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jim procter <j.procter@dundee.ac.uk> in jabaws

JWS-128 patch out log4j references in the compbio.FileUtil class, and corresponding calls to methods in the JABAWS client and engine code.

    • -22
    • +12
    /compbio-utils/compbio/util/FileUtil.java
    • -2
    • +2
    /engine/compbio/engine/client/Util.java
JWS-128 compbio-utils sources added to compilation tree and log4j logging dependence removed

    • -3
    • +19
    /.settings/org.eclipse.wst.common.component
    • -0
    • +48
    /compbio-utils/compbio/util/FileParser.java
    • -0
    • +389
    /compbio-utils/compbio/util/FileUtil.java
    • -0
    • +229
    /compbio-utils/compbio/util/FileWatcher.java
    • -0
    • +92
    /compbio-utils/compbio/util/Grep.java
    • -0
    • +36
    /compbio-utils/compbio/util/Gzip.java
    • -0
    • +40
    /compbio-utils/compbio/util/NullOutputStream.java
    • -0
    • +107
    /compbio-utils/compbio/util/PropertyHelper.java
    • -0
    • +29
    /compbio-utils/compbio/util/SysPrefs.java
    • -0
    • +199
    /compbio-utils/compbio/util/Timer.java
    • -0
    • +48
    /compbio-utils/compbio/util/Util.java
    • -0
    • +28
    /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

    • -0
    • +98
    /log/log4j2.dundee.properties
    • -0
    • +86
    /log/log4j2.properties
Additional sphinx-generated stuff for website

    • -0
    • +12
    /website/docs/_static/documentation_options.js
    • -0
    • +10872
    /website/docs/_static/jquery-3.5.1.js
    • -0
    • +297
    /website/docs/_static/language_data.js
    • -0
    • +2042
    /website/docs/_static/underscore-1.13.1.js
Updated logging config for statdb task during build

    • -0
    • +35
    /log/log4j.statdb.properties
Classpath for eclipse project

Update changelog and rebuild docs

    • -0
    • +8
    /website/docs/_sources/changelog.rst.txt
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    • +322
    /website/docs/_static/basic.css
    • -23
    • +59
    /website/docs/_static/doctools.js
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    • +118
    /website/docs/_static/searchtools.js
    • -31
    • +6
    /website/docs/_static/underscore.js
    • -204
    • +208
    /website/docs/advanced.html
    • -219
    • +209
    /website/docs/develop.html
  1. … 13 more files in changeset.
Version bump and additional authors

Log4j2 property for config file

upgrade log4j to 2.16.0 - patched against log4shell

    • binary
    /WEB-INF/lib/log4j-1.2-api-2.16.0.jar
    • binary
    /WEB-INF/lib/log4j-api-2.16.0.jar
    • binary
    /WEB-INF/lib/log4j-core-2.16.0.jar