jabaws/webservices/compbio/ws

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Friday 26 May 2017
5:19 pm

Fábio Madeira

JWS-120 Fixes the exception raised by the ChunkHolder method in GenericMetadataService. This behavior was expected for services which do not support execution statistics. This solution was found in the compbio.ws.server.JronnWS.java.

Options
    • -0
    • +11
    ./DisemblWS.java
    • -0
    • +11
    ./GlobPlotWS.java
    • -0
    • +11
    ./IUPredWS.java
Tuesday 28 Feb 2017
12:21 pm

Fábio Madeira

JWS-113 Commented Jpred entries in the datamodel, runner and webservices java source code.

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    • -151
    • +151
    ./JpredWS.java
    • -18
    • +18
    ./WSUtil.java
  3. … 13 more files in changeset.
Monday 30 Sep 2013
2:30 pm

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

Google analytics receives message with actual Jabaws version

Options
    • -2
    • +4
    ./GAUtils.java
2:26 pm

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

Roll back some changes in WSDL of RegistryWS for some time: restore back compatibility

Options
    • -2
    • +2
    ./RegistryWS.java
    • -19
    • +0
    ./resource/RegistryWS.wsdl
    • -14
    • +0
    ./resource/RegistryWS_schema1.xsd
  4. … 1 more file in changeset.
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
    • -14
    • +7
    ./MafftWS.java
    • -6
    • +3
    ./SequenceAnnotationService.java
    • -3
    • +4
    ./WSUtil.java
  4. … 24 more files in changeset.
Tuesday 24 Sep 2013
5:35 pm

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

Assign JABAService.V2_SERVICE_NAMESPACE to all new services: JpredWS, RNAalifoldWS, MSAprobsWS, GLprobsWS

Options
    • -1
    • +1
    ./ClustalOWS.java
    • -1
    • +1
    ./GLprobsWS.java
    • -1
    • +1
    ./JpredWS.java
    • -1
    • +1
    ./MSAprobsWS.java
    • -146
    • +3
    ./resource/GLprobsWS.wsdl
    • -374
    • +0
    ./resource/GLprobsWS_schema1.xsd
    • -146
    • +3
    ./resource/JpredWS.wsdl
    • -374
    • +0
    ./resource/JpredWS_schema1.xsd
    • -146
    • +3
    ./resource/MSAprobsWS.wsdl
    • -374
    • +0
    ./resource/MSAprobsWS_schema1.xsd
    • -0
    • +149
    ./resource/MsaWS.wsdl
    • -0
    • +374
    ./resource/MsaWS_schema1.xsd
  13. … 2 more files in changeset.
3:11 pm

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

Add all needed infrastructure for MSAprobs and GLprobs

Options
    • -0
    • +157
    ./GLprobsWS.java
    • -0
    • +157
    ./MSAprobsWS.java
    • -0
    • +2
    ./resource/ClustalWS_schema1.xsd
    • -0
    • +292
    ./resource/GLprobsWS.wsdl
    • -0
    • +374
    ./resource/GLprobsWS_schema1.xsd
    • -0
    • +2
    ./resource/JpredWS_schema1.xsd
    • -0
    • +292
    ./resource/MSAprobsWS.wsdl
    • -0
    • +374
    ./resource/MSAprobsWS_schema1.xsd
    • -0
    • +2
    ./resource/MafftWS_schema1.xsd
    • -0
    • +2
    ./resource/MuscleWS_schema1.xsd
    • -0
    • +2
    ./resource/RegistryWS_schema1.xsd
    • -0
    • +2
    ./resource/TcoffeeWS_schema1.xsd
  13. … 23 more files in changeset.
Friday 20 Sep 2013
3:32 pm

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

Refactoring: rename duplicated Util classes

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    • -7
    • +5
    ./ClustalOWS.java
    • -7
    • +5
    ./ClustalWS.java
    • -5
    • +14
    ./GAUtils.java
    • -4
    • +5
    ./GenericMetadataService.java
    • -4
    • +5
    ./JpredWS.java
    • -10
    • +5
    ./MafftWS.java
    • -1
    • +2
    ./MainManager.java
    • -12
    • +6
    ./MuscleWS.java
    • -3
    • +4
    ./ProbconsWS.java
    • -3
    • +3
    ./SetExecutableFlag.java
    • -7
    • +5
    ./TcoffeeWS.java
    • -14
    • +9
    ./WSUtil.java
  13. … 51 more files in changeset.
Thursday 19 Sep 2013
1:47 pm

