From 8c5809e7cce4bd4a1f47fd94565fc0a01bfd8eb5 Mon Sep 17 00:00:00 2001 From: =?utf8?q?F=C3=A1bio=20Madeira?= Date: Mon, 6 Mar 2017 14:09:17 +0000 Subject: [PATCH] JWS-109 Updated the Documentation pages. Fixed the links and fixed chuncks of text to improve readability. --- website/man_about.jsp | 77 ++++++++++++++++++++++------------------- website/man_client.jsp | 52 ++++++++++++++++++++++++---- website/man_configuration.jsp | 28 ++++++++------- website/man_dev.jsp | 58 ++++++++++++++----------------- website/man_docs.jsp | 27 +++++++++++---- website/man_server_dev.jsp | 26 +++++++------- website/man_servervm.jsp | 20 +++++++---- website/man_serverwar.jsp | 22 ++++++------ website/man_stats.jsp | 2 +- 9 files changed, 188 insertions(+), 124 deletions(-) diff --git a/website/man_about.jsp b/website/man_about.jsp index a4444e9..62edca5 100644 --- a/website/man_about.jsp +++ b/website/man_about.jsp @@ -26,10 +26,10 @@ @@ -51,17 +51,46 @@ 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. + (see the list of currently supported programs). Future versions of JABAWS will incorporate other tools.

Getting JABAWS

- JABAWS consists of a server and a 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 + JABAWS consists of a server and a 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 (VA). + 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 (WAR). + 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. + in writing your own client, the + JABAWS command line (CLI) client is what you need. +

+

+ Back to top +

+ + + + +
+
+
+
+

What is the JABAWS Client?

+
+
+

A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web + services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web + services on any instance of JABAWS Server available over the web. The basic client is useful if you would like + to test or execute the programs provided by the JABAWS server in your own scripts, but you do not want to handle + any web service specific details. The client is an open source software, so you can also use the source code to + as an example how to manipulate with JABAWS web services in your own code. + Jalview, a multiple sequence alignment and analysis application, is a good + example of a graphical JABAWS client. This client uses the same functionality as the + JABAWS command line (CLI) client, but + instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.

Back to top @@ -78,7 +107,7 @@

    -
  • Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.
    • +
  • Can be deployed on most operating systems, as a VMware or compatible Virtual Appliance, as well as a Tomcat Java Web Application.
  • Comes complete with sources and binaries for all the bioinformatics programs that it runs.
  • Can operate as a stand alone server or one that submits jobs to a cluster via DRMAA.
  • Easy to access from Jalview using its graphical client, or using the JABAWS command line client.
    • @@ -98,7 +127,7 @@
    -

    JABA Web Services Programs

    +

    Bioinformatics tools included in JABAWS

    JABAWS currently provides access to the following programs:

    @@ -155,7 +184,7 @@
    - JABAWS Version 2.2 (Released XX Feb 2017) + JABAWS Version 2.2 (Released XX March 2017)

    The website was improved and several service programs were update:

    • The versions of several application programs provided by JABAWS were bumped to the latest available. @@ -170,7 +199,7 @@ The pre-configured JABAWS Amazon Machine Image (AMI), which allowed for JABAWS to be run in the Amazon EC2 cloud, is no longer provided - due to very limited use by the scientific community. + due to very limited use by the scientific community peers.
    @@ -227,30 +256,6 @@
    -
    -
    -
    -
    -

    What is the JABAWS Client?

    -
    -
    -

    A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web - services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web - services on any instance of JABAWS Server available over the web. The basic client is useful if you would like - to test or execute the programs provided by theJABAWS server in your own scripts, but you do not want to handle - any web service specific details. The client is an open source software, so you can also use the source code to - as an example how to manipulate with JABAWS web services in your own code. - Jalview, a multiple sequence alignment and analysis application, is a good - example of a graphical JABAWS client. This client uses the same functionality as the command line client, but - instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface. -

    -

    - Back to top -

    -
    -
    -
    -
    diff --git a/website/man_client.jsp b/website/man_client.jsp index 1925d2c..69a71e8 100644 --- a/website/man_client.jsp +++ b/website/man_client.jsp @@ -16,24 +16,55 @@
  • Documentation
  • Develop JABAWS
    • -
    +
    -

    JABAWS Command Line Client Usage

    +

    Command Line Client

    +
    +
    + + + + +
    +
    +
    +
    +
    +
    +
    +
    +

    Overview of the Command Line Client

    The command line client comes as a part of - client package + client package which you are welcome to download. The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via - JABAWS API. Using this client you could align sequences + JABAWS API. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.

