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asfgit merged 1 commit into from
Dec 10, 2020
Merged

dependency updates for vagrant example #318

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189 changes: 86 additions & 103 deletions extras/vagrantExample/src/main/vagrant/Vagrantfile
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -33,9 +33,7 @@

Vagrant.configure(2) do |config|

config.vm.box = "ubuntu/trusty64"
config.vm.box_url = "https://cloud-images.ubuntu.com/vagrant/trusty/current/trusty-server-cloudimg-amd64-vagrant-disk1.box"

config.vm.box = "bento/ubuntu-18.04"
config.vm.provider "virtualbox" do |vb|
vb.name = "rya-example-box"
vb.memory = "4096"
Expand All @@ -46,57 +44,40 @@ Vagrant.configure(2) do |config|
config.vm.hostname = "rya-example-box"

config.vm.provision "shell", inline: <<-SHELL

###set -x ## turn on command echo with expanded variables
set -x ## turn on command echo with expanded variables
# List of dependency versions
export ACCUMULO_VERSION=1.6.5
###export ACCUMULO_VERSION=1.7.1
export ACCUMULO_VERSION=1.6.6
export HADOOP_VERSION=2.7.2
export RYA_EXAMPLE_VERSION=4.0.0-incubating-SNAPSHOT
# TODO: Eventually this version of the Rya distribution will be on maven...and then we can use the following instead
#export RYA_EXAMPLE_VERSION=4.0.0-incubating
export RDF4J_VERSION=2.3.1
export ZOOKEEPER_VERSION=3.4.5-cdh4.5.0

mavenRepoUrl=http://repo1.maven.org/maven2/

### IMPORTANT: Verify this exists in the Maven repos. As you know, I am writing this before it exists.
export RYA_EXAMPLE_VERSION=4.0.1
export RDF4J_VERSION=2.5.5
export ZOOKEEPER_VERSION=3.4.5-cdh5.16.1
mavenRepoUrl=https://repo1.maven.org/maven2/
echo "Updating host file with permanent ip"
sudo sed -i 's/127.0.1.1/192.168.33.10/' /etc/hosts
cat >> /etc/hosts <<EOF
192.168.33.10 zoo1 zoo2 zoo3
127.0.0.1 localhost
192.168.33.10 zoo1 zoo2 zoo3 leader1
EOF

sudo -E apt-get -qq update

echo "Installing Java installer..."
sudo -E add-apt-repository ppa:webupd8team/java || exit $?
sudo -E apt-get -qq update || exit $?
echo debconf shared/accepted-oracle-license-v1-1 select true | \
sudo -E /usr/bin/debconf-set-selections
echo debconf shared/accepted-oracle-license-v1-1 seen true | \
sudo -E /usr/bin/debconf-set-selections
sudo mkdir --parents /var/cache/oracle-jdk8-installer || exit $?
echo verbose=off >> /var/cache/oracle-jdk8-installer/wgetrc || exit $?

echo "Installing Java..."
sudo -E apt-get -qq install -y oracle-java8-installer || exit $?
sudo ln --force -s /usr/lib/jvm/java-8-oracle/ /usr/lib/jvm/default-java

# if you want dev tools like javac, change this to openjdk-8-jdk-headless
sudo -E apt-get install -y openjdk-8-jre || exit $?

echo "Installing Tomcat..."
sudo -E apt-get install -y tomcat7 || exit $?

sudo useradd -r -m -U -d /opt/tomcat -s /bin/false tomcat
sudo -E apt-get install -y tomcat9 || exit $?
sudo usermod -a -G tomcat vagrant
echo "Installing Unzip..."
apt-get install unzip || exit $?

echo "Setting up environment..."
export JAVA_HOME=/usr/lib/jvm/java-8-oracle
export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/jre
export HADOOP_HOME=/home/vagrant/hadoop-${HADOOP_VERSION}
export ZOOKEEPER_HOME=/home/vagrant/zookeeper-${ZOOKEEPER_VERSION}
export ZOO_LOG_DIR=${ZOOKEEPER_HOME}/logs/
export ACCUMULO_HOME=/home/vagrant/accumulo-${ACCUMULO_VERSION}
export PATHADD=$JAVA_HOME/bin:$ZOOKEEPER_HOME/bin:$ACCUMULO_HOME/bin:$HADOOP_HOME/bin
export PATH=$PATH:$PATHADD

export HADOOP_PREFIX="$HADOOP_HOME"
export HADOOP_CONF_DIR="$HADOOP_PREFIX/etc/hadoop"
export ACCUMULO_LOG_DIR=$ACCUMULO_HOME/logs
Expand All @@ -110,14 +91,12 @@ EOF
# Shell environment includes Accumulo resources.
ACCUMULO_RC=/home/vagrant/.accumulo_rc.sh
cat > ${ACCUMULO_RC} <<EOF

