From a4b91e312a2515be6d3d052b85398f815865a50b Mon Sep 17 00:00:00 2001 From: =?utf8?q?F=C3=A1bio=20Madeira?= Date: Mon, 10 Apr 2017 18:08:36 +0100 Subject: [PATCH] JWS-109 General improvements and further fixes to typos and proofreading. --- website/about.jsp | 3 +- website/download.jsp | 143 +++++++++++++++++----------------- website/getting_started.jsp | 141 +++++++++++++++++---------------- website/index.jsp | 20 ++--- website/statpages/MonthlySummary.jsp | 2 +- website/statpages/ServicesStatus.jsp | 2 +- 6 files changed, 156 insertions(+), 155 deletions(-) diff --git a/website/about.jsp b/website/about.jsp index 0dded22..686b96a 100644 --- a/website/about.jsp +++ b/website/about.jsp @@ -79,7 +79,8 @@

Peter V. Troshin, James B. Procter and Geoffrey J. Barton - Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS - Bioinformatics 2011. 27 (14): 2001-2002. doi: + Bioinformatics 2011. 27 (14): 2001-2002. doi: + 10.1093/bioinformatics/btr304.

diff --git a/website/download.jsp b/website/download.jsp index bfbe57c..8933729 100644 --- a/website/download.jsp +++ b/website/download.jsp @@ -19,10 +19,10 @@

- Read the quickstart guides - to better decide which JABAWS distribution better suits your needs. - Additional information is available in the - JABAWS documentation pages. + Read the Getting Started + guides to better decide which JABAWS distribution better suits your needs. + Additional information is available in the + documentation pages.


@@ -34,22 +34,22 @@ I want to use JABAWS for... - JABAWS Virtual Appliance (VA) - Running JABAWS services through Jalview on my - computer with a private server + Command Line Interface (CLI) + Accessing a public or private + JABAWS server from my own software - JABAWS Web Application aRchive (WAR) + Web Application aRchive (WAR) Running JABAWS for my group, lab, or organization on the local infrastructure - JABAWS Command Line Interface (CLI) - Accessing a public or private - JABAWS server from my own software + Virtual Appliance (VA) + Running JABAWS services through Jalview on my + computer with a private server - JABAWS Source Code + Source Code Extend the functionally of JABAWS by adding new features and services. @@ -61,46 +61,56 @@
-
-
-
-
-

Current Version

-
-
-

- The current version of JABAWS is 2.2.0, released on XX March 2017. We advise you to update to JABAWS 2.2 as this version is fully backward compatible with JABAWS v1.0, v2.0 and v2.1. - Please consult the documentation pages - for the changelog and more information on compatibility between versions.

-

-
-
-
-
-
+<%--
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--%> + <%--
--%> + <%--

Current Version

--%> + <%--
--%> + <%--
--%> + <%--

--%> + <%--The current version of JABAWS is 2.2.0, released on XX March 2017. We advise you to update to JABAWS 2.2 as this version is fully backward compatible with JABAWS v1.0, v2.0 and v2.1.--%> + <%--Please consult the documentation pages--%> + <%--for the changelog and more information on compatibility between versions.

--%> + <%--

--%> + <%--
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-

JABAWS Server Virtual Appliance (VA)

+

Command Line Interface (CLI)

- The JABAWS virtual appliance (VA) is a way of running a fully functional JABAWS instance - on your own computer. In order to use the VA, you have to install software from VMWare to run - the virtual machine. We recommend VMWare Player - which is available for free for Windows and Linux users. Once the VA is running, you can - configure Jalview to use your local - JABAWS VA with these instructions. - + The command line client is an executable Java program for scripting + against JABAWS web services. It is also useful as an example of how to + access JABAWS services if you intend to use JABAWS in your own + program, with functions demonstrating how to discover command line + parameters and presets supported by a service, and how to run, + monitor and retrieve the results of a job. + + Note: The client is used in Jalview + to autogenerate a graphical user interface for JABA services. +

- Please check the JABAWS document pages - for further instructions. + The command line client displays help when executed without arguments, + more details is available from the JABAWS + document pages.

Back to top @@ -113,7 +123,7 @@

-

JABAWS Server Web Application aRchive (WAR)

+

Web Application aRchive (WAR)

@@ -123,8 +133,8 @@ Finally, you can use this version on a computer cluster. The server is provided as a self-contained Web Application aRchive (WAR) containing all necessary binaries. The WAR file can be deployed on any web - application server supporting the Java servlet specification (version 2.4 or above), i.e. - Tomcat 7.0. + application server supporting the Java Servlet Specification (version 2.4 or above), i.e. + Tomcat 8.5.

  • @@ -133,7 +143,7 @@ (includes source and precompiled Linux x86 and Windows binaries)

- Please check the JABAWS document pages + Please check the JABAWS document pages for further instructions.