    +
    +
    +
    +
    +
    +
    +
    +
    +

    Command Line Client Usage

    +
    +
    + 
    java -jar jaba-client.jar
    Usage:
 java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]
 -h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
@@ -51,7 +82,17 @@ Please note that if input file is specified other actions are ignored
 -o=<outputFile> - full path to the file where to write an alignment
 -f=<parameterInputFile> - the name of the file with the list of parameters to use.
    
 Please note that -r and -f options cannot be used together. Alignment is done with either preset or aparameters from the file, but not both!
    - +
    +
    +
    +
    +
    +
    +
    +
    +

    Example Usage

    +
    +

    Align sequences from input.fasta file using Mafft web service with default settings, print alignment in Clustal format to console. @@ -106,7 +147,6 @@ MTADGPRELLQLRAAV -h=http://mylabserver.myuni.edu. This comes handy if your favorite server is off and you need to do the job yesterday.

    -
    diff --git a/website/man_configuration.jsp b/website/man_configuration.jsp index cb967bf..9d8680f 100644 --- a/website/man_configuration.jsp +++ b/website/man_configuration.jsp @@ -14,7 +14,7 @@
    1. Home
    2. Documentation
      3. -
    3. Develop JABAWS
      4. +
    4. Configuring JABAWS
    @@ -34,7 +34,7 @@
  • Limiting the size of the job accepted by JABAWS Server
  • Using a different version of the alignment program with JABAWS
  • Load balancing
    • -
  • Testing JABA Web Services
    • +
  • Testing JABAWS Web-Services
  • JABAWS requests logging
  • JABAWS internal logging
  • JABAWS War File Content
    • @@ -179,7 +179,7 @@ LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64 

    local.X.bin.windows=<path to executable under windows system, optional>
 local.X.bin=<path to the executable under non-windows system, optional>
-cluster.X.bin=<path to the executable on the cluster, all cluster nodes must see it, optional><
+cluster.X.bin=<path to the executable on the cluster, all cluster nodes must see it, optional>
 X.bin.env=<semicolon separated list of environment variables for executable, use hash symbol as name value separator, optional>
 X.--aamatrix.path=<path to the directory containing substitution matrices, optional>
 X.presets.file=<path to the preset configuration file, optional>
@@ -187,7 +187,7 @@ X.parameters.file=<path to the parameters configuration file, optional>
 X.limits.file=<path to the limits configuration file, optional>
 X.cluster.settings=<list of the cluster specific options, optional>
    -

    Where X is either clustal, muscle, mafft, probcons or tcoffee.

    +

    Where X any of the bioinformatics tools available (e.g. clustalw, muscle, mafft, probcons, t-coffee, etc.).

    Default JABAWS configuration includes path to local executables @@ -268,7 +268,7 @@ mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000

    Environment variables can be defined in property

    x.bin.env

    - Where x is one of five executables supported by JABAWS. Several environment + Where x is one of thw executables supported by JABAWS. Several environment variables can be specified in the same line. For example. 

    mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;
    @@ -413,7 +413,7 @@ mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000
    -

    Testing JABA Web Services

    +

    Testing JABAWS Web-Services

    @@ -595,6 +595,10 @@ mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000 log4j.properties - log configuration file (optional) + static + Static content such as CSS, JavaScript and Image files + + Help Pages @@ -603,17 +607,17 @@ mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000 dm_javadoc - javadoc for JABAWS client (the link is available from How To - pages) + JavaDoc for the JABAWS Data Model - prog_docs - documentation for programs that JABAWS uses + full_javadoc + JavaDoc for the complete JABAWS - images - images referenced by html pages + prog_docs + Documentation for programs that are included in JABAWS +

    Back to top diff --git a/website/man_dev.jsp b/website/man_dev.jsp index 3605da6..217b850 100644 --- a/website/man_dev.jsp +++ b/website/man_dev.jsp @@ -14,7 +14,7 @@

    1. Home
    2. Documentation
      3. -
    3. Develop JABAWS
      4. +
    4. Accessing JABAWS
    @@ -52,7 +52,7 @@

    - All JABA multiple sequence alignment web services comply to the same + All JABAWS multiple sequence alignment web services comply to the same interface, thus the function described below are available from all the services.

