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-<title>Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual</title>\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</title>\r
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- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
+ <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
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<h2 id="headtitle">JABAWS MANUAL</h2>\r
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<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><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
<p>Authentication lets you see the detailed usage statistics. 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. In other cases you need to ask your system administrator for it. </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><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
</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><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>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><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
<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
+<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
+ # 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
+<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
+ # 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
+<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
<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
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<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
git://source.jalview.org / jabaws.git / blobdiff