From: pvtroshin Date: Wed, 7 Dec 2011 11:54:34 +0000 (+0000) Subject: web pages updates to point to new download location also the redirect servlet X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bc3346bd7c1c518fad867d4c60a53779e7516588;p=jabaws.git web pages updates to point to new download location also the redirect servlet git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4788 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml index b348e84..37710f0 100644 --- a/WEB-INF/web.xml +++ b/WEB-INF/web.xml @@ -54,6 +54,11 @@ ServiceStatus compbio.stat.servlet.ServiceStatus + + + DownloadRedirector + compbio.stat.servlet.DownloadRedirector + WebService Status with no UI. Accepts web service name as a parameter @@ -155,8 +160,14 @@ listings / + + DownloadRedirector + /download + + + DisplayStat /DisplayStat diff --git a/webservices/compbio/stat/servlet/DownloadRedirector.java b/webservices/compbio/stat/servlet/DownloadRedirector.java new file mode 100644 index 0000000..af078c2 --- /dev/null +++ b/webservices/compbio/stat/servlet/DownloadRedirector.java @@ -0,0 +1,23 @@ +package compbio.stat.servlet; + +import java.io.IOException; + +import javax.servlet.ServletException; +import javax.servlet.http.HttpServlet; +import javax.servlet.http.HttpServletRequest; +import javax.servlet.http.HttpServletResponse; + +public class DownloadRedirector extends HttpServlet { + + @Override + protected void doGet(HttpServletRequest req, HttpServletResponse resp) + throws ServletException, IOException { + resp.sendRedirect("http://www.compbio.dundee.ac.uk/download"); + } + @Override + protected void doPost(HttpServletRequest req, HttpServletResponse resp) + throws ServletException, IOException { + doGet(req, resp); + } + +} diff --git a/website/contacts.html b/website/contacts.html index d3d1334..0b8bbe5 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -28,7 +28,7 @@ page
Home Getting Started Manual -Download +Download Usage Statistics Services Status Contact Us diff --git a/website/download.html b/website/download.html deleted file mode 100644 index bfac660..0000000 --- a/website/download.html +++ /dev/null @@ -1,130 +0,0 @@ - - - - - - -Java Bioinformatics Analysis Web Services (JABAWS) download -page - - - - -
- - - -
- - - -
-

JABAWS Server Virtual Appliance

-

JABAWS virtual machine is a way of running fully functional JABA Web Services on your own computer. To use virtual machine (VM) you have to install a software for running it. We would recommend VMWare Player for Windows and Linux users or VMware Fusion for Mac users. Jalview can use your local JABAWS VA.

-
    -
  • JABAWS Virtual Appliance: download (520M)
    • -
-

Please check out our manual for the detailed instructions.

- - -

JABAWS Server Web Application

-

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. You can also use this version for Mac and Linux computers if you do not want to use virtualization. Finally, you can use this version with a cluster.
- 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 the Java servlet specification v. 2.4 or above, i.e. Tomcat 7.0.

-
    -
  • A JABAWS WAR for all platforms (comes with precompiled Linux x86 and Windows binaries): download -(55M)
    • -
  • A JABAWS WAR for Mac (comes with precompiled Mac binaries): download (51M)
    • -
- - -

Please bear in mind that if you deploy JABAWS WAR on Windows, not all web services will be functional. Use the JABAWS Server VA package instead. - -

- -

JABAWS Command Line Client

-

The command line client is an executable Java program for scripting against JABA web services. Its 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 the Jalview 2.6.1 source code to autogenerate a graphical user interface for JABA services.

-
    -
  • Command line client - -
    • -
-

The command line client will display help documentation if it is run with no arguments, the same information is also given in the command line client's manual page.

-

Version

-

Current JABAWS version is 2.0 release date 15 August 2011.

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- - - - - -
- -
- - - -
- - - -
- - - diff --git a/website/index.html b/website/index.html index fde5fa7..c18c434 100644 --- a/website/index.html +++ b/website/index.html @@ -31,7 +31,7 @@ page Home Getting Started Manual - Download + Download Usage Statistics Services Status Contact Us @@ -51,7 +51,7 @@ page

For Users

- The Server: JABAWS Virtual Appliance: (520M) + The Server: JABAWS Virtual Appliance: (520M) or use JABAWS on Amazon Webservices Cloud
The Client: Jalview (18M)

To use JABA Web Services on most operating systems, just download and install the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!

@@ -64,7 +64,7 @@ page

For System Administrators

The Server: JABAWS Web Application aRchive (55M)

+"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive (55M)

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

@@ -74,11 +74,11 @@ page

For Bioinformaticians/Developers

The Server: JABAWS Web Application aRchive (55M) +"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive (55M)
The Client: - Command Line Client binary | source + Command Line Client binary | source @@ -92,14 +92,14 @@ Check out the quick start guide for furt

Public JABAWS Server

-

You can access our public JABA Web Services with our command line client, Jalview, or with your own program. Jalview is configured to use this public JABAWS server by default.

+

You can access our public JABA Web Services with our command line client, Jalview, or with your own program. Jalview is configured to use this public JABAWS server by default.