    Functions for initiating the alignment @@ -71,8 +71,8 @@ Limit limit = getLimit(String name) LimitsManager lm = getLimits() PresetManager pm = getPresets()

    - Please refer to a data model - javadoc for a detailed description of each methods. + Please refer to a Data Model + JavaDoc for a detailed description of each methods.

    Back to top @@ -115,7 +115,7 @@ PresetManager pm = getPresets() compbio-util-1.3.jar and compbio-annotation-1.0.jar.

    - Please refer to a data model javadoc + Please refer to a Data Model JavaDoc for a detailed description of each class and its methods.

    @@ -136,7 +136,7 @@ PresetManager pm = getPresets() For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the - download page. + download page. Please note that for now all the examples are in Java, other languages will follow if there is sufficient demand.

    @@ -182,7 +182,7 @@ MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal + "Port& MsaWS specification, thus from the caller point of view all JABAWS web services can be represented by MsaWS interface. The full documentation of MsaWS functions is available from - the javadoc. + the JavaDoc.

    @@ -200,30 +200,30 @@ MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal + "Port&

    Multiple sequence alignment services

    - diff --git a/website/man_server_dev.jsp b/website/man_server_dev.jsp index c276e11..1e60fab 100644 --- a/website/man_server_dev.jsp +++ b/website/man_server_dev.jsp @@ -14,7 +14,7 @@
    1. Home
    2. Documentation
      3. -
    3. Develop JABAWS
      4. +
    4. Developing JABAWS
    @@ -48,10 +48,10 @@

    This page is for anyone who wants to add a new webservice into the JABAWS framework.

    -

    Data model javadoc- read this if your are coding +

    Data Model JavaDoc - read this if your are coding against JABA Web Services

    -

    Complete javadoc - for developers who want to +

    Complete JavaDoc - for developers who want to use JABAWS framework and use Engines and Executables directly

    @@ -68,7 +68,7 @@

    The source code

    -

    Publicly available Git repository: +

    Publicly available Git repository: http://source.jalview.org/gitweb/?p=jabaws.git;a=summary

    Another publicly available JABAWS repository, containing the code for each @@ -208,17 +208,17 @@

    Several testing groups are supported:

      -
    • All tests (Test)
      • -
    • Cluster tests (Run_cluster_dependent_test)
      • -
    • Cluster independent tests ()
      • -
    • Windows only tests (All_cluster_independent_windows_only_tests)
      • -
    • Performance and stability tests (Long_tests)
      • -
    • Re-run failed tests (Rerun_failed_tests)
      • -
    • Run custom test (CustomTest)
      • +
    • All tests ('Test')
      • +
    • Cluster tests ('Run_cluster_dependent_test')
      • +
    • Cluster independent tests ('All_cluster_independent_tests')
      • +
    • Windows only tests ('All_cluster_independent_windows_only_tests')
      • +
    • Performance and stability tests ('Long_tests')
      • +
    • Re-run failed tests ('Rerun_failed_tests')
      • +
    • Run custom test ('CustomTest')

    - To run the tests you need to download all sources from repository. + To run the tests you need to download all sources from repository. Once you have done that, enter into the command line mode, change directory to the project directory and type:

    @@ -266,7 +266,7 @@
    -

    Preparing distributive's

    +

    Preparing distributives

    diff --git a/website/man_servervm.jsp b/website/man_servervm.jsp index 347456d..bf5c439 100644 --- a/website/man_servervm.jsp +++ b/website/man_servervm.jsp @@ -48,7 +48,7 @@

    The JABAWS Virtual Appliance is a - way to run JABAWS server locally without the need to connect to the internet or configure JABAWS. + way to run a JABAWS server locally, without the need to connect to the internet or configure JABAWS. What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM), running an installation of the JABAWS Web Application Archive (WAR) on TurnKey Linux 12.1 (Tomcat edition). Once this has @@ -58,7 +58,7 @@ VMware Player, but you will need to install it first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and VMware Fusion on Mac. - However, you are not limited to these virtualization systems and can use the JABAWS appliance with + However, you are not limited to these virtualization systems and can use the JABAWS Appliance with any other virtualization platform. You can use VMware OVF tool to prepare JABAWS image for a different virtualization platform e.g. @@ -78,17 +78,23 @@

