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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
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    /compbio-utils/compbio/util/FileUtil.java
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    /engine/compbio/engine/client/ConfExecutable.java
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    /engine/compbio/engine/client/EngineUtil.java
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    /engine/compbio/engine/client/Util.java
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    /engine/compbio/engine/local/ExecutableWrapper.java
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
    • -3
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    /.classpath
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    /.settings/org.eclipse.wst.common.component
    • binary
    /WEB-INF/lib/compbio-util-1.4.jar
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    /build.xml
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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
  16. … 19 more files in changeset.
Monday 20 Dec 2021
5:34 pm

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

Patch log config

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    /log/log4j2.dundee.properties
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    /log/log4j2.properties
Friday 17 Dec 2021
5:25 pm

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

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

Options
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    /build.xml
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    /log/log4j.properties
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    /log/log4j.properties.dundee
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    /log/log4j2.dundee.properties
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    /log/log4j2.properties
5:11 pm

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

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
5:09 pm

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

Updated logging config for statdb task during build

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    /build.xml
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    /log/log4j.properties.statdb
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    • +35
    /log/log4j.statdb.properties
5:07 pm

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

Classpath for eclipse project

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    /.classpath
5:06 pm

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

Update changelog and rebuild docs

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    /docs/v_2_2_0/changelog.rst
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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/jquery.js
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    /website/docs/_static/pygments.css
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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/changelog.html
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    /website/docs/citations.html
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    /website/docs/client.html
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    /website/docs/develop.html
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    /website/docs/docker.html
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    /website/docs/genindex.html
  16. … 13 more files in changeset.
11:21 am

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

Version bump and additional authors

Options
    • -2
    • +2
    /build.xml
11:21 am

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

Log4j2 property for config file

Options
    • -1
    • +1
    /build.xml
Wednesday 15 Dec 2021
12:22 pm

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

upgrade log4j to 2.16.0 - patched against log4shell

Options
    • binary
    /WEB-INF/lib/log4j-1.2-api-2.16.0.jar
    • binary
    /WEB-INF/lib/log4j-1.2.15.jar
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    /WEB-INF/lib/log4j-api-2.16.0.jar
    • binary
    /WEB-INF/lib/log4j-core-2.16.0.jar
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    /build.xml
Tuesday 27 Mar 2018
10:07 am

Fábio Madeira

Updated the Jabaws 2.2 reference and bumped the date

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    /website/index.jsp
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    /website/template_footer.jsp
Friday 18 Aug 2017
5:18 pm

Fábio Madeira

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

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    /webservices/compbio/data/msa/JABAService.java
3:22 pm

Fábio Madeira

JWS-109 & JWS-116 Bumped the release date and fixed the text regarding the Elixir-UK.

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    /docs/v_2_2_0/changelog.rst
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    /website/docs/_sources/changelog.rst.txt
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    /website/docs/changelog.html
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    /website/docs/index.html
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    /website/docs/jabaws_manual.pdf
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    /website/docs/objects.inv
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    /website/docs/searchindex.js
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    /website/index.jsp
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    /website/template_footer.jsp
Monday 26 Jun 2017
3:51 pm

Fábio Madeira

JWS-112 Uploaded a new aacon jar, following a minor update made to AAcon's output format.

Options
    • binary
    /binaries/windows/compbio-conservation-1.1.jar
3:49 pm

Fábio Madeira

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/changelog.rst
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    /docs/v_2_2_0/docker.rst
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    /docs/v_2_2_0/getting_started.rst
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    /docs/v_2_2_0/index.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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    /website/docs/_sources/getting_started.rst.txt
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    /website/docs/_sources/index.rst.txt
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    /website/docs/_static/basic.css
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    /website/docs/_static/pygments.css
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    /website/docs/_static/searchtools.js
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    /website/docs/_static/websupport.js
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    /website/docs/advanced.html
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    /website/docs/changelog.html
  16. … 15 more files in changeset.
3:47 pm

Fábio Madeira

JWS-122 & JWS-109 Minor updates to the homepage to point out new Docker support and bump date.

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    /website/index.jsp
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    /website/template_footer.jsp
3:46 pm

Fábio Madeira

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

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    /docker/Dockerfile
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    /docker/Executable.properties
Thursday 08 Jun 2017
5:43 pm

Fábio Madeira

JWS-121 Minor bug fix on the timeexec - wrong units.

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    /webservices/compbio/stat/servlet/AnnualStat.java
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    /webservices/compbio/stat/servlet/ServiceStatus.java
Friday 02 Jun 2017
4:41 pm

Jim Procter

4:40 pm

Jim Procter

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

4:31 pm

Jim Procter

  • More
  • CR-2
  • started review
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
3:19 pm

Fábio Madeira

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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    /docs/v_2_2_0/changelog.rst
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    /website/docs/_sources/changelog.rst.txt
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    /website/docs/changelog.html
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    /website/docs/index.html
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    /website/docs/jabaws_manual.pdf
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    /website/docs/objects.inv
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    /website/docs/searchindex.js
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    /website/index.jsp
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    /website/statpages/ServicesStatus.jsp
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    /website/template_footer.jsp
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    /website/template_header.jsp
3:16 pm

Fábio Madeira

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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    /WEB-INF/web.xml
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    /webservices/compbio/stat/servlet/AnnualStatRefresher.java
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    /webservices/compbio/stat/servlet/ServiceStatusRefresher.java
3:13 pm

Fábio Madeira

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.

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    /website/refresh_service_status.sh
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    /website/service_status.jsp
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    /website/template_header.jsp
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    /website/usage_statistics.jsp
3:07 pm

Fábio Madeira

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.

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    /conf/Engine.local.properties
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    /webservices/compbio/stat/servlet/AnnualStat.java
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    /webservices/compbio/stat/servlet/ServiceStatus.java
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    /website/statpages/MonthlySummary.jsp
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    /website/statpages/ServicesStatus.jsp
3:00 pm

Fábio Madeira

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.

Options
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    /webservices/compbio/stat/servlet/util/RefreshIterator.java
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    /webservices/compbio/stat/servlet/util/ScheduleIterator.java
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    /webservices/compbio/stat/servlet/util/Scheduler.java
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    /webservices/compbio/stat/servlet/util/SchedulerTask.java
2:54 pm

Fábio Madeira

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

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    /WEB-INF/web.xml
Wednesday 31 May 2017
5:37 pm

Fábio Madeira

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/service_status.jsp
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    /website/statpages/MonthlySummary.jsp
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    /website/statpages/ServicesStatus.jsp
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    /website/usage_statistics.jsp
5:01 pm

Fábio Madeira

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.

Options
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    /webservices/compbio/stat/servlet/AnnualStat.java
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    /website/statpages/MonthlySummary.jsp
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    /website/statpages/ServicesStatus.jsp