jabaws

engine

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Tuesday 10 May
12:26 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
    • -1
    • +1
    ./compbio/engine/client/ConfExecutable.java
    • -2
    • +2
    ./compbio/engine/client/EngineUtil.java
    • -2
    • +2
    ./compbio/engine/client/Util.java
    • -2
    • +2
    ./compbio/engine/local/ExecutableWrapper.java
  5. … 1 more file in changeset.
Monday 28 Feb
12:26 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
    • -5
    • +5
    ./compbio/engine/client/ConfExecutable.java
    • -26
    • +24
    ./compbio/engine/client/EngineUtil.java
    • -26
    • +24
    ./compbio/engine/client/Util.java
    • -2
    • +4
    ./compbio/engine/local/ExecutableWrapper.java
  5. … 30 more files in changeset.
Tuesday 11 Apr 2017
5:44 pm

Fábio Madeira

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

Options
    • -0
    • +417
    ./compbio/engine/client/Util.java
    • -0
    • +100
    ./compbio/engine/cluster/drmaa/AsyncJobRunner.java
    • -0
    • +95
    ./compbio/engine/cluster/drmaa/ClusterUtil.java
    • -0
    • +395
    ./compbio/engine/cluster/drmaa/JobRunner.java
  5. … 9 more files in changeset.
Monday 14 Oct 2013
10:56 am

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Diable printing environmental variables in procInput.txt

Options
    • -0
    • +3
    ./compbio/engine/local/ExecutableWrapper.java
Thursday 26 Sep 2013
2:30 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

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

Options
    • -65
    • +35
    ./compbio/engine/Configurator.java
    • -0
    • +95
    ./compbio/engine/cluster/drmaa/AsyncClusterRunner.java
    • -98
    • +0
    ./compbio/engine/cluster/drmaa/AsyncJobRunner.java
    • -0
    • +385
    ./compbio/engine/cluster/drmaa/ClusterRunner.java
    • -57
    • +46
    ./compbio/engine/cluster/drmaa/ClusterSession.java
    • -392
    • +0
    ./compbio/engine/cluster/drmaa/JobRunner.java
    • -147
    • +151
    ./compbio/engine/local/ExecutableWrapper.java
  8. … 20 more files in changeset.
Friday 20 Sep 2013
3:32 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Refactoring: rename duplicated Util classes

Options
    • -4
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    ./compbio/engine/ClusterJobId.java
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    ./compbio/engine/Configurator.java
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    ./compbio/engine/Job.java
    • -2
    • +3
    ./compbio/engine/SubmissionManager.java
    • -6
    • +4
    ./compbio/engine/client/ConfExecutable.java
    • -0
    • +417
    ./compbio/engine/client/EngineUtil.java
    • -5
    • +1
    ./compbio/engine/client/EnvVariableProcessor.java
    • -4
    • +3
    ./compbio/engine/client/SkeletalExecutable.java
    • -417
    • +0
    ./compbio/engine/client/Util.java
    • -3
    • +3
    ./compbio/engine/cluster/drmaa/AsyncJobRunner.java
    • -0
    • +87
    ./compbio/engine/cluster/drmaa/ClusterEngineUtil.java
    • -12
    • +10
    ./compbio/engine/cluster/drmaa/ClusterSession.java
    • -95
    • +0
    ./compbio/engine/cluster/drmaa/ClusterUtil.java
    • -16
    • +13
    ./compbio/engine/cluster/drmaa/JobRunner.java
    • -4
    • +3
    ./compbio/engine/conf/DirectoryManager.java
  16. … 48 more files in changeset.
Tuesday 17 Sep 2013
11:46 am

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Remove unused imports

Options
    • -1
    • +0
    ./compbio/engine/client/ConfiguredExecutable.java
  2. … 1 more file in changeset.
11:22 am

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Clean up logging system

Options
    • -4
    • +2
    ./compbio/engine/LoadBalancer.java
    • -2
    • +1
    ./compbio/engine/client/ConfExecutable.java
    • -2
    • +1
    ./compbio/engine/conf/RunnerConfigMarshaller.java
    • -1
    • +0
    ./compbio/engine/local/ExecutableWrapper.java
  5. … 24 more files in changeset.
Thursday 08 Aug 2013
2:23 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

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

Options
    • -121
    • +121
    ./compbio/engine/local/ExecutableWrapper.java
2:23 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

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

Options
    • -121
    • +121
    ./compbio/engine/local/ExecutableWrapper.java
2:19 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Improve coding style

Options
    • -8
    • +4
    ./compbio/engine/SubmissionManager.java
    • -12
    • +6
    ./compbio/engine/client/ConfExecutable.java
    • -6
    • +4
    ./compbio/engine/cluster/drmaa/AsyncJobRunner.java
    • -10
    • +8
    ./compbio/engine/local/LocalRunner.java
2:19 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Improve coding style

Options
    • -8
    • +4
    ./compbio/engine/SubmissionManager.java
    • -12
    • +6
    ./compbio/engine/client/ConfExecutable.java
    • -6
    • +4
    ./compbio/engine/cluster/drmaa/AsyncJobRunner.java
    • -10
    • +8
    ./compbio/engine/local/LocalRunner.java
Friday 02 Aug 2013
11:41 am