    When to use the Virtual Appliance

    -

    The appliance best suits users who would like to use the JABA web services locally. This might be because they do not want to access +

    The appliance best suits users who would like to use the JABAWS web-services locally. + This might be because they do not want to access systems over an internet, or just want to keep their data private. It is also - the recommended option for users who want to install JABAWS on Windows, which does not support all the bioinformatics programs that JABAWS can run. + the recommended option for users who want to install JABAWS on Windows, which does not support all the + bioinformatics programs that JABAWS can run.

    - For servers that will be used heavily, we recommend that a JABAWS Server WAR distribution is deployed, rather than the Virtual Appliance version of JABAWS. + For servers that will be used heavily, we recommend that a + JABAWS Server WAR distribution is deployed, rather than the + Virtual Appliance version of JABAWS. This is because the JABAWS appliance is pre-configured to use only 1 CPU and 512M of memory - (where the minimum amount of memory required for a JABAWS server is about 378M), which is unlikely to be sufficient for heavy computation. + (where the minimum amount of memory required for a JABAWS server is about 378M), which is unlikely to + be sufficient for heavy computation. It is possible to reconfigure the virtual appliance so it uses more computation resources, - but for most production environments, the JABAWS WAR distribution will be easier to deploy and fine tune to take advantage of the available resources. + but for most production environments, the JABAWS WAR distribution will be easier to deploy and fine + tune to take advantage of the available resources.

    Back to top diff --git a/website/man_serverwar.jsp b/website/man_serverwar.jsp index 6a538a9..54d943a 100644 --- a/website/man_serverwar.jsp +++ b/website/man_serverwar.jsp @@ -26,7 +26,7 @@

    • System Requirements
    • Installing the JABAWS WAR file
      • -
    • Preparing executables for use with JABAWS
      • +
    • Preparing executables to use with JABAWS
    • Using the pre-compiled i386 binaries on Linux
    • Recompiling the bundled programs for your system
    • Reuse the binaries that are already in your system
      • @@ -105,8 +105,8 @@ the localhost:8080 and jaba.war file is put into the <tomcat server root>/webapps directory, - the deployed application from the jaba.war file then can be accessed by this - URL http://localhost:8080/jaba. + the deployed application from the jabaws.war file then can be accessed by this + URL http://localhost:8080/jabaws.

      For any other web application server, please follow your server's specific deployment procedure @@ -130,7 +130,7 @@

      -

      Preparing executables for use with JABAWS

      +

      Preparing executables to use with JABAWS

      @@ -171,9 +171,11 @@

      You can try the JABAWS functionality with the JABAWS test client or have a look at deploying on Tomcat tips if you experience any problems.
      - Note: You may want to enable logging, - as described here. + href="#usingWsTester"> test client or have a look at + deploying on Tomcat + tips if you experience any problems.
      + Note: You may want to enable logging, + as described here.

      Back to top @@ -263,7 +265,7 @@ symbolic links to them. Then the default configuration will work for you. More information about the Executable.properties file is given in the - JABAWS Configuration chapter. + JABAWS Configuration page.

      Back to top @@ -452,10 +454,10 @@ Service ProbconsWS IS NOT FUNCTIONAL

      To stop Tomcat from automatically undeploying your application if the war file is removed use an explicit application descriptor. It could come in different flavors, - the one I prefer is to drop a context descriptor file into + the one we prefer is to drop a context descriptor file into <tomcatRoot>conf/Catalina/localhost directory. Name your context file the same as your application folder e.g. if your - JABAWS resides in webappl/jabaws folder, then call the context file jabaws.xml. + JABAWS resides in webapps/jabaws folder, then call the context file jabaws.xml. Below is an example of content this file might have. 

      <?xml version="1.0" encoding="UTF-8"?>
diff --git a/website/man_stats.jsp b/website/man_stats.jsp
index 76a53c8..2ecab15 100644
--- a/website/man_stats.jsp
+++ b/website/man_stats.jsp
@@ -196,7 +196,7 @@
             
      
                 
      
                     JABAWS- job details
      
+                         width="600" height="340" />
      
                 
      
                     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
-- 
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