  • The JABAWS public web services address is http://www.compbio.dundee.ac.uk/jabaws
  • A detailed web services description is available from here: WSDL List
-

These web services will reject submissions containing more then 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.

+

These web services will reject submissions containing more then 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.

Reference

diff --git a/website/man_about.html b/website/man_about.html index ffaf2a0..edc4008 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -37,7 +37,7 @@ JABAWS JABAWS Development
- Download + Download Usage Statistics Services Status Contact Us @@ -110,7 +110,7 @@ functionality as the command line client, but instead allows JABAWS services to any programming language or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home page, and you can use this to automatically generate service bindings for your program. If you use Java, however, then you may wish to use our -client package to access JABAWS. +client package to access JABAWS. This package is based on the autogenerated source code produced by wsimport, which is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify working with JABAWS. For more information please refer to the data model javadoc. diff --git a/website/man_awscloud.html b/website/man_awscloud.html index ea4f060..21cd30c 100644 --- a/website/man_awscloud.html +++ b/website/man_awscloud.html @@ -44,7 +44,7 @@ JABAWS JABAWS Development
-Download +Download Usage Statistics Services Status Contact Us diff --git a/website/man_awscloud_bs.html b/website/man_awscloud_bs.html index d747998..16cbb87 100644 --- a/website/man_awscloud_bs.html +++ b/website/man_awscloud_bs.html @@ -44,7 +44,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us diff --git a/website/man_awscloud_ec2.html b/website/man_awscloud_ec2.html index 88ea662..a1121b7 100644 --- a/website/man_awscloud_ec2.html +++ b/website/man_awscloud_ec2.html @@ -44,7 +44,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us diff --git a/website/man_client.html b/website/man_client.html index 473b653..d84f2a6 100644 --- a/website/man_client.html +++ b/website/man_client.html @@ -39,7 +39,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us @@ -51,7 +51,7 @@

JABAWS MANUAL

JABAWS Command Line Client Usage

-

The command line client comes as a part of 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 using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.

+

The command line client comes as a part of 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 using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.

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
-s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS] diff --git a/website/man_configuration.html b/website/man_configuration.html index b401c8c..f5348ec 100644 --- a/website/man_configuration.html +++ b/website/man_configuration.html @@ -39,7 +39,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us diff --git a/website/man_dev.html b/website/man_dev.html index 0831503..f541bd4 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -39,7 +39,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us @@ -107,7 +107,7 @@

Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.
Please refer to a data model javadoc for a detailed description of each class and its methods.

Connecting to JABAWS

-

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. Please note that for now all the examples are in Java other languages will follow given a sufficient demand.

+

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. Please note that for now all the examples are in Java other languages will follow given a sufficient demand.

Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee.

import java.net.URL;
import javax.xml.namespace.QName;
@@ -214,7 +214,7 @@ FileOutputStream outStream = new FileOutputStream(file);
ClustalAlignmentUtil.writeClustalAlignment(outStream, align);

A complete client example

-

Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a PDF version of this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a JABAWS binary client. Please make sure that the client is in the Java class path before running this example.

+

Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a PDF version of this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a JABAWS binary client. Please make sure that the client is in the Java class path before running this example.

 import java.io.ByteArrayInputStream;
 import java.io.FileNotFoundException;
diff --git a/website/man_server_dev.html b/website/man_server_dev.html
index f1196f0..3edfaa2 100644
--- a/website/man_server_dev.html
+++ b/website/man_server_dev.html
@@ -38,7 +38,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/man_servervm.html b/website/man_servervm.html
index 234f426..d2001f6 100644
--- a/website/man_servervm.html
+++ b/website/man_servervm.html
@@ -39,7 +39,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/man_serverwar.html b/website/man_serverwar.html
index f50e8c5..76c58f5 100644
--- a/website/man_serverwar.html
+++ b/website/man_serverwar.html
@@ -39,7 +39,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/man_stats.html b/website/man_stats.html
index 4e12de7..487aa13 100644
--- a/website/man_stats.html
+++ b/website/man_stats.html
@@ -39,7 +39,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/manual_qs_client.html b/website/manual_qs_client.html
index 9c07636..49c926c 100644
--- a/website/manual_qs_client.html
+++ b/website/manual_qs_client.html
@@ -24,7 +24,7 @@
 Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	 Services Status
 	Contact Us
@@ -67,7 +67,7 @@
 
 
The JABAWS command line client

 
  • Download the Client Jar (80 K)
    • 
+"http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">Download the Client Jar (80 K)
 

 
This is a single java archive which contains the JABAWS command line client. 
 It requires Java version 1.6 to run, and allows anyone who wants to connect 
diff --git a/website/manual_qs_va.html b/website/manual_qs_va.html
index 7d706fc..cdae95a 100644
--- a/website/manual_qs_va.html
+++ b/website/manual_qs_va.html
@@ -24,7 +24,7 @@
 Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	 Services Status
 	Contact Us
@@ -61,7 +61,7 @@
 
 
 
Running JABAWS on your local machine

-