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Merge pull request #8511 from IQSS/develop
Version 5.10
2 parents fb24c87 + 27a733f commit a57ce53

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‎.github/workflows/maven_unit_test.yml

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@@ -4,22 +4,34 @@ on:
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push:
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paths:
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- "**.java"
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- "pom.xml"
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- "modules/**/pom.xml"
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pull_request:
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paths:
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- "**.java"
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- "pom.xml"
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- "modules/**/pom.xml"
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jobs:
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unittest:
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name: (JDK ${{ matrix.jdk }} / ${{ matrix.os }}) Unit Tests
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name: (${{ matrix.status}} / JDK ${{ matrix.jdk }}) Unit Tests
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strategy:
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fail-fast: false
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matrix:
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os: [ ubuntu-latest ]
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jdk: [ '11' ]
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experimental: [false]
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status: ["Stable"]
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#
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# JDK 17 builds disabled due to non-essential fails marking CI jobs as completely failed within
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# Github Projects, PR lists etc. This was consensus on Slack #dv-tech. See issue #8094
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# (This is a limitation of how Github is currently handling these things.)
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#
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#include:
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# - os: ubuntu-latest
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# jdk: '16'
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runs-on: ${{ matrix.os }}
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# - jdk: '17'
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# experimental: true
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# status: "Experimental"
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continue-on-error: ${{ matrix.experimental }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up JDK ${{ matrix.jdk }}
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key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
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restore-keys: ${{ runner.os }}-m2
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- name: Build with Maven
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run: mvn -DcompilerArgument=-Xlint:unchecked -P all-unit-tests clean test
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run: mvn -DcompilerArgument=-Xlint:unchecked -Dtarget.java.version=${{ matrix.jdk }} -P all-unit-tests clean test
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- name: Maven Code Coverage
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env:
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CI_NAME: github

‎.gitignore

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scripts/search/data/binary/trees.png.thumb140
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src/main/webapp/resources/images/cc0.png.thumb140
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src/main/webapp/resources/images/dataverseproject.png.thumb140
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# apache-maven is downloaded by docker-aio
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apache-maven*

‎README.md

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1-
Dataverse®
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Dataverse®
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===============
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Dataverse is an [open source][] software platform for sharing, finding, citing, and preserving research data (developed by the [Data Science and Products team](http://www.iq.harvard.edu/people/people/data-science-products) at the [Institute for Quantitative Social Science](http://iq.harvard.edu/) and the [Dataverse community][]).

‎checkstyle.xml

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</module>
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-->
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<module name="IllegalImport">
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<property name="illegalPkgs" value="org.apache.commons.lang"/>
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<property name="illegalPkgs" value="org.apache.commons.lang, org.apache.log4j"/>
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</module>
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<!-- <module name="RedundantImport"/> -->
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<!-- <module name="UnusedImports">

‎conf/docker-aio/0prep_deps.sh

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@@ -9,11 +9,11 @@ if [ ! -e dv/deps/payara-5.2021.5.zip ]; then
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wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2021.5/payara-5.2021.5.zip -O dv/deps/payara-5.2021.5.zip
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fi
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if [ ! -e dv/deps/solr-8.8.1dv.tgz ]; then
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if [ ! -e dv/deps/solr-8.11.1dv.tgz ]; then
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echo "solr dependency prep"
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# schema changes *should* be the only ones...
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cd dv/deps/
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wget https://archive.apache.org/dist/lucene/solr/8.8.1/solr-8.8.1.tgz -O solr-8.8.1dv.tgz
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wget https://archive.apache.org/dist/lucene/solr/8.11.1/solr-8.11.1.tgz -O solr-8.11.1dv.tgz
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cd ../../
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fi
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‎conf/docker-aio/1prep.sh