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Impove coding style

Options
    • -29
    • +12
    ./compbio/engine/client/SkeletalExecutable.java
    • -9
    • +7
    ./compbio/engine/conf/PropertyHelperManager.java
  3. … 2 more files in changeset.
Monday 29 Jul 2013
12:55 pm

Sasha <Main-laptop2>

Refactoring and code style improving

Options
    • -9
    • +5
    ./compbio/engine/local/ExecutableWrapper.java
  2. … 3 more files in changeset.
Friday 14 Jun 2013
12:03 pm

Sasha <Main-laptop2>

Code for cleaning up old job directories

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    • -2
    • +4
    ./compbio/engine/Cleaner.java
    • -2
    • +1
    ./compbio/engine/local/LocalExecutorService.java
  3. … 4 more files in changeset.
Friday 26 Apr 2013
6:26 pm

Sasha <asherstnev@main-laptop2>

Delete old job directory automatically

Options
    • -11
    • +23
    ./compbio/engine/Cleaner.java
  2. … 6 more files in changeset.
6:24 pm

Sasha <asherstnev@main-laptop2>

Add new methods

Options
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    • +52
    ./compbio/engine/conf/PropertyHelperManager.java
6:23 pm

Sasha <asherstnev@main-laptop2>

re-formatting code

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    • -14
    • +9
    ./compbio/engine/Configurator.java
Wednesday 06 Jun 2012
7:02 pm

jprocter <jprocter@compbio.dundee.ac.uk>

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

Options
    • -1
    • +12
    ./compbio/engine/client/PathValidator.java
Tuesday 15 May 2012
4:55 pm

jprocter <jprocter@compbio.dundee.ac.uk>

remove jabaws 3 development code

Options
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    ./compbio/engine/cluster/drmaa/_DrmaaExample.java
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    • +0
    ./compbio/engine/cluster/drmaa/_JobStatus.java
    • -152
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    ./compbio/engine/cluster/dundee/_Queue.java
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    ./compbio/engine/cluster/dundee/_QueueConstraints.java
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    ./compbio/engine/conf/_Key.java
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    • +0
    ./compbio/engine/local/_TrackingExecutor.java
  7. … 39 more files in changeset.
Tuesday 11 Oct 2011
12:37 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

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

Options
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    • +3
    ./compbio/engine/conf/PropertyHelperManager.java
  2. … 12 more files in changeset.
Thursday 25 Aug 2011
4:46 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

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

Options
    • -0
    • +10
    ./compbio/engine/client/Util.java
Friday 12 Aug 2011
2:35 pm

pvtroshin <pvtroshin@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

Options
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    ./compbio/engine/Cleaner.java
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    ./compbio/engine/FilePuller.java
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    ./compbio/engine/PulledFileCache.java
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    ./compbio/engine/client/CommandBuilder.java
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    ./compbio/engine/client/ConfExecutable.java
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    ./compbio/engine/client/PathValidator.java
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    ./compbio/engine/client/PipedExecutable.java
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    ./compbio/engine/client/Util.java
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    ./compbio/engine/cluster/drmaa/AsyncJobRunner.java
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    ./compbio/engine/cluster/drmaa/ClusterSession.java
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    ./compbio/engine/cluster/drmaa/_DrmaaExample.java
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    • +1
    ./compbio/engine/cluster/drmaa/_JobStatus.java
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    ./compbio/engine/cluster/dundee/_Queue.java
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    ./compbio/engine/cluster/dundee/_QueueConstraints.java
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    • +4
    ./compbio/engine/conf/PropertyHelperManager.java
  16. … 17 more files in changeset.
Wednesday 06 Jul 2011
11:56 am

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

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

Options
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    • +10
    ./compbio/engine/client/Util.java
  2. … 3 more files in changeset.
Friday 01 Jul 2011
10:41 am

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

remove assert

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

Options
    • -1
    • +0
    ./compbio/engine/client/Util.java
Thursday 30 Jun 2011
6:22 pm

pvtroshin <pvtroshin@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

Options
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    • +61
    ./compbio/engine/client/Util.java
  2. … 3 more files in changeset.
Thursday 23 Jun 2011
3:15 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

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

Options
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    • +10
    ./compbio/engine/conf/PropertyHelperManager.java
  2. … 3 more files in changeset.
Wednesday 22 Jun 2011
6:11 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Fix for testcases

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

Options
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    ./compbio/engine/client/EnvVariableProcessor.java
    • -1
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    ./compbio/engine/client/PathValidator.java
  3. … 10 more files in changeset.
Tuesday 21 Jun 2011
1:06 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

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

Options
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    ./compbio/engine/client/ClusterNativeSpecExecutable.java
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    ./compbio/engine/client/ConfExecutable.java
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    ./compbio/engine/client/Executable.java
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    ./compbio/engine/client/SkeletalExecutable.java
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    ./compbio/engine/cluster/drmaa/JobRunner.java
  6. … 5 more files in changeset.
Friday 17 Jun 2011
3:06 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

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

Options
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    ./compbio/engine/client/EnvVariableProcessor.java
  2. … 47 more files in changeset.