From 697980fd79f3cc008c62d8a48ce70f4c1f9160c9 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Mon, 30 Sep 2013 14:32:41 +0100 Subject: [PATCH] Lots of changes for Jabaws 2.1 website --- website/contacts.html | 40 +++--- website/develhome.html | 130 ------------------ website/index.html | 120 ++++++++++------ website/jabaws_funding.html | 47 +++---- website/man_about.html | 94 ++++++++----- website/man_awscloud.html | 61 ++++----- website/man_awscloud_bs.html | 85 ++++++------ website/man_awscloud_ec2.html | 117 +++++++++------- website/man_client.html | 68 ++++----- website/man_configuration.html | 49 ++++--- website/man_dev.html | 49 ++++--- website/man_server_dev.html | 297 +++++++++++++++++++++++----------------- website/man_servervm.html | 73 +++++----- website/man_serverwar.html | 52 ++++--- website/man_stats.html | 70 +++++----- website/manual_qs_amazon.html | 41 +++--- website/manual_qs_client.html | 44 +++--- website/manual_qs_va.html | 50 +++---- website/manual_qs_war.html | 60 ++++---- website/print.css | 14 +- website/quick_start.html | 30 ++-- website/ws.css | 118 +++++++++++----- 22 files changed, 877 insertions(+), 832 deletions(-) delete mode 100644 website/develhome.html diff --git a/website/contacts.html b/website/contacts.html index 187c06c..a046c99 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -1,12 +1,13 @@ - + Java Bioinformatics Analysis Web Services (JABAWS) download page - + + + @@ -14,28 +15,29 @@
-
Home - Getting Started - Manual - Download - Usage Statistics - Services Status - Contact Us - Barton Group - Funding + - +

Contact Us

@@ -49,7 +51,7 @@ Dundee,
DD1 5EH,
Scotland, UK

- +

diff --git a/website/develhome.html b/website/develhome.html deleted file mode 100644 index e6a0901..0000000 --- a/website/develhome.html +++ /dev/null @@ -1,130 +0,0 @@ - - - - - -Java Bioinformatics Analyses Web Services (JABAWS) developers documentation - - - - - - -
- - - -
- - - -
-

JABAWS Javadoc

-

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

-

Starting up from the source code

-

SVN source repository:https://svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA_r1
-The repository contains a complete JABAWS Eclipse project. To use Eclipse with this repository you need to install Eclipse SVN plugin which could be found here: http://subclipse.tigris.org/servlets/ProjectProcess?pageID=p4wYuA. Eclipse update web site address is http://subclipse.tigris.org/update_1.4.x Take care to install 1.4.x version of the plugin, as SVN repository will not work with more recent clients. it would help to install TestNG plugin as well which could be downloaded from http://testng.org/doc/download.html. Please note however that no generated code is stored in the repository. That is to say that if you like to obtain client or server packages it is better to download them from the download section of this web site. Of cause If you want to make a modification to the source code you would need to generate distributives yourself. To do that first generate JAX-WS artifacts using build-server task from wsbuild.xml ant script, than you could use build.xml tasks to generate any of the distributives you need.

-

Structure of the project

-JABAWS layers -

Layers in the source code are defined in a different source folders which are: -
/webservices
- /runner
- /engine
- /datamodel

-

JABAWS project is split into 4 layers. From bottom-up the first layer consists from the value classes used by all other layers of the hierarchy, in particular web services. So, to be able to use JABAWS one needs to have these classes. At the same time classes on this layer does not have any dependencies on the layers above.

-

The second layer contains code for execution of the wrappers, which are the abstraction describing native executables. The code on this level code engine. JABAWS can execute tasks locally that is on the same machine as JVM and on the cluster. Thus currently code on this layer contain two engines. This layer depends on the layer underneath, the data model layer, but is completely independent from the code above.

-

The third layer consists of the wrappers for the native executables and classes to handle their configuration. It depends on the engines and the data model, but know nothing about the web services.

-

Finally, the upper layer contains the web services, that depend on all the layers below.