export JAVA_HOME=\'$JAVA_HOME\'
export HADOOP_HOME=\'$HADOOP_HOME\'
export ZOOKEEPER_HOME=\'$ZOOKEEPER_HOME\'
export ZOO_LOG_DIR=\'$ZOO_LOG_DIR\'
export ACCUMULO_HOME=\'$ACCUMULO_HOME\'
export PATH=\\$PATH:$PATHADD

export HADOOP_PREFIX=\'$HADOOP_PREFIX\'
export HADOOP_CONF_DIR=\'$HADOOP_CONF_DIR\'
export ACCUMULO_LOG_DIR=\'$ACCUMULO_LOG_DIR\'
Expand All @@ -133,9 +112,7 @@ EOF
function ryaps() { ps -ef | grep java | tr ' ' '\\n' | egrep '^org\\.apache|^tracer|^master|^monitor|^tserver|^gc' | sed '/\\.Main/ N ; s/\\n/ /' ; }
EOF
source ${ACCUMULO_RC} || exit 151

# include it at the beginning of both shell configuration files.

for BASHRC in /home/vagrant/.bashrc /home/vagrant/.bash_profile ;
do touch ${BASHRC} ;
cat - ${BASHRC} > ${BASHRC}.new <<EOF && mv ${BASHRC}.new ${BASHRC} || exit 152
Expand All @@ -145,7 +122,6 @@ EOF
echo "Acquiring and Extracting ..."

function echoerr() { printf "%s\n" "$*" >&2; }

function download {
### curl --fail treat http status >= 400 as an error. --location follow redirects status>=300
curl --silent --show-error --fail --location "$@"
Expand Down Expand Up @@ -174,31 +150,27 @@ EOF
fi
done
}

echo "- Hadoop"
hadoopUrl=https://archive.apache.org/dist/hadoop/common/hadoop-${HADOOP_VERSION}/hadoop-${HADOOP_VERSION}.tar.gz
if [[ ! -d ${HADOOP_HOME} ]] ; then
echo "Downloading $hadoopUrl"
download $hadoopUrl \
| tar -zxC /home/vagrant || exit 101
fi

echo "- Zookeeper"
zookeeperUrl=http://archive-primary.cloudera.com/cdh4/cdh/4/zookeeper-${ZOOKEEPER_VERSION}.tar.gz
zookeeperUrl=http://archive.cloudera.com/cdh5/cdh/5/zookeeper-${ZOOKEEPER_VERSION}.tar.gz
if [[ ! -d ${ZOOKEEPER_HOME} ]] ; then
echo "Downloading $zookeeperUrl"
download $zookeeperUrl \
| tar -zxC /home/vagrant || exit 102
fi

echo "- Accumulo"
accumuloUrl=https://archive.apache.org/dist/accumulo/${ACCUMULO_VERSION}/accumulo-${ACCUMULO_VERSION}-bin.tar.gz
if [[ ! -d ${ACCUMULO_HOME} ]] ; then
echo "Downloading $accumuloUrl"
download $accumuloUrl \
| tar -zxC /home/vagrant || exit 103
fi

echo "Configuring Zookeeper..."
sudo mkdir --parents /var/zookeeper
sudo chown vagrant:vagrant /var/zookeeper
Expand All @@ -208,15 +180,12 @@ EOF
# Conflicts with Accumulo and maybe Zookeeper
sudo rm --force ${HADOOP_HOME}/share/hadoop/common/lib/slf4j-api-1.7.10.jar
sudo rm --force ${HADOOP_HOME}/share/hadoop/common/lib/slf4j-log4j12-1.7.10.jar

# Assure logs are creatable and writeable
sudo mkdir --parents ${ZOO_LOG_DIR}
sudo touch "${ZOO_LOG_DIR}/zookeeper.out"
sudo chmod -R a+wX ${ZOO_LOG_DIR}

echo "Running Zookeeper..."
sudo -E ${ZOOKEEPER_HOME}/bin/zkServer.sh start

echo "Configuring Accumulo..."
cp ${ACCUMULO_HOME}/conf/examples/1GB/standalone/* ${ACCUMULO_HOME}/conf/
rm --force ${ACCUMULO_HOME}/conf/accumulo-site.xml
Expand Down Expand Up @@ -271,7 +240,6 @@ EOF
cat > ${ACCUMULO_HOME}/conf/masters <<EOF
rya-example-box
EOF