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

Re-generate WS artefacts: option.furtherDetails is xs:string now

Options
    • -1
    • +1
    ./resource/AAConWS_schema1.xsd
    • -1
    • +1
    ./resource/ClustalWS_schema1.xsd
    • -1
    • +1
    ./resource/DisemblWS_schema1.xsd
    • -1
    • +1
    ./resource/GlobPlotWS_schema1.xsd
    • -1
    • +1
    ./resource/IUPredWS_schema1.xsd
    • -1
    • +1
    ./resource/JpredWS_schema1.xsd
    • -1
    • +1
    ./resource/JronnWS_schema1.xsd
    • -1
    • +1
    ./resource/MafftWS_schema1.xsd
    • -1
    • +1
    ./resource/MuscleWS_schema1.xsd
    • -1
    • +1
    ./resource/RNAalifoldWS_schema1.xsd
    • -1
    • +1
    ./resource/TcoffeeWS_schema1.xsd
Tuesday 17 Sep 2013
3:35 pm

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

Final fixing of Jpred problem with casting

Options
    • -2
    • +11
    ./resource/ClustalWS_schema1.xsd
    • -2
    • +11
    ./resource/JpredWS_schema1.xsd
    • -2
    • +11
    ./resource/MafftWS_schema1.xsd
    • -2
    • +11
    ./resource/MuscleWS_schema1.xsd
    • -2
    • +11
    ./resource/TcoffeeWS_schema1.xsd
  6. … 3 more files in changeset.
3:20 pm

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

Fix probem with metadata

Options
    • -27
    • +14
    ./ClustalOWS.java
    • -23
    • +13
    ./ClustalWS.java
    • -1
    • +0
    ./JpredWS.java
    • -9
    • +7
    ./MafftWS.java
    • -2
    • +2
    ./MuscleWS.java
    • -2
    • +2
    ./ProbconsWS.java
    • -12
    • +7
    ./TcoffeeWS.java
  8. … 1 more file in changeset.
11:22 am

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

Clean up logging system

Options
    • -4
    • +2
    ./GAUtils.java
    • -43
    • +3
    ./WSUtil.java
  3. … 26 more files in changeset.
Wednesday 11 Sep 2013
5:13 pm

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

Fix problem with the JpredWS service. Now Jws2Client is able to test the service

Options
    • -1
    • +2
    ./JpredWS.java
  2. … 3 more files in changeset.
Tuesday 10 Sep 2013
4:09 pm

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

New version of wsdl and xsd files for all services

Options
    • -28
    • +28
    ./resource/AAConWS.wsdl
    • -18
    • +26
    ./resource/AAConWS_schema1.xsd
    • -28
    • +28
    ./resource/ClustalWS.wsdl
    • -28
    • +28
    ./resource/ClustalWS_schema1.xsd
    • -28
    • +28
    ./resource/DisemblWS.wsdl
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    • +26
    ./resource/DisemblWS_schema1.xsd
    • -28
    • +28
    ./resource/GlobPlotWS.wsdl
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    • +26
    ./resource/GlobPlotWS_schema1.xsd
    • -28
    • +28
    ./resource/IUPredWS.wsdl
    • -28
    • +36
    ./resource/IUPredWS_schema1.xsd
    • -28
    • +28
    ./resource/JpredWS.wsdl
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    ./resource/JpredWS_schema1.xsd
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    • +28
    ./resource/JronnWS.wsdl
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    • +26
    ./resource/JronnWS_schema1.xsd
    • -28
    • +28
    ./resource/MafftWS.wsdl
  16. … 9 more files in changeset.
4:06 pm

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

Add "safe type casting" warnings

Options
    • -5
    • +6
    ./SequenceAnnotationService.java
4:02 pm

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

Add "safe type cast" warnings

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    • -13
    • +6
    ./RNAalifoldWS.java
Friday 06 Sep 2013
5:23 pm

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

Merge branch 'JABAWS_Release_2_5' into develop

Conflicts:

.project

WEB-INF/sun-jaxws.xml

conf/Executable.properties

testsrc/compbio/data/sequence/SequenceUtilTester.java

webservices/compbio/data/msa/Category.java

webservices/compbio/ws/client/Jws2Client.java

webservices/compbio/ws/client/Services.java

webservices/compbio/ws/client/WSTester.java

webservices/compbio/ws/server/WSUtil.java

webservices/compbio/ws/server/resource/AAConWS.wsdl

webservices/compbio/ws/server/resource/AAConWS_schema1.xsd

webservices/compbio/ws/server/resource/ClustalWS.wsdl

webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd

webservices/compbio/ws/server/resource/DisemblWS.wsdl

webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd

webservices/compbio/ws/server/resource/GlobPlotWS.wsdl

webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd

webservices/compbio/ws/server/resource/IUPredWS.wsdl

webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd

webservices/compbio/ws/server/resource/JronnWS.wsdl

webservices/compbio/ws/server/resource/JronnWS_schema1.xsd

webservices/compbio/ws/server/resource/MafftWS.wsdl

webservices/compbio/ws/server/resource/MafftWS_schema1.xsd

webservices/compbio/ws/server/resource/MuscleWS.wsdl

webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd

webservices/compbio/ws/server/resource/RegistryWS.wsdl

webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd

webservices/compbio/ws/server/resource/TcoffeeWS.wsdl

webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd

wsbuild.xml

Options
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    • +23
    ./WSUtil.java
  2. … 11 more files in changeset.
4:26 pm