-

The layer isolation is archived though specially designed compilation task which is executed sequentially in several stages so that the first layer compiles before any other layers, second layer compiles after that and process continies before all the code is compiled. Any violation of the layer boundaries results in the compilation failure. Use Ant "Compile" or "Complile_with_debug" tasks to perform the staged compilation.

-

A client package contains only classes from data model layer and a simple web services client. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Framework exclude the web services layer. Server package contains all the code.

- -

Running tests

-

The test results for the JABAWS package offered for download can be found here: Test Results
-JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied with JABAWS together with an ant tasks to run the test cases.

-

The best way to ensure that JABAWS framework is completely functional on your system is to run all test cases. -Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding those that depends on the cluster. -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)
    • -
-

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: - ant -f build.xml <test group name>

-

. Make sure you have Apache Ant - installed and path to ant executable is defined in your path environmental variable. - Replace test group name with the one of the names given in the list above to run required group of tests e.g for running cluster only tests - use the following - command: ant -f build.xml Run_cluster_dependent_test - If you work under Linux you could use a simple script from the root folder of repository called runtests.sh This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, which you can define once for your system and then reuse. -

-

-

A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in test-output/testng-failed.xml. and is used in the ant task called Rerun_failed_tests. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: ant -f build.xml Rerun_failed_tests CustomTest runs the test defined in the project root directory file called temp-testng-customsuite.xml. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure.

-

For cluster execution make sure that the property LD_LIBRARY_PATH defined in build.xml points to cluster engine LD libraries directory in your local system.

- -

Preparing distributive's

-

There are a number of ant tasks aimed for preparing distributives for download. - Currently a few types of JABAWS packages are offered -

    -
  1. Client only (contains classes required to access JABA Web Services)
    2. -
  2. Platform specific JABAWS (windows and other)
    3. -
  3. JABA Web Services without JAXWS libraries ( a the runtime dependency)
    4. -
  4. JABAWS without binaries
    5. -
  5. JABAWS without binaries and jax-ws
    6. -
  6. JABAWS framework
    7. -
-

- Corresponding build task names are: -
    -
  1. min-jaba-client
    2. -
  2. jaba-windows, jaba-complete
    3. -
  3. jaba-without-jaxws
    4. -
  4. jaba-no-binaries
    5. -
  5. jaba-no-jaxws-no-binaries
    6. -
  6. full-jaba-client
    7. -
- -

The easiest way to build all distributives is to call build-all ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory.

-

If you made any changes to the data model and would like to generate a complete JABAWS distro make sure you have rebuilt jaxws artifact as described below.

-

Building web services artifacts

-

Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in webservices/compbio/ws/server/resource directory. It is not necessary to edit them if any of the JABAWS clients are used. However, if you would like to generate portable artifacts using wsimport based on the generated WSDL files then, <soap:address location="REPLACE_WITH_ACTUAL_URL"/>

- -

must be replaced with an actual server URL including the web services context path. For example:

-

http://www.compbio.ac.uk:8080/ws

-

JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible.

-
- -
-
- - - - - - - diff --git a/website/index.html b/website/index.html index b2812e7..4865866 100644 --- a/website/index.html +++ b/website/index.html @@ -1,62 +1,78 @@ - + Java Bioinformatics Analyses Web Services (JABAWS) main page - + + -
-
- + +

JABAWS 2.1

-

JABAWS -is free software which provides web services conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. -Services for multiple sequence alignment include Clustal Omega, Clustal W, -MAFFT, MUSCLE, -TCOFFEE and PROBCONS. Analysis services allow -prediction of the protein secondary structure with Jpred and protein disorder with DisEMBL, -IUPred, Jronn (a Java implementation of Ronn by P. Troshin and G. Barton, unpublished), -and GlobPlot; and calculation of amino acid alignment conservation with AACon. The -secondary structure for an RNA aligment can be predicted with the RNAalifold program from the Vienna RNA package. -

- -JABA 2.1 Web Services installations can be accessed from the Jalview desktop application (version 2.8 onwards) -and the JABAWS command-line client, and provide multiple alignment -and sequence analysis calculations limited only by your own computing resources.
+

