From 5be9c8c2ff3353e57cb1b626efcf0088522419ff Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Wed, 13 Jul 2011 11:31:08 +0000 Subject: [PATCH] new web site design and updates to the web pages git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4411 e3abac25-378b-4346-85de-24260fe3988d --- website/contacts.html | 12 +-- website/download.html | 22 ++--- website/index.html | 20 ++--- website/man_about.html | 33 +++++--- website/man_client.html | 13 +-- website/man_configuration.html | 45 +++-------- website/man_dev.html | 14 ++-- website/man_jaba_internals.html | 144 +++++++++++++++++++++++++++++++++ website/man_servervm.html | 13 +-- website/man_serverwar.html | 14 ++-- website/man_stats.html | 168 +++++++++++++++++++++++++++++++++++++++ website/manual_qs_client.html | 13 +-- website/manual_qs_va.html | 12 +-- website/manual_qs_war.html | 13 +-- website/quick_start.html | 13 +-- website/ws.css | 16 ++-- 16 files changed, 448 insertions(+), 117 deletions(-) create mode 100644 website/man_jaba_internals.html create mode 100644 website/man_stats.html diff --git a/website/contacts.html b/website/contacts.html index 21a4fc4..d9b49b1 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -16,11 +16,12 @@ page
+ +
@@ -29,7 +30,8 @@ page Manual Download Contact Us -Barton Group +Usage Statistics +Barton Group
diff --git a/website/download.html b/website/download.html index c64991e..fe56e7d 100644 --- a/website/download.html +++ b/website/download.html @@ -17,11 +17,12 @@ page
+ +
@@ -30,7 +31,8 @@ page Manual Download Contact Us -Barton Group +Usage Statistics +Barton Group
@@ -47,12 +49,12 @@ page

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 Web Application aRchive (WAR) containing all necessary binaries. WAR file can be deployed on any web application server -supporting at least version 2.4 of the Java servlet specification, i.e. Tomcat 6.0.

+supporting at least version 2.4 of the Java servlet specification, i.e. Tomcat 7.0.

@@ -66,9 +68,9 @@ aRchive (WAR) containing all necessary binaries. WAR file can be deployed o
  • Command line client
    • @@ -91,7 +93,7 @@ aRchive (WAR) containing all necessary binaries. WAR file can be deployed o
  • A complete Eclipse project package: download (82M)
  • JABAWS source only package: download (250K)
    • +"archive/jabaws-src-2.0.jar">download (250K) diff --git a/website/index.html b/website/index.html index 52826d9..c2ed799 100644 --- a/website/index.html +++ b/website/index.html @@ -18,9 +18,9 @@ page
    @@ -33,15 +33,15 @@ page Manual Download Contact Us - Usage stats + Usage Statistics Barton Group

    JABAWS 2

    -

    JABAWS:MSA is free software which provides five web services for multiple sequence alignment: Clustal W, JABAWS2.0:Disorder 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 DisEMBL, IUPred, Ronn, GlobPlot, conservation is calculated by AACon, multiple sequence alignment services are the Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS conveniently packaged to run on your local computer, server or cluster. +"http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"> TCOFFEE and PROBCONS. JABA Web Services can be accessed from the Jalview multiple sequence alignment editor and analysis workbench to allow multiple alignment calculations limited only by your own local computing resources.

    @@ -63,7 +63,7 @@ page

    For System Administrators

    The Server: JABAWS Web Application aRchive (45M)

    +"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive (51M)

    JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. Please check the quick start guide for installation instructions.

    @@ -73,11 +73,11 @@ page

    For Bioinformaticians/Developers

    The Server: JABAWS Web Application aRchive (45M) +"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive (51M)
    The Client: - Command Line Client binary | source + Command Line Client binary | source diff --git a/website/man_about.html b/website/man_about.html index ac1c686..3758bfe 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -13,9 +13,9 @@
    @@ -31,12 +31,15 @@ Server
    Configuration     CMD Client + Usage Statistics Accessing
    JABAWS
    Download Contact Us - Barton Group
    + Usage Statistics + Barton Group
    +
    @@ -53,8 +56,8 @@

    What is JABAWS?

    -

    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 the list of currently supported programs) from Jalview. - 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.

    +

    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 the list of currently supported programs) from Jalview. + Future versions of JABAWS will incorporate many other tools.

    Getting JABAWS

    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.

    JABAWS Benefits

    @@ -69,14 +72,26 @@

    JABA Web Services Programs

    JABAWS currently provides access to the following programs:

    +

    Multiple Sequence Alignement

    +

    Protein disorder prediction

    + +

    Amino Acid conservation

    +

    What is JABAWS client?

