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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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    /compbio-utils/compbio/util/FileUtil.java
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    /engine/compbio/engine/client/Util.java
JWS-128 compbio-utils sources added to compilation tree and log4j logging dependence removed

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    /.settings/org.eclipse.wst.common.component
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    /compbio-utils/compbio/util/FileParser.java
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    /compbio-utils/compbio/util/FileUtil.java
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    /compbio-utils/compbio/util/FileWatcher.java
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    /compbio-utils/compbio/util/Grep.java
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    /compbio-utils/compbio/util/Gzip.java
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    /compbio-utils/compbio/util/NullOutputStream.java
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    /compbio-utils/compbio/util/PropertyHelper.java
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    /compbio-utils/compbio/util/SysPrefs.java
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    /compbio-utils/compbio/util/Timer.java
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    /compbio-utils/compbio/util/Util.java
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    /compbio-utils/compbio/util/log4j.properties
  1. … 19 more files in changeset.
Patch log config

Minimal log4j->log4j2 config properties - some of these are not used in JABAWS 2

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    /log/log4j2.dundee.properties
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    /log/log4j2.properties
Additional sphinx-generated stuff for website

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    /website/docs/_static/documentation_options.js
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    /website/docs/_static/jquery-3.5.1.js
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    /website/docs/_static/language_data.js
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    /website/docs/_static/underscore-1.13.1.js
Updated logging config for statdb task during build

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    /log/log4j.statdb.properties
Classpath for eclipse project

Update changelog and rebuild docs

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    /website/docs/_sources/changelog.rst.txt
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    /website/docs/_static/basic.css
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    /website/docs/_static/doctools.js
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    /website/docs/_static/searchtools.js
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    /website/docs/_static/underscore.js
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    /website/docs/advanced.html
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    /website/docs/develop.html
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Version bump and additional authors

Log4j2 property for config file

upgrade log4j to 2.16.0 - patched against log4shell

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    /WEB-INF/lib/log4j-1.2-api-2.16.0.jar
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    /WEB-INF/lib/log4j-api-2.16.0.jar
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    /WEB-INF/lib/log4j-core-2.16.0.jar
Updated the Jabaws 2.2 reference and bumped the date

JWS-114 Bumped the version of the webservices 'JABAWS_VERSION' to 2.2.

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    /webservices/compbio/data/msa/JABAService.java
JWS-109 & JWS-116 Bumped the release date and fixed the text regarding the Elixir-UK.

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    /website/docs/_sources/changelog.rst.txt
JWS-112 Uploaded a new aacon jar, following a minor update made to AAcon's output format.

JWS-122 & JWS-116 New documentation entry with instructions on how to use the JABAWS Docker image and new built html pages.

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    /docs/v_2_2_0/docker.rst
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    /website/docs/_sources/changelog.rst.txt
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    /website/docs/_sources/docker.rst.txt
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JWS-122 & JWS-109 Minor updates to the homepage to point out new Docker support and bump date.

JWS-122 Added a Dockerfile and some container image specific Executable.properties.

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    /docker/Executable.properties
JWS-121 Minor bug fix on the timeexec - wrong units.

JWS-109 & JWS-116 Added the new chaching as new entries to index.jsp and the docs’ changelog. Also bumped the release/update dates.

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    /website/docs/_sources/changelog.rst.txt
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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    /webservices/compbio/stat/servlet/AnnualStatRefresher.java
JWS-121 & JWS-109 Service Status now gives an indication of the health of service. Fixed the links to the Service Status and Usage Statistics pages. Also removed now unecessary files.

JWS-121 Improved the AnnualStat and ServiceStatus classes so they start the scheduler in the init() method and refresh the in memory cache every X minutes. The number of minutes is defined in the Engine.local.properties config. In memory values are cached in the ServletContext.

JWS-121 Added new scheduler utility classes so that usage statistics and service status can be monitored in a cronjob-like manner. RefreshIterator implements a ScheduleIterator that runs a new task every X minutes.

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    /webservices/compbio/stat/servlet/util/RefreshIterator.java
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    /webservices/compbio/stat/servlet/util/Scheduler.java
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    /webservices/compbio/stat/servlet/util/SchedulerTask.java
JWS-110 Commented out the servlet entries for the Download redirects no longer needed.

JWS-121 & JWS-109 Improved the way the service_status.jsp and usage_statistics.jsp work to load cached htmls or to redirect on error (i.e. missing cached htmls). This is a very hacky temporary solution. The provided script can be used to refresh the cached htmls every x minutes.

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    /website/refresh_service_status.sh
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    /website/statpages/MonthlySummary.jsp
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    /website/statpages/ServicesStatus.jsp
JWS-121 & JWS-111 Adding ‘timestamp’ (string formatted date + time) to the HttpServletRequest to be used in the jsp and setting ‘timexec’ as seconds instead of millisecs.

JWS-121 Added new jsp enpoints that try loading chached service status and usage statistics pages. If not available there is a redirect to the main endpoints. Also fixed the header and footer links to match the new endpoints.

JWS-109 Some minor fixes for broken links and missing space.

JWS-119 & JWS-109 Fixed the relative paths to the documentation pages and bumped the date.