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JWS-128 patch out log4j references in the compbio.FileUtil class, and corresponding calls to methods in the JABAWS client and engine code.

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JWS-128 compbio-utils sources added to compilation tree and log4j logging dependence removed

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JWS-114 Bumping varied config files and jetbrains xmls. Also adding some java classes that are generated during the compilation.

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    ./client/Util.java
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    ./cluster/drmaa/AsyncJobRunner.java
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    ./cluster/drmaa/ClusterUtil.java
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    ./cluster/drmaa/JobRunner.java
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Diable printing environmental variables in procInput.txt

Refactoring (renaming) 2 classes: AsyncJobRunner.java -> AsyncClusterRunner.java and JobRunner.java -> ClusterRunner.java

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    ./cluster/drmaa/AsyncClusterRunner.java
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    ./cluster/drmaa/AsyncJobRunner.java
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    ./cluster/drmaa/ClusterRunner.java
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    ./cluster/drmaa/ClusterSession.java
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    ./local/ExecutableWrapper.java
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Refactoring: rename duplicated Util classes

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    ./client/EngineUtil.java
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    ./cluster/drmaa/ClusterEngineUtil.java
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    ./cluster/drmaa/ClusterSession.java
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Remove unused imports

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Clean up logging system

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Add a file with the runnig command and environment in each wrok dir

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    ./local/ExecutableWrapper.java
Add a file with the runnig command and environment in each wrok dir

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    ./local/ExecutableWrapper.java
Improve coding style

Improve coding style

Impove coding style

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    ./client/SkeletalExecutable.java
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Refactoring and code style improving

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Code for cleaning up old job directories

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Delete old job directory automatically

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Add new methods

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    ./conf/PropertyHelperManager.java
re-formatting code

JWS-44 - attempt to make a file executable if it is supposed to be executable according to jabaws configuration.

remove jabaws 3 development code

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    ./cluster/drmaa/_DrmaaExample.java
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    ./cluster/dundee/_QueueConstraints.java
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Google Analytics statistics is added

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4651 e3abac25-378b-4346-85de-24260fe3988d

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An attempt to automatically make binaries executables - not successful but the code is commented out and let in for future use

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4548 e3abac25-378b-4346-85de-24260fe3988d

Javadoc fixes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4508 e3abac25-378b-4346-85de-24260fe3988d

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    ./cluster/drmaa/ClusterSession.java
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    ./cluster/dundee/_QueueConstraints.java
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Better method for searching JAVA

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4392 e3abac25-378b-4346-85de-24260fe3988d

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remove assert

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4378 e3abac25-378b-4346-85de-24260fe3988d

obtain JAVA executable path from the JAVA_HOME variable. Does not require path to java for jar libraries.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4376 e3abac25-378b-4346-85de-24260fe3988d

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update to compbio.utils and a few small changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4327 e3abac25-378b-4346-85de-24260fe3988d

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Fix for testcases

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4307 e3abac25-378b-4346-85de-24260fe3988d

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Get rind of NativeClusterJob interface as pretty much every jobs best to use some cluster settings, and they are simply defined in the executable conf file and passed by the SkeletalExecutable.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4294 e3abac25-378b-4346-85de-24260fe3988d

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    ./client/ClusterNativeSpecExecutable.java
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Refactoring of all SequenceAnnotation web services New version of Metro Definition for IUPred exec Stubs regenerated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4280 e3abac25-378b-4346-85de-24260fe3988d

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