+JABAWS +is free software which provides web services conveniently +packaged to run on your local computer, server, cluster or Amazon EC2 instance. +

+ +

Services for multiple sequence alignment include +Clustal Omega, +Clustal W, +MAFFT, +MUSCLE, +T-Coffee, +ProbCons, +MSAProbs, and +GLProbs. +Analysis services allow prediction of the protein secondary structure with +Jpred and protein disorder with +DisEMBL, +IUPred, +Jronn (a Java implementation of Ronn by P. Troshin and G. Barton, unpublished), and +GlobPlot; and calculation of amino acid alignment conservation +with AACon. +The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the +Vienna RNA package. +

+ +

+JABAWS 2.1 installation can be accessed from the Jalview desktop +application (version 2.8 onwards) and the JABAWS command-line client. +JABAWS 2.1 is able to provide multiple alignment and sequence analysis calculations limited only by your own +computing resources.

+
@@ -105,7 +125,7 @@ Check out the quick start guide for furt

Public JABAWS Server

-

You can access our public JABA Web Services with our command line client, +

You can access our public JABAWS web services with our command line client, Jalview, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2.1. The latest versions of Jalview are configured to use public JABAWS server by default.

    @@ -117,12 +137,22 @@ title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=

    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.

    + + +

    Previous versions of JABAWS

    -

    We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and - contains some important bug fixes. Please consult the manual for more information - on compatibility between versions.

    Should you require them, however, old versions of JABAWS are available here:

    +

    +We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and contains +some important bug fixes. Please consult the manual +for more information on compatibility between versions.

    Should you require them, however, old versions of JABAWS are available here:

    + + + +

    Reference

    Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for diff --git a/website/jabaws_funding.html b/website/jabaws_funding.html index af9aac1..27c009c 100644 --- a/website/jabaws_funding.html +++ b/website/jabaws_funding.html @@ -1,12 +1,12 @@ - + Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual - + + @@ -14,30 +14,29 @@

@@ -66,7 +82,7 @@ and sequence analysis calculations limited only by your own computing resources. The Server: JABAWS Virtual Appliance: (440M) or JABAWS on Amazon Webservices Cloud
The Main Client: Jalview (18M) -

To use JABA Web Services on most operating systems, just download and install +

To use JABAWS 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!

@@ -76,9 +92,13 @@ and sequence analysis calculations limited only by your own computing resources.

For System Administrators

-

The Server: 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.

+

+ The Server: 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. +

- - - - - + + + + +
JABAWS-2.1Disorder
JABAWS-2.1Disorder
-
-
Home - Getting Started - Manual - Download - Usage Statistics - Services Status - Contact Us - Barton Group - Funding + -

JABAWS FUNDING

@@ -54,12 +53,14 @@ Geoff Barton. Further support comes from Wellcome Trust Strategic Grant: 100476. - - - + + + +
-
ENFIN
Wellcome Trust
SULSA
ENFINWellcome TrustSULSA
+

+

diff --git a/website/man_about.html b/website/man_about.html index 2c72efc..9304cb9 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -1,13 +1,13 @@ - + -Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual - - +Java Bioinformatics Analyses Web Services (JABAWS): Manual + + + @@ -18,7 +18,7 @@ - +
JABAWS-2.1JABAWS-2.1 Disorder
@@ -27,26 +27,23 @@
-
Home - Getting Started - Manual - - Download - Usage Statistics - Services Status - Contact Us - Barton Group - Funding + @@ -105,12 +102,14 @@

JABAWS currently provides access to the following programs:

Multiple Sequence Alignement

Protein Secondary structure prediction

    @@ -133,14 +132,37 @@
  • RNAalifold from ViennaRNA (2.0)
-All these codes including Jronn and AAcon are available at the Download section (registration is required). +All these codes including Jronn and AAcon are available at the Download +section (registration is required). -

What is new in JABAWS 2.1?

-JABAWS Version 2.1 (Released 1st Oct 2013)

JABAWS 2.1 includes several bug fixes and minor updates for JABAWS Version 2.0. These are listed below:

+ + +

What is new in JABAWS 2.1?