    A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web services. The most basic JABAWS client is a command line Java application which can call any of the JABAWS web services methods diff --git a/website/man_client.html b/website/man_client.html index ce35521..2f2fc53 100644 --- a/website/man_client.html +++ b/website/man_client.html @@ -15,11 +15,12 @@

    + +
    diff --git a/website/man_configuration.html b/website/man_configuration.html index 5122e08..4e20c50 100644 --- a/website/man_configuration.html +++ b/website/man_configuration.html @@ -15,11 +15,12 @@
    + +
    @@ -57,12 +60,11 @@ 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 Usage Statistics

    • JABAWS Configuration

    There are three parts of the system you can configure. The local @@ -127,8 +129,8 @@ 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 @@ -258,27 +260,6 @@ By default limits are set well in excess of what you may want to offer to the u

    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 package) to test your JABAWS installation as described here. If you downloaded a JABAWS @@ -336,9 +317,6 @@ class="hightlight">log4j.properties and uncomment section of

    If 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

    @@ -409,7 +387,6 @@ class="hightlight">log4j.properties and uncomment section of
    images referenced by html pages
    -

     

    diff --git a/website/man_stats.html b/website/man_stats.html new file mode 100644 index 0000000..8c24989 --- /dev/null +++ b/website/man_stats.html @@ -0,0 +1,168 @@ + + + + + +Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual + + + + + +
    + + +
    + + + +
    +

    JABAWS MANUAL

    + +

    JABAWS Usage Statistics

    + +

    Summary of Usage

    +

    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 admin. There is a link at the bottom of the page that would let you login, if you have not done so.

    +

    If you are using JABAWS VA (Virtual Appliance) then the username is jabaws and password is not defined, e.g. empty.

    +

    If you have deployed a JABAWS WAR file, then please see the configuring privileged access for Tomcat web application server section for further details.

    +

    JABAWS usage statistics

    +

    The table contains the number of jobs processed by JABAWS per month, for the whole period when the statistics was collected

    +

    For each month the table contains the following information.

    +
      +
    • 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.
      • +
    • Total - the total number of jobs accepted by JABAWS
      • +
    • Incomplete - the number of jobs for which the result file was not found or was empty excluding cancelled
      • +
    • Cancelled - the number of jobs cancelled by the user
      • +
    • Abandoned - the number of jobs which result(s) were not collected
      • +
    +

    The summary for each column is displayed in the last row of the table.

    +

    Detailed Usage Statistic

    +

    Detailed execution statistics for each month is available for authenticated users only.

    +

    JABAWS one month usage statistics

    +

    Each table contains the number of jobs processed by JABAWS during the period of time specified in the title.

    +
      +
    • The "All Jobs" table contains the summary of all jobs.
      • +
    • "Local Jobs" table - contains the summary of the jobs calculated by the local engine.
      • +
    • "Cluster Jobs" table - contains the summary of the jobs calculated by the cluster.
      • +
    +Each table contains the following information for each web service +
      +
    • Total - the total number of jobs accepted by a particular JABA service
      • +
    • Incomplete - the number of jobs for which the result file was not found or was empty excluding cancelled
      • +
    • Cancelled - the number of jobs cancelled by the user
      • +
    • Abandoned - the number of jobs which result(s) were not collected
      • +
    +

    Job List

    +

    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 Configuring JABAWS execution statistics section for further details.

    +

    JABAWS - job list

    +

    Columns

    +
      +
    • JobID - the JABAWS job id, unique for every job
      • +
    • Cluster JobID - cluster job id
      • +
    • InputSize - input size in bytes
      • +
    • ResultSize - result size in bytes
      • +
    • Runtime (s) - job's runtime in seconds
      • +
    • Start time (s)- job's start time and date
      • +
    • Finish time (s)- job's finish time and date
      • +
    • isCancelled - whether the job was cancelled
      • +
    • isCollected - whether the job was collected. False for the jobs that has been initiated but which results has never been retrieved
      • +
    • 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.
      • +
    +

    JABAWS Job Directory Content

    +

    JABAWS- job details

    +

    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.

    +

    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.

    +

    RunnerConfig.xml file contains a complete description of the job and JABAWS can restart the job based on this description.

    +

    procError.txt and procOutput.txt files contains the content of the standard out and standard error streams of the process.

    +

    result.txt file contains the results.

    +

    input.txt file contains input into the process.

    +

    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).

    +

    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 Configuring JABAWS execution statistics section for further details.

    +

    Configuring JABAWS execution statistics

    +

    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.

    +

    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.

