From: Fábio Madeira Date: Mon, 13 Feb 2017 16:55:52 +0000 (+0000) Subject: JWS-109 Automatic relative path refactoring by IntelliJ. Some paths other relative... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=234dc373ab3f4f964ea751b35753f6f8149d0e56;p=jabaws.git JWS-109 Automatic relative path refactoring by IntelliJ. Some paths other relative paths are now probably wrong. --- diff --git a/website/v_2_1_0/contacts.html b/website/v_2_1_0/contacts.html index dc2e943..a44176c 100644 --- a/website/v_2_1_0/contacts.html +++ b/website/v_2_1_0/contacts.html @@ -16,9 +16,9 @@ diff --git a/website/v_2_1_0/index.html b/website/v_2_1_0/index.html index 556c8af..93c1f30 100644 --- a/website/v_2_1_0/index.html +++ b/website/v_2_1_0/index.html @@ -16,9 +16,9 @@ diff --git a/website/v_2_1_0/jabaws_funding.html b/website/v_2_1_0/jabaws_funding.html index 08d3786..433fc8a 100644 --- a/website/v_2_1_0/jabaws_funding.html +++ b/website/v_2_1_0/jabaws_funding.html @@ -15,9 +15,9 @@ @@ -54,10 +54,10 @@ Further support comes from Wellcome Trust Strategic Grant: 100476. - - - - + + + +
ENFINWellcome TrustSULSAENFINWellcome TrustSULSA


diff --git a/website/v_2_1_0/man_about.html b/website/v_2_1_0/man_about.html index ffa16f4..669ede5 100644 --- a/website/v_2_1_0/man_about.html +++ b/website/v_2_1_0/man_about.html @@ -17,9 +17,9 @@ @@ -217,7 +217,7 @@ section (registration is required). you may wish to use our 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. In addition, this offers some additional methods that simplify - working with JABAWS. For more information please refer to the data model javadoc. + working with JABAWS. For more information please refer to the data model javadoc.

diff --git a/website/v_2_1_0/man_awscloud.html b/website/v_2_1_0/man_awscloud.html index 35576d2..4e1e512 100644 --- a/website/v_2_1_0/man_awscloud.html +++ b/website/v_2_1_0/man_awscloud.html @@ -17,9 +17,9 @@ diff --git a/website/v_2_1_0/man_awscloud_bs.html b/website/v_2_1_0/man_awscloud_bs.html index 4b1ec87..810383f 100644 --- a/website/v_2_1_0/man_awscloud_bs.html +++ b/website/v_2_1_0/man_awscloud_bs.html @@ -17,9 +17,9 @@ @@ -60,19 +60,19 @@
  • Create Amazon Web Services account.
  • Log in into the Amazon Web Services (AWS) console and switch to AWS Elastic Beanstalk view. - Elastic Beanstalk launch JABAWS war step 1 + Elastic Beanstalk launch JABAWS war step 1
  • Create a new Beanstalk application by uploading JABAWS war file: - Elastic Beanstalk launch JABAWS war step 2 + Elastic Beanstalk launch JABAWS war step 2
  • Give a name to your JABAWS instance. This name will be a part of the access URL for your JABAWS. - Elastic Beanstalk launch JABAWS war step 3 + Elastic Beanstalk launch JABAWS war step 3
  • Choose the type of hardware you want to run JABAWS on. - Elastic Beanstalk launch JABAWS war step 4 + Elastic Beanstalk launch JABAWS war step 4
  • If everything goes well you should be able to access your JABAWS on http://jabaws.elasticbeanstalk.com - Elastic Beanstalk launch JABAWS war + Elastic Beanstalk launch JABAWS war

    •  

    diff --git a/website/v_2_1_0/man_awscloud_ec2.html b/website/v_2_1_0/man_awscloud_ec2.html index b8b8939..ba26ec6 100644 --- a/website/v_2_1_0/man_awscloud_ec2.html +++ b/website/v_2_1_0/man_awscloud_ec2.html @@ -17,9 +17,9 @@ @@ -60,31 +60,31 @@
  • Create Amazon Web Services account.
  • Log in into the Amazon Web Services (AWS) console. Make sure you are in the EU West (Ireland) region. JABAWS image is not available in other regions as yet. See marker 1.
  • Click on "Launch Instance" button marker 2. - AWS console + AWS console
  • Go to the "Community AMI" tab and search for JABAWS, then click select. - select AMI
    • + select AMI
  • Choose the "hardware" for your JABAWS server instance. "Large" instance should be sufficient for a single user needs. If you are planning to use this instance as a server for the lab, you may want to select a more powerful machine. Once you have chosen the hardware click continue. - select hardware + select hardware
  • You should not need to customize anything on this page, continue to the next page. - keys + keys
  • At the "Create a key pair" step, choose "Proceed without a key pair" unless you want to access JABAWS server via SSH. - +
  • Create a new security group with a single HTTP (80) port as shown below. You may want to add SSH (22) port if you are planning to manage your instance via SSH. For starting/stopping your JABAWS instance, SSH is not necessary, you can do this from the Amazon Webservices Console (AWS). - ese + ese
  • Review the configuration and launch the instance, then click "view your instances on the Instances page". - +
  • At this point you should have JABAWS instance up and running. Your AWS console should look something like this: - +
  • Now you can run JABAWS web services by accessing the public DNS address of your JABAWS server instance. For instance, to register it with Jalview, just add the new JABAWS web server. Prefix your instance public diff --git a/website/v_2_1_0/man_client.html b/website/v_2_1_0/man_client.html index c23ef14..08d5a39 100644 --- a/website/v_2_1_0/man_client.html +++ b/website/v_2_1_0/man_client.html @@ -17,9 +17,9 @@ @@ -55,7 +55,7 @@