+JABAWS Version 2.1 (Released 1st Oct 2013) +

Several new web services are available in this version of JABAWS:

+
    +
  • Two multiple sequence aligners: MSAprobs and GLprobs. Both services return the standard Alignment object
    • +
  • RNAalifoldWS returns RNAStructScoreManager which is the standard ScoreManager objects with several additional methods.
    • +
  • + JpredWS returns the JpredAligment object which is the standard Alignment with additional methods for extracting + Jpred predictions. These predictions are supplied as additional sequences in the aligment. +
    • +
+ +

Some bugs have been fixed and several improvements have been done:

+
    +
  • WS status servlet returns version and some additional information on each web service
    • +
  • a bug with path to help in the client
    • +
  • Fix two bug with the Google Analytics library: no-stop due to running thread
    • +
  • GoogleAnalytics gets proper JABAWS version
    • +
+ + +JABAWS Version 2.0.1 (Released 2nd Jul 2013)

JABAWS 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2.0. These are listed below:

  • Disembl returned swapped strings for HOTLOOPS and REM465
  • Jronn failed to process jobs with more than 3 sequences
    • -
  • JABAWS could not deal with FASTA records with '>' symbols in the record identificator
    • +
  • JABAWS could not deal with FASTA records with '>' symbols in the record identificator
  • Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores in one call
  • JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties
    • diff --git a/website/man_awscloud.html b/website/man_awscloud.html index 521a5b7..ada42f4 100644 --- a/website/man_awscloud.html +++ b/website/man_awscloud.html @@ -1,50 +1,52 @@ - + + -Java Bioinformatics Analyses Web Services (JABAWS) Server Amazon Cloud Manual +Java Bioinformatics Analyses Web Services (JABAWS): Manual - + +
    + -
    -
    Home - Getting Started - Manual - - Download - Usage Statistics - Services Status - Contact Us - Barton Group - Funding + @@ -52,11 +54,6 @@

    JABAWS MANUAL

    -

    JABAWS Server in the Amazon Cloud

    -

    JABAWS on the Cloud

    We provide pre-configured JABAWS Amazon Machine Image (AMI) which you can use on the Amazon EC2 cloud. Typical use cases are

    @@ -68,7 +65,9 @@

    If you know what to do than JABAWS AMI ID is ami-d1d5e9a5, manifest 846107356395/JABAWS 2 to get you started, if not please refer to How to use JABAWS on the Amazon EC2 cloud pages.

    Alternatively you can use JABAWS on the Amazon Elastic BeanStalk. You may want to use this option to deploy JABAWS in the cluster configuration.

    +









    +
    diff --git a/website/man_awscloud_bs.html b/website/man_awscloud_bs.html index a916eab..405184c 100644 --- a/website/man_awscloud_bs.html +++ b/website/man_awscloud_bs.html @@ -1,51 +1,52 @@ - + + -Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual +Java Bioinformatics Analyses Web Services (JABAWS): Manual - + + -
    + -
    -
    Home - Getting Started - Manual - - Download - Usage Statistics - Services Status - Contact Us - Barton Group - Funding + @@ -56,18 +57,23 @@

    How to use JABAWS on Amazon Elastic Beanstalk

      -
    1. Create Amazon Web Services account.
      2. -
    2. Log in into the Amazon Web Services (AWS) console and switch to AWS Elastic Beanstalk view.
      3. - Elastic Beanstalk launch JABAWS war step 1 -
    3. Create a new Beanstalk application by uploading JABAWS war file
      4. - Elastic Beanstalk launch JABAWS war step 2 -
    4. Give a name to your JABAWS instance. This name will be a part of the access URL for your JABAWS.
      5. - Elastic Beanstalk launch JABAWS war step 3 - -
    5. Choose the type of hardware you want to run JABAWS on.
      6. -Elastic Beanstalk launch JABAWS war step 4 -
    6. If everything goes well you should be able to access your JABAWS on http://jabaws.elasticbeanstalk.com
      7. -Elastic Beanstalk launch JABAWS war +
    7. Create Amazon Web Services account. +
      8. +
    8. Log in into the Amazon Web Services (AWS) console and switch to AWS Elastic Beanstalk view. + Elastic Beanstalk launch JABAWS war step 1 +
      9. +
    9. Create a new Beanstalk application by uploading JABAWS war file: + Elastic Beanstalk launch JABAWS war step 2 +
      10. +
    10. 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 +
      11. +
    11. Choose the type of hardware you want to run JABAWS on. + Elastic Beanstalk launch JABAWS war step 4 +
      12. +
    12. If everything goes well you should be able to access your JABAWS on http://jabaws.elasticbeanstalk.com + Elastic Beanstalk launch JABAWS war +

