google Analytics</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
just pass whatever is specified in this line directly to the\r
cluster submission library. This is how DRMAA itself treats this\r
settings. More exactly DRMAA <span class="hightlight">JobTemplate.setNativeSpecification()</span> function will be called.</p>\r
-\r
+<p>For further details and examples of configuration please refer to the <span class="hightlight">Executable.properties</span> file supplied with JABAWS.</p>\r
<h3><a name="setexecenv" />Defining Environment Variables for\r
Executables</h3>\r
\r
<h3><a name="settinglimit" id="settinglimit"></a>Limiting the size of the job accepted by JABAWS </h3>\r
<p>JABAWS can be configured to reject excessively large tasks. This is useful if you operate JABAWS service for many users. By defining a maximum allowed task size you can provide an even service for all users and prevents waist of resources on the tasks too large to complete successfully. You can define the maximum number of sequences and the maximum average sequence length that JABAWS accepts for each JABA Web Service independently. \r
Furthermore, you can define different limits for different presets of the same web service. <br />\r
-By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing <span class="hightlight">conf/settings/<X>Limit.xml</span> files.</p>\r
+By default limits are disabled. You can enable them by editing <span class="hightlight">conf/Executable.properties</span> file. You can adjust the limits according to your needs by editing <span class="hightlight">conf/settings/<X>Limit.xml</span> files. </p>\r
<h3><a name="diffbin" id="diffbin"></a>Using a different version of the alignment program with JABAWS</h3>\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
+<p>Access <span class="code"><your_JABAWS_server_URL>/ServiceStatus</span> to test all web services. Each time you access this URL, all services are tested. You can test a particular web service by adding its name at the end of this URL. For example <span class="code">http://localhost:8080/jabaws/ServiceStatus/MuscleWS </span>will test MuscleWS webservice only. For production configuration we recommend prohibiting requests to this URL for non authenticated users to prevent excessive load on the server. </p>\r
+<p>Alternatively, 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
server package, you can use <span class=\r
"hightlight"><your_jaba_context_name>/WEB-INF/lib/jaba-client.jar</span> to test JABAWS installation as described in <a href=\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
<tr>\r
name of the executable</td>\r
</tr>\r
<tr>\r
+ <td>ExecutionStatistics</td>\r
+ <td>The database for storing the execution statistics. </td>\r
+ </tr>\r
+ <tr>\r
+ <td>statpages</td>\r
+ <td>Web pages for usage statistics visialization and webservices status queries. </td>\r
+ </tr>\r
+ <tr>\r
<td>jobsout/</td>\r
<td>Contains directories generated when running an individual executable. E.g. input and output files and some other task\r
related data. (optional)</td>\r
binaries.</td>\r
</tr>\r
<tr>\r
+ <td>binaries/windows</td>\r
+ <td>Contains binaries for MS Windows operating system. </td>\r
+ </tr>\r
+ <tr>\r
<td>binaries/matrices</td>\r
<td>Substitution matrices\r
<!-- what format ? --></td>\r
<td>images referenced by html pages</td>\r
</tr>\r
</table>\r
-<p> </p>\r
+<h3><a name="ga" id="ga"></a>JABAWS and Google Analytics </h3>\r
+<p>JABAWS reports web services usage to our group Google Analytics (GA) account. JABAWS usage statistics are collected for funding and reporting purposes, and no private information is collected. The data sent by JABAWS is as follows: </p>\r
+<ol>\r
+ <li>The IP address of the JABAWS server machine (the server IP can anonymized see <span class="hightlight">conf/GA.properties</span> config file)</li>\r
+ <li>The name of the web service that was called. </li>\r
+ <li>A few details of the system such as JABAWS version, java version, user language, color depth, screen\r
+ resolution and character encoding.</li>\r
+</ol>\r
+<p> Google Analytics can be disabled or adjusted by removing/editing <span class="hightlight">conf/GA.properties</span> Google Analytics (GA) settings file. We would appreciate it greatly if you could leave it on!</p>\r
+<p>All calls to GA are very lightweight, completed asynchronously, create very little overhead and do not influence the server response time or performance.</p>\r
</div>\r
<!-- content end-->\r
-<div id="copyright">Last update: 7 January 2011<br />\r
+<div id="copyright">Last update: 16 September 2011<br />\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
</div>\r
git://source.jalview.org / jabaws.git / blobdiff