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# this was based off the phoenix deployment; and is likely uglier and bulkier than necessary in a perfect world
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mkdir -p testdata/doc/sphinx-guides/source/_static/util/
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cp ../solr/8.8.1/schema*.xml testdata/
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cp ../solr/8.8.1/solrconfig.xml testdata/
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cp ../solr/8.11.1/schema*.xml testdata/
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cp ../solr/8.11.1/solrconfig.xml testdata/
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cp ../jhove/jhove.conf testdata/
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cp ../jhove/jhoveConfig.xsd testdata/
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cd ../../

‎conf/docker-aio/c8.dockerfile

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@@ -23,7 +23,7 @@ COPY testdata/sushi_sample_logs.json /tmp/
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COPY disableipv6.conf /etc/sysctl.d/
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RUN rm /etc/httpd/conf/*
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COPY httpd.conf /etc/httpd/conf
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RUN cd /opt ; tar zxf /tmp/dv/deps/solr-8.8.1dv.tgz
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RUN cd /opt ; tar zxf /tmp/dv/deps/solr-8.11.1dv.tgz
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RUN cd /opt ; unzip /tmp/dv/deps/payara-5.2021.5.zip ; ln -s /opt/payara5 /opt/glassfish4
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# this copy of domain.xml is the result of running `asadmin set server.monitoring-service.module-monitoring-levels.jvm=LOW` on a default glassfish installation (aka - enable the glassfish REST monitir endpoint for the jvm`
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# copy configuration related files
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RUN cp /tmp/dv/pg_hba.conf /var/lib/pgsql/13/data/
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RUN cp -r /opt/solr-8.8.1/server/solr/configsets/_default /opt/solr-8.8.1/server/solr/collection1
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RUN cp /tmp/dv/schema*.xml /opt/solr-8.8.1/server/solr/collection1/conf/
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RUN cp /tmp/dv/solrconfig.xml /opt/solr-8.8.1/server/solr/collection1/conf/solrconfig.xml
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RUN cp -r /opt/solr-8.11.1/server/solr/configsets/_default /opt/solr-8.11.1/server/solr/collection1
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RUN cp /tmp/dv/schema*.xml /opt/solr-8.11.1/server/solr/collection1/conf/
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RUN cp /tmp/dv/solrconfig.xml /opt/solr-8.11.1/server/solr/collection1/conf/solrconfig.xml
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# skipping payara user and solr user (run both as root)
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‎conf/docker-aio/dv/install/default.config

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POSTGRES_USER dvnapp
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POSTGRES_PASSWORD secret
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SOLR_LOCATION idx
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TWORAVENS_LOCATION NOT INSTALLED
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RSERVE_HOST localhost
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RSERVE_PORT 6311
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RSERVE_USER rserve

‎conf/docker-aio/entrypoint.bash

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#!/usr/bin/env bash
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export LANG=en_US.UTF-8
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sudo -u postgres /usr/pgsql-13/bin/pg_ctl start -D /var/lib/pgsql/13/data &
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cd /opt/solr-8.8.1/
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cd /opt/solr-8.11.1/
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# TODO: Run Solr as non-root and remove "-force".
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bin/solr start -force
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bin/solr create_core -c collection1 -d server/solr/collection1/conf -force

‎conf/docker-aio/httpd.conf

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CustomLog logs/access_log combined
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# proxy config (aka - what to send to glassfish or not)
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ProxyPassMatch ^/RApacheInfo$ !
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ProxyPassMatch ^/custom !
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ProxyPassMatch ^/dataexplore !
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ProxyPassMatch ^/Shibboleth.sso !
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ProxyPassMatch ^/shibboleth-ds !
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# pass everything else to Glassfish

‎conf/docker-aio/testdata/httpd.conf

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CustomLog logs/access_log combined
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# proxy config (aka - what to send to glassfish or not)
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ProxyPassMatch ^/RApacheInfo$ !
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ProxyPassMatch ^/custom !
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ProxyPassMatch ^/dataexplore !
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ProxyPassMatch ^/Shibboleth.sso !
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ProxyPassMatch ^/shibboleth-ds !
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# pass everything else to Glassfish

‎conf/httpd/conf.d/dataverse.conf

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# don't pass paths used by rApache and TwoRavens to Glassfish
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ProxyPassMatch ^/RApacheInfo$ !
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ProxyPassMatch ^/dataexplore !
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ProxyPassMatch ^/custom !
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ProxyPassMatch ^/rookzelig !
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# don't pass paths used by Shibboleth to Glassfish
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ProxyPassMatch ^/Shibboleth.sso !
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ProxyPassMatch ^/shibboleth-ds !