     

    @@ -76,7 +82,6 @@
    - -
    +

The code structure

  • datamodel contains the JABAWS datamodel
    • @@ -107,107 +106,150 @@

    A client package contains only classes from data model layer and a simple web services client. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Framework exclude the web services layer. Server package contains all the code.

    Running tests

    -

    JABAWS uses TestNG framework for testing. The test results for the JABAWS package offered for download can be found here: Test Results
    -JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied with JABAWS together with an ant tasks to run the test cases.

    +

    +JABAWS uses TestNG framework for testing. The test results for the JABAWS package offered for download can be found here: +Test Results
    +JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse +which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied +with JABAWS together with an ant tasks to run the test cases.

    The best way to ensure that JABAWS framework is completely functional on your system is to run all test cases. -Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding those that depends on the cluster. -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)

    +Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support +of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding +those that depends on the cluster.

    +

    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)
      • +

    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: ant -f build.xml <test group name>

    -

    . Make sure you have Apache Ant +

    Make sure you have Apache Ant installed and path to ant executable is defined in your path environmental variable. Replace test group name with the one of the names given in the list above to run required group of tests e.g for running cluster only tests use the following command: ant -f build.xml Run_cluster_dependent_test - If you work under Linux you could use a simple script from the root folder of repository called runtests.sh This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, which you can define once for your system and then reuse.

    -

    -

    A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in test-output/testng-failed.xml. and is used in the ant task called Rerun_failed_tests. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: ant -f build.xml Rerun_failed_tests CustomTest runs the test defined in the project root directory file called temp-testng-customsuite.xml. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure.

    + If you work under Linux you could use a simple script from the root folder of repository called runtests.sh + This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, + which you can define once for your system and then reuse.

    +

    + A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in + test-output/testng-failed.xml. and is used in the ant task called + Rerun_failed_tests. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: ant -f build.xml Rerun_failed_tests CustomTest runs the test defined in the project root directory file called temp-testng-customsuite.xml. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure.

    For cluster execution make sure that the property LD_LIBRARY_PATH defined in build.xml points to cluster engine LD libraries directory in your local system.

    Preparing distributive's

    -

    There are a number of ant tasks aimed for preparing distributives for download. - Currently a few types of JABAWS packages are offered -

    Client only (contains classes required to access JABA Web Services)

    -

    Platform specific JABAWS (windows and other)

    -

    JABAWS without binaries

    -

    JABAWS framework

    -

    - Corresponding build task names are: -

    min-jaba-client

    -

    jaba-windows, jaba-complete

    -

    jaba-no-binaries

    -

    full-jaba-client

    -

    The easiest way to build all distributives is to call build-all ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory.

    -

    If you made any changes to the data model and would like to generate a complete JABAWS distro make sure you have rebuilt jaxws artifact as described below.

    +

    There are a number of ant tasks aimed for preparing distributives for download. Currently a few types of JABAWS packages are offered:

    +
      +
    1. Client only (contains classes required to access JABA Web Services)
      2. +
    2. Platform specific JABAWS (windows and other)
      3. +
    3. JABAWS without binaries
      4. +
    4. JABAWS framework
      5. +
    +

    Corresponding build task names are:

    +
      +
    1. min-jaba-client
      2. +
    2. jaba-windows, jaba-complete
      3. +
    3. jaba-no-binaries
      4. +
    4. full-jaba-client
      5. +
    +

    The easiest way to build all distributives is to call build-all ant task. + There are more tasks defined in build.xml than described here. They are mostly self explanatory.