@@ -143,44 +153,30 @@

-
+
-

JABAWS Command Line Client

+

Virtual Appliance (VA)

- The command line client is an executable Java program for scripting - against JABA web services. It is also useful as an example of how to - access JABAWS services if you intend to use JABAWS in your own - program, with functions demonstrating how to discover command line - parameters and presets supported by a service, and how to run, - monitor and retrieve the results of a job. - - Note: The client is used in Jalview - to autogenerate a graphical user interface for JABA services. - + The JABAWS Virtual Appliance (VA) is a way of running a fully functional JABAWS instance + on your own computer. In order to use the VA, you have to install software from VMWare to run + the virtual machine. We recommend VMWare Player + which is available for free for Windows and Linux users. Once the VA is running, you can + configure Jalview to use your local + JABAWS VA with these instructions. +

- The command line client displays help when executed without arguments, - more details is available from the JABAWS - document pages. + Please check the JABAWS document pages + for further instructions.

Back to top @@ -216,6 +212,7 @@ Binaries of the programs included in JABAWS

  • JABAWS Git repository http://source.jalview.org/git/jabaws.git + and Git-tracker 
    git clone http://source.jalview.org/git/jabaws.git
    • diff --git a/website/getting_started.jsp b/website/getting_started.jsp index 46731e3..19978f3 100644 --- a/website/getting_started.jsp +++ b/website/getting_started.jsp @@ -19,9 +19,9 @@

    - Choose the JABAWS distribution that better suits your needs and read the quickstart guides below. - Detailed information is available in the - JABAWS documentation pages. + Choose the JABAWS distribution that better suits your needs and read the Getting Started guides below. + Detailed information is available in the + documentation pages.


    @@ -38,20 +38,21 @@ public server - JABAWS Virtual Appliance (VA) - Running JABAWS services through Jalview on my - computer with a private server + Command Line Interface (CLI) + Accessing a public or private + JABAWS server from my own software - JABAWS Web Application aRchive (WAR) + Web Application aRchive (WAR) Running JABAWS for my group, lab, or organization on the local infrastructure - JABAWS Command Line Interface (CLI) - Accessing a public or private - JABAWS server from my own software + Virtual Appliance (VA) + Running JABAWS services through Jalview on my + computer with a private server +
    @@ -81,53 +82,37 @@
    -
    +
    -

    JABAWS Virtual Appliance (VA)

    +

    Command Line Interface (CLI)

    - -

    - The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a - virtual machine on your laptop or desktop computer. A complete guide - to the JABAWS VA is given in the documentation pages, - but for the impatient, brief instructions are given below: -

    - -

    - If you work on Windows, Linux or Unix: + This is a single Java archive which contains the JABAWS command line interface (CLI) client. + It allows anyone who wants to connect to the JABAWS web-services running at the + University of Dundee's Public Server, or to run a local private JABAWS server from their own software. + You can read more about how to use JABAWS command line (CLI) client given in the + documentation pages, + but a brief instructions are given below:

      -
    1. Download JABAWS Virtual Appliance
      2. -
    2. Download and install VMWare Player
      3. -
    3. Unpack the JABAWS virtual appliance and open it with VMware Player
      4. +
    4. Download the Client Jar file
      5. +
    5. Download and install Java + (version 1.7)
      6. +
    6. Provided that you have the Java ready to run, you can get command line help by changing to + the directory where you downloaded the client jar, and typing:
      + 
      java -jar jaba-client.jar
      +
    - -

    - If you work on Mac do the same using - - VMware Fusion. -

    - -

    Testing

    - To check that your JABAWS virtual appliance is working visit the Services Status - page available from the main JABAWS menu. For this enter the JABAWS URL for your - new server into a web browser. This is shown once the appliance is booted up. -

    -

    - Alternatively you can use Jalview to complete the testing. + The JABA Web Services are WS-I compliant. This means that you can access them from any + language that has libraries or functions for consuming interoperable SOAP web services. + More information on how to develop software that access JABAWS services is provided in the + documentation pages. +

    -
      -
    1. Launch the desktop version of Jalview
      2. -
    2. Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), select the - Webservices panel and press the - New Service URL button.
      3. -
    3. Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.
      4. -

    Back to top

    @@ -139,7 +124,7 @@
    -

    JABAWS Web Application aRchive (WAR)

    +

    Web Application aRchive (WAR)

    @@ -148,13 +133,13 @@ The JABAWS Web Application aRchive (WAR) is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable their local JABAWS server to use the cluster or perform very large tasks. Complete documentation is provided in the - documentation pages, but brief instructions are given below: + documentation pages, but brief instructions are given below:

