JABAWS MANUAL
-JABAWS Configuration
+JABAWS Server Configuration
- JABAWS Configuration
- Local Engine Configuration @@ -57,12 +63,11 @@ with Mafft
- Limiting the size of the job accepted by JABAWS Server
- Using a different version of the alignment program with JABAWS
- Load balancing -
- Reviewing JABAWS configuration via web browser
- Testing JABA Web Services
- JABAWS requests logging
- JABAWS internal logging -
- Monitoring JABAWS
- JABAWS War File Content +
- JABAWS and Google Analytics
JABAWS Configuration
There are three parts of the system you can configure. The local @@ -127,8 +132,8 @@ environment variables have to be defined. They tell the cluster engine where to find DRMAA libraries. These variables should be defined when the web application server starts up, e.g.
-SGE_ROOT=/gridware/sge
- LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64
SGE_ROOT=/gridware/sge
+ LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64
Finally, do not forget to configure executables for the cluster execution, they may be the same as for the local execution but may @@ -203,7 +208,7 @@ can access and execute them.
just pass whatever is specified in this line directly to the cluster submission library. This is how DRMAA itself treats this settings. More exactly DRMAA JobTemplate.setNativeSpecification() function will be called. - +For further details and examples of configuration please refer to the Executable.properties file supplied with JABAWS.
Defining Environment Variables for Executables
@@ -253,34 +258,14 @@ defined in Limiting the size of the job accepted by JABAWSJABAWS 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.
Furthermore, you can define different limits for different presets of the same web service.
-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 conf/settings/<X>Limit.xml files.
Using a different version of the alignment program with JABAWS
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 ExecutableNameParamaters.xml configuration file.
Load balancing
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 "# LocalEngineExecutionLimit #" preset in <ServiceName>Limits.xml 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.
-Reviewing JABAWS configuration via web browser
-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 admin 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 conf/tomcat-user.xml file. <role rolename="admin"/>
- <user username="admin" password="your password here " roles="admin"/>
Once this is done make sure the servlet that returns the web application directory listings is enabled. Look in the <tomcatroot>/conf/web.xml file for the following <param-name>listings</param-name>
- <param-value>true</param-value>
The whole section that defines default listing servlet is below
- <servlet>
- <servlet-name>default</servlet-name>
- <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>
- <init-param>
- <param-name>debug</param-name>
- <param-value>0</param-value>
- </init-param>
- <init-param>
- <param-name>listings</param-name>
- <param-value>true</param-value>
- </init-param>
- <load-on-startup>1</load-on-startup>
- </servlet>
-
These listings are read only by default.
Testing JABA Web Services
-You can use a command line client (part of the client only +
Access <your_JABAWS_server_URL>/ServiceStatus 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 http://localhost:8080/jabaws/ServiceStatus/MuscleWS 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.
+Alternatively, you can use a command line client (part of the client only package) to test your JABAWS installation as described here. If you downloaded a JABAWS server package, you can use <your_jaba_context_name>/WEB-INF/lib/jaba-client.jar to test JABAWS installation as described in log4j.properties
and uncomment section ofIf you would like to know who is using your services, you might want to enable Tomcat request logging.
-Monitoring JABAWS
-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.
- 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!
JABAWS War File Content
| ExecutionStatistics | +The database for storing the execution statistics. | +|
| statpages | +Web pages for usage statistics visialization and webservices status queries. | +|
| jobsout/ | Contains directories generated when running an individual executable. E.g. input and output files and some other task related data. (optional) | @@ -372,6 +362,10 @@ class="hightlight">log4j.properties and uncomment section of binaries.|
| binaries/windows | +Contains binaries for MS Windows operating system. | +|
| binaries/matrices | Substitution matrices | @@ -409,10 +403,19 @@ class="hightlight">log4j.properties and uncomment section ofimages referenced by html pages |
+
JABAWS and Google Analytics
+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:
+-
+
- The IP address of the JABAWS server machine (the server IP can anonymized see conf/GA.properties config file) +
- The name of the web service that was called. +
- A few details of the system such as JABAWS version, java version, user language, color depth, screen + resolution and character encoding. +
Google Analytics can be disabled or adjusted by removing/editing conf/GA.properties Google Analytics (GA) settings file. We would appreciate it greatly if you could leave it on!
+All calls to GA are very lightweight, completed asynchronously, create very little overhead and do not influence the server response time or performance.