‎conf/solr/8.8.1/readme.md renamed to ‎conf/solr/8.11.1/readme.md

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‎conf/solr/8.8.1/schema.xml renamed to ‎conf/solr/8.11.1/schema.xml

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<field name="characteristicOfSources" type="text_en" multiValued="false" stored="true" indexed="true"/>
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<field name="city" type="text_en" multiValued="true" stored="true" indexed="true"/>
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<field name="cleaningOperations" type="text_en" multiValued="false" stored="true" indexed="true"/>
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<field name="collectionMode" type="text_en" multiValued="false" stored="true" indexed="true"/>
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<field name="collectionMode" type="text_en" multiValued="true" stored="true" indexed="true"/>
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<field name="collectorTraining" type="text_en" multiValued="false" stored="true" indexed="true"/>
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<field name="contributor" type="text_en" multiValued="true" stored="true" indexed="true"/>
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<field name="contributorName" type="text_en" multiValued="true" stored="true" indexed="true"/>

‎conf/solr/8.8.1/solrconfig.xml renamed to ‎conf/solr/8.11.1/solrconfig.xml

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to occupy. Note that when this option is specified, the size
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and initialSize parameters are ignored.
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-->
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<filterCache class="solr.FastLRUCache"
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<filterCache class="solr.search.CaffeineCache"
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size="512"
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initialSize="512"
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autowarmCount="0"/>
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maxRamMB - the maximum amount of RAM (in MB) that this cache is allowed
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to occupy
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-->
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<queryResultCache class="solr.LRUCache"
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<queryResultCache class="solr.search.CaffeineCache"
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size="512"
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initialSize="512"
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autowarmCount="0"/>
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document). Since Lucene internal document ids are transient,
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this cache will not be autowarmed.
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-->
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<documentCache class="solr.LRUCache"
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<documentCache class="solr.search.CaffeineCache"
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size="512"
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initialSize="512"
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autowarmCount="0"/>
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<!-- custom cache currently used by block join -->
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<cache name="perSegFilter"
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class="solr.search.LRUCache"
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class="solr.search.CaffeineCache"
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size="10"
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initialSize="0"
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autowarmCount="10"

‎conf/solr/8.8.1/update-fields.sh renamed to ‎conf/solr/8.11.1/update-fields.sh

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‎conf/vagrant/etc/yum.repos.d/shibboleth.repo

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[security_shibboleth]
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name=Shibboleth (CentOS_8)
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[shibboleth]
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name=Shibboleth (rockylinux8)
3+
# Please report any problems to https://shibboleth.atlassian.net/jira
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type=rpm-md
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baseurl=http://download.opensuse.org/repositories/security:/shibboleth/CentOS_8/
5+
mirrorlist=https://shibboleth.net/cgi-bin/mirrorlist.cgi/rockylinux8
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gpgcheck=1
6-
gpgkey=http://download.opensuse.org/repositories/security:/shibboleth/CentOS_8/repodata/repomd.xml.key
7+
gpgkey=https://shibboleth.net/downloads/service-provider/RPMS/repomd.xml.key
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https://shibboleth.net/downloads/service-provider/RPMS/cantor.repomd.xml.key
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enabled=1

‎doc/Architecture/components.uml

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}
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node "RserveServer1" {
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component "rApache" {
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}
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database "Rserve" {
4644
}
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}
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Clients --> LoadBalancer
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Clients --> rApache
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LoadBalancer --> Apache1
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LoadBalancer --> Apache2

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