    +

    If you made any changes to the data model and would like to generate a complete JABAWS + distro make sure you have rebuilt jaxws artifact as described below.

    Building web services artifacts

    -

    Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in webservices/compbio/ws/server/resource directory. It is not necessary to edit them if any of the JABAWS clients are used. JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible.

    +

    Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. + To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in + webservices/compbio/ws/server/resource directory. It is not necessary to + edit them if any of the JABAWS clients are used. JABAWS are the standard JAX-WS web services, which are + WS-I basic profile compatible.

    Rough guide - adding a new web service

      -
    1. Add a new executable which you'd like to wrap as a JABAWS web service to the binaries folder. If it has the source code and can be - recompiled for different platforms include it under binaries/src. - Edit binaries/src setexecutableflag.sh and compilebin.sh scripts accordingly.
      2. -
    2. Make sure that all the dependencies of the software being installed are satisfied. - If there are other binaries they should be included as well. Keep the dependent - binaries in subfolder for the main executable. Update compilebin and setexecflag
      3. - scripts accordingly.
    3. Make sure that the new executable
      4. - does not have any hard links to its dependencies, e.g. is able to run from - any installation folder and does not contain any hard coded paths. -
    4. Describe executable in conf/Exectuable.properties file. The lowercase name of the - wrapper should be included in the name of the property for example Clustal - properties all include clustal as a part of the name e.g. local.clustalw.bin. - The same property for Mafft will be called local.mafft.bin. For more help please refer to the Executable.properties file.
      5. -
    5. Describe the executable supported parameters in the <ExecutableName>Parameters.xml, presets in the <ExecutableName>Presets.xml and the execution limits in the <ExecutableName>Limit.xml. By convention these files are stored in conf/settings. All of these are optional. If the - executable does not support parameters you do not have to mention the - XXXParameter.xml file in the Executable.properties file at all. The same is true for - Presets and Limits.
      6. -
    6. Create a Java wrapper class for your executable. Create it within runner - source directory. Examples of other wrappers can be found in compbio.runner.msa - or compbio.runner.disorder packages. Wrapper should extend SkeletalExecutable<T> - implements PipedExecutable<T> if you need to pass the input or collect the - results from the standard in/out. Please see Mafft code as example. Wrapper - should expend SkeletalExecutable<T> if input/output can be set as a parameter - for an executable. Please see ClustalW code as example.
      7. -
    7. Create a testcase suit for your wrapper and run the test cases.
      8. -
    8. Create parser for the output files of your executable. Suggested location - compbio.data.sequence.SequenceUtil
      9. -
    9. Test the parser
      10. -
    10. Decide which web services interfaces your executable is going to match. - For example if the executable output can be represented as
      - SequenceAnnotation then SequenceAnnotation interface might be appropriate. - For multiple sequence alignment an Msa interface should be used.
      11. -
    11. If you find a web interface that matches your returning data type, then - implement a web service which confirms to it within a webservices source folder.
      12. -
    12. Register web service in WEB-INF/ web.xml and sun-jaxws.xml
      13. -
    13. Add generated wsdl to wsbuild.xml ant script to generate the stubs.
      14. -
    14. Run build-server task in wsbuild file. Watch for errors. If the task fails
      - that means that JAXB cannot serialize some of your new data structures. Add
      - appropriate annotations to your data types. - Also check that
      - - you do not have interfaces to serialize. JAXB cannot serialize them.
      - - you have a default no args constructor (can be private if you do not need it)
      - - JAXB cannot serialize a Map, use custom data structure instead!
      - - Enum cannot be serialized as its abstract class (do not confuse with enum
      - which is fine)
      - - Fields serialization leave a little more space for manoeuvre, so use it. If
      - you do then you can accept and return interfaces, e.g. List, Map; abstract
      - classes etc, from your methods.
      -
      - If you have the data on the server side, but nothing is coming through to the
      - client, this is a JAXB serialization problem. They tend to be very silent and
      - thus hard to debug. Check your data structure can be serialized!
      15. -
    15. Modify the client to work with your new web service. Update Services - enumeration to include new service and ensure that all the methods of this - enumeration take into account the new service. Update the client help text - (client_help.txt) and insert it into the Constraints class.
      16. -
    16. Test the web service with the client
      17. -
    17. Test on the cluster.
      18. +
    18. +

      Add a new executable which you'd like to wrap as a JABAWS web service to the binaries folder. + If it has the source code and can be recompiled for different platforms include it under + binaries/src. Edit setexecutableflag.sh + and compilebin.sh scripts in binaries/src + accordingly.