    +

    # Enable/disable cluster statistics collector true = enable, false = disable
    + cluster.stat.collector.enable=false +
    + # Maximum amount of time the job is considered be running in hours. Optional defaults to 7 days (168h)
    + cluster.stat.maxruntime=24

    +

    # Enable/disable cluster statistics collector true = enable, false = disable
    + local.stat.collector.enable=true +
    + # Maximum amount of time the job is considered to be running in hours. Optional defaults to 24 hours
    + local.stat.maxruntime=6

    +

    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.

    +

    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 "jabaws.xml" for jabaws. Where the TOMCAT_ROOT is the location of the Tomcat web application server. Here is an example of such a file:

    +

    <?xml version="1.0" encoding="UTF-8"?>
    +<Context antiResourceLocking="false" privileged="true" allowLinking="true"/>

    +

    The key option here is this: allowLinking="true". Please also make sure that you have defined the user in role "admin" as described below.

    +

    Configuring a privileged access for Tomcat web application server

    +

    Access to configuration files, detailed job execution statistics and job directories are allowed only for authenticated users in role "admin".

    +

    If you use Tomcat, then the simplest way to set up privileged access is to use a plain text configuration file conf/tomcat-user.xml. Here is an example of such configuration file defining user "peter" in role "admin". <tomcat-users>
    + <role rolename="admin"/>
    + <user username="peter" password="your password here " roles="admin"/>
    + </tomcat-users>

    +

    For more information on users and roles please consult Apache-Tomcat help pages.

    +


    +

    +
    + + + +
    + + +
    + + + + + + + + diff --git a/website/manual_qs_client.html b/website/manual_qs_client.html index a8b6599..1f7c595 100644 --- a/website/manual_qs_client.html +++ b/website/manual_qs_client.html @@ -11,10 +11,11 @@
    - @@ -25,7 +26,9 @@ Manual Download Contact Us - Barton Group
    + Usage Statistics + Barton Group
    +
    diff --git a/website/manual_qs_va.html b/website/manual_qs_va.html index e0c928e..be95fc1 100644 --- a/website/manual_qs_va.html +++ b/website/manual_qs_va.html @@ -11,10 +11,11 @@
    - @@ -25,7 +26,8 @@ Manual Download Contact Us - Barton Group
    + Usage Statistics + Barton Group
    diff --git a/website/manual_qs_war.html b/website/manual_qs_war.html index 0887429..9fbc23c 100644 --- a/website/manual_qs_war.html +++ b/website/manual_qs_war.html @@ -11,10 +11,11 @@
    - @@ -26,7 +27,9 @@ Manual Download Contact Us - Barton Group + Usage Statistics + Barton Group +
    diff --git a/website/quick_start.html b/website/quick_start.html index e74d380..e3617dd 100644 --- a/website/quick_start.html +++ b/website/quick_start.html @@ -11,10 +11,11 @@
    - @@ -25,7 +26,9 @@ Manual Download Contact Us - Barton Group
    + Usage Statistics + Barton Group
    +
    diff --git a/website/ws.css b/website/ws.css index f77b973..1b68222 100644 --- a/website/ws.css +++ b/website/ws.css @@ -71,6 +71,7 @@ background:#09c; border-color:09c; } */ + /* #container .round { display:block; margin-right:10px; @@ -83,7 +84,7 @@ border-color:09c; background-repeat:repeat-x; } - /* + #container .example5 div a { padding:3px 20px; border: 1px solid #ccc; @@ -107,15 +108,15 @@ See index.html banner commented out code for an example of use .uniicon a img {border:none;} */ #panel { - width:150px; - background:url("images/panel_bg.gif") repeat-y ; + width:161px; + background:url("images/panel_bg_long.png") repeat-y ; float:left; font-family:Verdana, Arial, Helvetica, sans-serif; padding-top:1em; } #content { - margin-left:157px; + margin-left:170px; border-bottom:solid 1px #6994af; margin-right:0.9em; } @@ -134,7 +135,7 @@ See index.html banner commented out code for an example of use } #wrapper { - background:url("images/panel_bg.gif") repeat-y left top; + background:url("images/panel_bg_long.png") repeat-y left top; margin:0; padding:0; } @@ -185,6 +186,7 @@ p { font-style:italic; } + .hightlight { font-style:italic; font-family:"Courier New", Courier, monospace; @@ -222,13 +224,11 @@ padding-left: 1em; } .u { text-decoration: underline; } -/* .headeru { text-shadow: #CCCCCC 15px -14px 2px;} font-size-adjust:+0.7 */ -/*.headeru { text-shadow: 1px 0 black, 0 -1px black;} */ + .headeru { text-shadow:0 1px 3px black; border-bottom: 1px solid white; } -/* .headeru { border-bottom:1px solid white; } */ #banner h1 { font-family:Helvetica, Arial, sans-serif; -- 1.7.10.2