    1. Download the JABAWS WAR file
      2. -
    2. Download and install Apache-Tomcat
      +
    3. Download and install Apache-Tomcat
      You will need at least Tomcat version 5.5 of - (we would recommend version 7.0) and at least Java 1.6 (i.e. JAVA 6). + (we would recommend version 8.5) and at least Java 1.7 (i.e. JAVA 7).
    4. Drop the JABAWS WAR file into tomcat/webapps directory.
    5. (Re)start the Tomcat.
      6. @@ -178,7 +163,7 @@
    6. If you are working on the command line, then use the command line client shipped with the JABAWS war to test it by running: - 
      java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jaba-client.jar -h=http://localhost:8080/jabaws
      + 
      java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jabaws-client.jar -h=http://localhost:8080/jabaws
      In this example we assumed that your JABAWS server URL is http://localhost:8080 and JABAWS context path is jabaws @@ -201,35 +186,53 @@
    -
    +
    -

    JABAWS Command Line Java Client

    +

    Virtual Appliance (VA)

    + +

    - This is a single Java archive which contains the JABAWS command line interface (CLI) client. - It allows anyone who wants to connect to the JABAWS web-services running at the - University of Dundee's Public Server, or to run a local private JABAWS server from their own software. - You can read more about how to use JABAWS command line (CLI) client given in the - documentation pages, - but a brief instructions are given below: + The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a + virtual machine on your laptop or desktop computer. A complete guide + to the JABAWS VA is given in the documentation pages, + but for the impatient, brief instructions are given below: +

    + +

    + If you work on Windows, Linux or Unix:

      -
    1. Download the Client Jar file
      2. -
    2. Download and install Java - (version 1.6)
      3. -
    3. Provided that you have the Java ready to run, you can get command line help by changing to - the directory where you downloaded the client jar, and typing:
      - 
      java -jar jaba-client.jar
      -
      4. +
    4. Download JABAWS Virtual Appliance
      5. +
    5. Download and install VMWare Player
      6. +
    6. Unpack the JABAWS virtual appliance and open it with VMware Player
    +

    - The JABA Web Services are WS-I compliant. This means that you can access them from any - language that has libraries or functions for consuming interoperable SOAP web services. - + If you work on Mac do the same using + + VMware Fusion. +

    + +

    Testing

    +

    + To check that your JABAWS virtual appliance is working visit the Services Status + page available from the main JABAWS menu. For this enter the JABAWS URL for your + new server into a web browser. This is shown once the appliance is booted up.

    +

    + Alternatively you can use Jalview to complete the testing. +

    +
      +
    1. Launch the desktop version of Jalview
      2. +
    2. Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), select the + Webservices panel and press the + New Service URL button.
      3. +
    3. Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.
      4. +
    diff --git a/website/index.jsp b/website/index.jsp index 0db7a64..c80ffb3 100644 --- a/website/index.jsp +++ b/website/index.jsp @@ -45,7 +45,7 @@

    JABAWS web-services can be accessed through the Jalview desktop - graphical user interface (GUI) (version 2.8 onwards) or the command line interface (CLI) client. + graphical user interface (GUI) (version 2.8 onwards) or the JABAWS Command Line Interface (CLI) client. In this way you can perform computations on your sequences using the publicly available servers running at the University of Dundee. Alternatively, JABAWS installation allows you to perform analysis limited only by your own computing resources, by running it in your local computer, server or cluster. @@ -139,24 +139,24 @@

    - You can access our public JABAWS web services with the - command line client, - Jalview, - or with your own program. The latest versions of Jalview (version 2.9 or later) are fully compatible + You can access our public JABAWS web services with Jalview, + JABAWS CLI, or + with your own program. + The latest versions of Jalview (version 2.9 or later) are fully compatible with JABAWS 2.2 and are configured to use the public JABAWS server by default.

    These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy - or on an unreliable network connection, then you can - download and - run the JABAWS Server on your own hardware. + or you are on an unreliable network connection, then you can + download and + run the JABAWS WAR on your own hardware.

    @@ -193,7 +193,7 @@

    Peter V. Troshin, James B. Procter and Geoffrey J. Barton - Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS - Bioinformatics 2011. 27 (14): 2001-2002. doi: + Bioinformatics 2011. 27 (14): 2001-2002. doi: 10.1093/bioinformatics/btr304.

    diff --git a/website/statpages/MonthlySummary.jsp b/website/statpages/MonthlySummary.jsp index 78b1fc5..a1f0090 100644 --- a/website/statpages/MonthlySummary.jsp +++ b/website/statpages/MonthlySummary.jsp @@ -97,7 +97,7 @@ Date: May 2011 The summary for each column is displayed in the last row of the table.
    -

    Please login as administrator to view the detailed statistics (help)

    +

    Please login as administrator to view the detailed statistics (help)
    diff --git a/website/statpages/ServicesStatus.jsp b/website/statpages/ServicesStatus.jsp index 62844a2..27b622e 100644 --- a/website/statpages/ServicesStatus.jsp +++ b/website/statpages/ServicesStatus.jsp @@ -193,7 +193,7 @@ TODO refactor

    If you would like to integrate JABAWS with automated health check system you may want to use the HTTP code response service checker. It responds with HTTP status code depending on the status of the web service. - For more information please refer to + For more information please refer to Testing JABAWS server help page.

    -- 1.7.10.2