      +
    19. +

      Make sure that all the dependencies of the software being installed are satisfied. + If there are other binaries they should be included as well. Keep the dependent + binaries in a subfolder for the main executable. Update + compilebin.sh and setexecflag.sh scripts accordingly.

      +
    20. +

      Make sure that the new executable does not have any hard links to its dependencies, e.g. is able to run from + any installation folder and does not contain any hard coded paths.

      +
    21. +

      Describe executable in conf/Exectuable.properties file. The lowercase name of the wrapper should be included + in the name of the property for example Clustal properties all include clustal as a part of the name e.g. local.clustalw.bin. + The same property for MAFFT will be called local.mafft.bin. For more help please refer to the Executable.properties file.

      +
    22. +

      Describe the executable supported parameters in the + <ExecutableName>Parameters.xml, presets in the + <ExecutableName>Presets.xml and the execution limits in the + <ExecutableName>Limit.xml. By convention these files are stored + in conf/settings. All of these are optional. If the executable + does not support parameters you do not have to mention the XXXParameter.xml file + in the Executable.properties file at all. The same is true for + Presets and Limits.

      +
    23. +

      Create a Java wrapper class for your executable. Create it within runner source directory. + Examples of other wrappers can be found in compbio.runner.msa or + in other compbio.runner.* packages. Wrapper should extend + SkeletalExecutable<T> and implement + PipedExecutable<T> + if you need to pass the input or collect the results from the standard in/out. Please see Mafft + code as example. Wrapper should expend SkeletalExecutable<T> + if input/output can be set as a parameter for an executable. Please see the ClustalW code as example.

      +
    24. +

      Create a testcase suit for your wrapper in testsrc and run the test cases.

      +
    25. +

      Create parser for the output files of your executable. Suggested location + compbio.data.sequence.SequenceUtil

      +
    26. +

      Test the parser

      +
    27. +

      Decide which web services interfaces your executable is going to match. For example + if the executable output can be represented as SequenceAnnotation then SequenceAnnotation + interface might be appropriate. For multiple sequence alignment an Msa interface should be used.

      +
    28. +

      If you find a web interface that matches your returning data type, then + implement a web service which confirms to it within a webservices source folder.

      +
    29. +

      Register web service in WEB-INF/web.xml + and WEB-INF/sun-jaxws.xml

      +
    30. +

      Add generated wsdl to wsbuild.xml ant script to generate the stubs.

      +
    31. +

      Run build-server task in wsbuild file. Watch for errors. If the task fails that means + that JAXB cannot serialize some of your new data structures. Add appropriate annotations to your data types. + Also check that:

      +
        +
      • you do not have interfaces to serialize, since JAXB cannot serialize them;
        • +
      • you have a default no args constructor (can be private if you do not need it);
        • +
      • JAXB cannot serialize Java Map class, use a custom data structure instead;
        • +
      • Enum cannot be serialized as its abstract class (do not confuse with enum which is fine);
        • +
      • Fields serialization leaves a little more space for manoeuvre. + If you do this then you may accept
        and return interfaces, e.g. List, Map; abstract classes etc, from your methods. +
        • +
      +

      If you have the data on the server side, but nothing is coming through to the + client, this is a JAXB serialization problem. They tend to be very silent and + thus hard to debug. Check your data structure can be serialized!

      +
    32. +

      Modify the client to work with your new web service. Update Services + enumeration to include new service and ensure that all the methods of this + enumeration take into account the new service. Update the client help text + (client_help.txt) and insert it into the Constraints class.

      +
    33. +

      Test the web service with the client.

      +
    34. +

      Test on the cluster.

      +

     

@@ -215,7 +257,6 @@ Several testing groups are supported:
-
+