WEB-INF

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

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upgrade log4j to 2.16.0 - patched against log4shell

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    ./lib/log4j-1.2-api-2.16.0.jar
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    ./lib/log4j-api-2.16.0.jar
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    ./lib/log4j-core-2.16.0.jar
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this looks like the same pattern of scheduler settings as in ServiceStatus - if you wanted to be more Java-ish, you'd have a generic ScheduledEventAttribute class that manipulated a given servlet c...

this looks like the same pattern of scheduler settings as in ServiceStatus - if you wanted to be more Java-ish, you'd have a generic ScheduledEventAttribute class that manipulated a given servlet context's attributes to create/update these stats

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JWS-121: Service status and usage statistics show cached results for faster loads
JWS-121: Service status and usage statistics show cached results for faster loads
JWS-121 Added new refresher methods and the respective servlets and mappings entries in web.xml. These are used to update the ServletContext values as an input from the user (clickable links) that point to the new endpoints.

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JWS-110 Commented out the servlet entries for the Download redirects no longer needed.

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

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    ./classes/lib/testng-5.10-jdk15.jar
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    ./classes/log4j.properties.dundee
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    ./classes/log4j.properties.full
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    ./classes/log4j.properties.statdb
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JWS-113 Commented Jpred entries in various configuration files.

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Add all needed infrastructure for MSAprobs and GLprobs

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Remove un-necessary Axis servlets

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

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Prepare JABAWS for generation of wsdl for Jpred

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Add untracked dir

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    ./classes/log4j.properties
Add untracked dir

Update GoogleAnalytics jar. bug fixed: tomcat did not stop after shutdown due to problem in the jar

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    ./lib/compbio-ga-1.1.jar
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update derby.jar and add version number to the library

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    ./lib/derby-10.8.2.2.jar
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Code for cleaning up old job directories

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Re-formatting files

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JWS-55 temporary fix for wrong security configuration

web pages updates to point to new download location also the redirect servlet

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4788 e3abac25-378b-4346-85de-24260fe3988d

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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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    ./lib/compbio-ga-1.0.jar
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allow head method for all jabaws servlets

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4590 e3abac25-378b-4346-85de-24260fe3988d

comment out services checkers from the security constrain

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4574 e3abac25-378b-4346-85de-24260fe3988d

Web services status checking servlets, new clustalo x32 binary from Fabian, other small changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4571 e3abac25-378b-4346-85de-24260fe3988d

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Adding listener for setting executable flag on the web application start up

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4563 e3abac25-378b-4346-85de-24260fe3988d

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ClustalO servlets

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4469 e3abac25-378b-4346-85de-24260fe3988d

Add servlet for public usage stats display.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4384 e3abac25-378b-4346-85de-24260fe3988d

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Build script improvements & updated util

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4337 e3abac25-378b-4346-85de-24260fe3988d

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