    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 +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]
    diff --git a/website/v_2_1_0/man_configuration.html b/website/v_2_1_0/man_configuration.html index e71aa99..f3203af 100644 --- a/website/v_2_1_0/man_configuration.html +++ b/website/v_2_1_0/man_configuration.html @@ -17,9 +17,9 @@ diff --git a/website/v_2_1_0/man_dev.html b/website/v_2_1_0/man_dev.html index 01a60e8..bee2443 100644 --- a/website/v_2_1_0/man_dev.html +++ b/website/v_2_1_0/man_dev.html @@ -17,9 +17,9 @@ @@ -80,7 +80,7 @@ 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.

    Structure of the template command line client

    @@ -105,7 +105,7 @@

    Additional utility libraries that 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.

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

    Connecting to JABAWS

    @@ -156,7 +156,7 @@ web service deployed in the University of Dundee.

    Where Services is enumeration of JABAWS web services. All JABAWS multiple sequence alignment methods confirm to 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. + interface. The full documentation of MsaWS functions is available from the javadoc.

    @@ -255,7 +255,7 @@ calculation has been completed before accessing the results. You can do it like The names of all the parameters supported by a web service e.g. "PAM300" can be obtained using options.getArguments() method. Further details on the methods available from RunnerConfig object are available from the - javadoc.

    + javadoc.

    Writing alignments to a file

    There is a utility method in the client library that does exactly that.

    Alignment alignment = align(...)
    @@ -401,7 +401,7 @@ public class Example { } } -For a more detailed description of all available types and their functions please refer to the data model javadoc. +For a more detailed description of all available types and their functions please refer to the data model javadoc.

    Building web services artifacts

    JABAWS are the standard JAX-WS SOAP web services, which are WS-I diff --git a/website/v_2_1_0/man_server_dev.html b/website/v_2_1_0/man_server_dev.html index 42f3768..8ae9f6d 100644 --- a/website/v_2_1_0/man_server_dev.html +++ b/website/v_2_1_0/man_server_dev.html @@ -17,9 +17,9 @@

    @@ -63,8 +63,8 @@

    The API

    -

    Data model javadoc- read this if your are coding against JABA Web Services

    -

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

    +

    Data model javadoc- read this if your are coding against JABA Web Services

    +

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

    The source code

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

    Another publicly available JABAWS repository, containing the code for each JABAWS public release, is located at jabaws.googlecode.com

    diff --git a/website/v_2_1_0/man_servervm.html b/website/v_2_1_0/man_servervm.html index cb081eb..099bfcd 100644 --- a/website/v_2_1_0/man_servervm.html +++ b/website/v_2_1_0/man_servervm.html @@ -17,9 +17,9 @@ @@ -98,7 +98,7 @@ but for most production environments, the JABAWS WAR distribution will be easie

    JABAWS Appliance details

    By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.

    The VMware Player screen shot below displays JABAWS VM CPU settings.

    -

    vmware cpu settings

    +

    vmware cpu settings

    JABAWS Virtual Appliance Configuration:

    VMware info

    @@ -141,9 +141,9 @@ To enable Jalview to work with your JABAWS appliance you need to go to Jalview-& New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview     help pages.

    -

    JABAWS welcome screen

    +

    JABAWS welcome screen

    If you click on Advanced Menu, you will see the configuration console, similar to the one below.

    -

    JABAWS welcome screen

    +

    JABAWS welcome screen

    If you need to configure a static IP address the configuration console will help you with this. Shutting down the VM is best from the configuration console as well.

    VM Network Settings

    diff --git a/website/v_2_1_0/man_serverwar.html b/website/v_2_1_0/man_serverwar.html index 892fba0..0f38b52 100644 --- a/website/v_2_1_0/man_serverwar.html +++ b/website/v_2_1_0/man_serverwar.html @@ -17,9 +17,9 @@

    diff --git a/website/v_2_1_0/man_stats.html b/website/v_2_1_0/man_stats.html index adbdcff..a3f13aa 100644 --- a/website/v_2_1_0/man_stats.html +++ b/website/v_2_1_0/man_stats.html @@ -17,9 +17,9 @@ @@ -64,7 +64,7 @@

    JABAWS comes with a web application for visualizing usage statistics. The screenshot below shows the main page of this application. The individual month is linked to detailed usage statistics (described later). Please note, 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 lets 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, i.e. 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

    +

    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.