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

Regenerate wsdl-s

Options
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    • +34
    ./resource/AAConWS.wsdl
    • -19
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    ./resource/AAConWS_schema1.xsd
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    ./resource/ClustalWS.wsdl
    • -22
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    ./resource/ClustalWS_schema1.xsd
    • -34
    • +34
    ./resource/DisemblWS.wsdl
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    ./resource/DisemblWS_schema1.xsd
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    ./resource/GlobPlotWS.wsdl
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    ./resource/GlobPlotWS_schema1.xsd
    • -34
    • +34
    ./resource/IUPredWS.wsdl
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    ./resource/IUPredWS_schema1.xsd
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    • +102
    ./resource/JpredWS.wsdl
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    ./resource/JpredWS_schema1.xsd
    • -34
    • +34
    ./resource/JronnWS.wsdl
    • -19
    • +19
    ./resource/JronnWS_schema1.xsd
    • -55
    • +55
    ./resource/MafftWS.wsdl
  16. … 7 more files in changeset.
4:25 pm

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

Switch to olde namespace

Options
    • -1
    • +1
    ./ClustalOWS.java
    • -6
    • +4
    ./JpredWS.java
4:25 pm

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

Different code style

Options
    • -18
    • +10
    ./ProbconsWS.java
3:29 pm

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

Switch JpredWS from SequenceAnnotation to MsaWS

Options
    • -30
    • +113
    ./JpredWS.java
  2. … 6 more files in changeset.
Thursday 05 Sep 2013
11:20 am

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

Roll back JpredWS JABAWS namespace: from V3 to V2. V3 will be a Matrix

Options
    • -1
    • +1
    ./JpredWS.java
    • -13
    • +13
    ./resource/RegistryWS.wsdl
  3. … 2 more files in changeset.
11:07 am

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

Change JAXWS java code and wsdl for changed methods in RegistryWS

Options
    • -0
    • +19
    ./resource/RegistryWS.wsdl
  2. … 2 more files in changeset.
10:52 am

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

Other necessary changes

Options
    • -2
    • +1
    ./JpredWS.java
    • -1
    • +0
    ./WSUtil.java
    • -0
    • +14
    ./resource/RegistryWS_schema1.xsd
  4. … 1 more file in changeset.
10:47 am

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

report both operating and non-operating services

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    • -7
    • +13
    ./RegistryWS.java
Saturday 31 Aug 2013
11:54 am

Daniel Barton

Parameter bug fixed, Jalview will now run some parameters

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    • -1
    • +1
    ./RNAalifoldWS.java
    • -2
    • +0
    ./WSUtil.java
  3. … 4 more files in changeset.
Friday 30 Aug 2013
10:57 am

Daniel Barton

Clean-up, refactoring, commenting. Parameters file containts only options since Jalview still can't deal with them

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    • -3
    • +1
    ./RNAalifoldWS.java
    • -25
    • +4
    ./WSUtil.java
  3. … 13 more files in changeset.
Thursday 22 Aug 2013
6:03 pm

Daniel Barton

WSTester updated to work plus hopefully all the other changes that need to go into the remote.

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    ./resource/AAConWS.wsdl
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    ./resource/AAConWS_schema1.xsd
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    ./resource/ClustalWS.wsdl
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    ./resource/ClustalWS_schema1.xsd
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    ./resource/DisemblWS.wsdl
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    ./resource/DisemblWS_schema1.xsd
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    ./resource/GlobPlotWS.wsdl
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    ./resource/GlobPlotWS_schema1.xsd
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    ./resource/IUPredWS.wsdl
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    ./resource/IUPredWS_schema1.xsd
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    ./resource/JronnWS.wsdl
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    ./resource/JronnWS_schema1.xsd
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    ./resource/MafftWS.wsdl
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    ./resource/MafftWS_schema1.xsd
    • -66
    • +66
    ./resource/MuscleWS.wsdl
  16. … 1295 more files in changeset.
2:00 pm

Daniel Barton

Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added to ScoreManager.

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    • -11
    • +2
    ./RNAalifoldWS.java
    • -1
    • +2
    ./WSUtil.java
  3. … 24 more files in changeset.
Wednesday 21 Aug 2013
12:27 pm

Daniel Barton

Reverted some testing changes in TestRNAalifoldWS so that it will run successfully.

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    • +40
    ./RNAalifoldWS.java
  2. … 1 more file in changeset.