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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.

JWS-112 Updated AACon to version 1.1.

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JWS-112 Updated the versions the tool versions that are shown in the ServiceStatus page

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

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Define path to UNIREF database in conf/Executable.properties

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Comment code for future options

Remove still unsupported methods of RegistryWS

Google analytics receives message with actual Jabaws version

Bug Fixg: testing RNAalifold jobs have been considered as real ones

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Add Jabaws version string available in Services

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

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    ./server/resource/RegistryWS_schema1.xsd
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Refactoring (renaming) 2 classes: AsyncJobRunner.java -> AsyncClusterRunner.java and JobRunner.java -> ClusterRunner.java

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    ./server/SequenceAnnotationService.java
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Assign JABAService.V2_SERVICE_NAMESPACE to all new services: JpredWS, RNAalifoldWS, MSAprobsWS, GLprobsWS

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    ./server/resource/GLprobsWS.wsdl
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    ./server/resource/GLprobsWS_schema1.xsd
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    ./server/resource/JpredWS_schema1.xsd
    • -146
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    ./server/resource/MSAprobsWS.wsdl
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    ./server/resource/MSAprobsWS_schema1.xsd
    • -0
    • +149
    ./server/resource/MsaWS.wsdl
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    • +374
    ./server/resource/MsaWS_schema1.xsd
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Add all needed infrastructure for MSAprobs and GLprobs

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    ./server/GLprobsWS.java
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    ./server/MSAprobsWS.java
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    ./server/resource/ClustalWS_schema1.xsd
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    • +292
    ./server/resource/GLprobsWS.wsdl
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    • +374
    ./server/resource/GLprobsWS_schema1.xsd
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    • +292
    ./server/resource/MSAprobsWS.wsdl
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    • +374
    ./server/resource/MSAprobsWS_schema1.xsd
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    ./server/resource/MuscleWS_schema1.xsd
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    • +2
    ./server/resource/RegistryWS_schema1.xsd
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    ./server/resource/TcoffeeWS_schema1.xsd
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Refactoring: rename duplicated Util classes

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JWS-17 re-design behaviour of Option.toString

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

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    ./server/resource/ClustalWS_schema1.xsd
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    ./server/resource/DisemblWS_schema1.xsd
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    ./server/resource/GlobPlotWS_schema1.xsd
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    • +1
    ./server/resource/IUPredWS_schema1.xsd
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    ./server/resource/MuscleWS_schema1.xsd
    • -1
    • +1
    ./server/resource/RNAalifoldWS_schema1.xsd
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    • +1
    ./server/resource/TcoffeeWS_schema1.xsd
JWS-17: fix problem with undefined URL for the furtherDetails tag

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Final fixing of Jpred problem with casting

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    ./server/resource/ClustalWS_schema1.xsd
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    ./server/resource/JpredWS_schema1.xsd
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    ./server/resource/MafftWS_schema1.xsd
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    • +11
    ./server/resource/MuscleWS_schema1.xsd
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    • +11
    ./server/resource/TcoffeeWS_schema1.xsd
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Fix probem with metadata

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Clean up logging system

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Re-design the ServiceStatus JSP page

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Define proper test for JpredWS

Fix problem with wrong casting Alignment -> JpredAlignment

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

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New version of wsdl and xsd files for all services

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    ./server/resource/AAConWS_schema1.xsd
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    ./server/resource/ClustalWS.wsdl
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    ./server/resource/ClustalWS_schema1.xsd
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    ./server/resource/DisemblWS.wsdl
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    • +26
    ./server/resource/DisemblWS_schema1.xsd
    • -28
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    ./server/resource/GlobPlotWS.wsdl
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    • +26
    ./server/resource/GlobPlotWS_schema1.xsd
    • -28
    • +36
    ./server/resource/IUPredWS_schema1.xsd
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    ./server/resource/JpredWS_schema1.xsd
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    • +26
    ./server/resource/JronnWS_schema1.xsd
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Add "safe type casting" warnings

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    ./server/SequenceAnnotationService.java
Fix problem with unknown services ("forward" compatibility)

Add "safe type cast" warnings

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

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