cat > ${ACCUMULO_HOME}/conf/slaves <<EOF
rya-example-box
EOF
Expand All @@ -280,112 +248,127 @@ EOF
mkdir --parents /data/accumulo/lib/ext

sudo chmod -R a+rwX ${ACCUMULO_HOME}/logs/

echo "Starting Accumulo..."
echo "Init will fail during a re-provision, but you can ignore it: 'FATAL: It appears the directories [...] were previously initialized.'"
echo "Also, you may see an indefinitely repeating: 'Waiting for accumulo to be initialized' which means Accumulo won't start."
echo "Either issue can be resolved by removing the directory: 'sudo rm -r /data/accumulo' then re-provision. Warning: this will erase all Rya/Accumulo data."
${ACCUMULO_HOME}/bin/accumulo init --instance-name dev --password root
${ACCUMULO_HOME}/bin/start-all.sh || exit 107

sudo chmod -R a+rwX ${ACCUMULO_HOME}/logs/

echo 'Done!'

# --------------------
echo "Installing RDF4J Server"
# creating log dir rdf4j-http-server-${RDF4J_VERSION}
sudo mkdir --parents /usr/share/tomcat7/.RDF4J
sudo chown -R tomcat7:tomcat7 /usr/share/tomcat7
sudo ln --force -s /usr/share/tomcat7/.RDF4J/Server/logs /var/log/tomcat7/rdf4j-server
rdf4jwar=/var/lib/tomcat7/webapps/rdf4j-server.war
# this is the rdf4j data dir. It might need to be registered with tomcat to write there.
export rdf4jServerBase=/opt/tomcat/
sudo install -d -o tomcat -m u=rwx,go=rx ${rdf4jServerBase}
sudo -u tomcat mkdir --parents ${rdf4jServerBase}/server/logs
sudo -u tomcat mkdir --parents ${rdf4jServerBase}/.RDF4J/server/logs
# tomcat v9 requires explicit permissions to the file system.
sudo mkdir --parents /etc/systemd/system/tomcat9.service.d
cat <<EOF | sudo tee --append /etc/systemd/system/tomcat9.service.d/logging-allow.conf
[Service]
ReadWritePaths=${rdf4jServerBase}
EOF
echo 'Restarting Tomcat (or starting)'
sudo -E systemctl daemon-reload || exit 1080
sudo -E systemctl enable tomcat9 || exit 1081
sudo -E systemctl restart tomcat9 || exit 1082
rdf4jwar=/var/lib/tomcat9/webapps/rdf4j-server.war
if [[ ! -s $rdf4jwar ]] ; then
echo "Downloading RDF4J Server"
download --output $rdf4jwar ${mavenRepoUrl}org/eclipse/rdf4j/rdf4j-http-server/${RDF4J_VERSION}/rdf4j-http-server-${RDF4J_VERSION}.war || exit 110
fi
echo "RDF4J http server deployed at http://rya-example-box:8080/rdf4j-server"

# --------------------
echo "Installing RDF4J Workbench"
workbench=/var/lib/tomcat7/webapps/rdf4j-workbench.war
workbench=/var/lib/tomcat9/webapps/rdf4j-workbench.war
if [[ ! -s $workbench ]] ; then
echo "Downloading RDF4J Workbench"
download --output $workbench ${mavenRepoUrl}org/eclipse/rdf4j/rdf4j-http-workbench/${RDF4J_VERSION}/rdf4j-http-workbench-${RDF4J_VERSION}.war || exit 111
fi
echo "RDF4J workbench deployed at http://rya-example-box:8080/rdf4j-workbench"

# ----------------------
echo "Installing Rya"
ryaIndexing=rya.indexing.example-${RYA_EXAMPLE_VERSION}-distribution
# Place in the vagrant folder from your dev project, example: extras/indexingExample/target/rya.indexing.example-4.0.1-distribution.zip
if [[ -s "/vagrant/${ryaIndexing}.zip" ]] ; then
echo "Using found local file: /vagrant/${ryaIndexing}.zip "
cp "/vagrant/${ryaIndexing}.zip" ./
fi
if [[ ! -s ${ryaIndexing}.zip ]] ; then
echo "Downloading ${ryaIndexing}.zip quietly, this will take some minutes with no output..."
download --output ${ryaIndexing}.zip https://www.dropbox.com/s/gruhp3a848k8ryu/${ryaIndexing}.zip?raw=1 || exit 112
# TODO: Eventually this version of the Rya distribution will be on maven...and then we can use the following instead
#download --output ${ryaIndexing}.zip ${mavenRepoUrl}org/apache/rya/rya.indexing.example/${RYA_EXAMPLE_VERSION}/${ryaIndexing}.zip || exit 112
download --output ${ryaIndexing}.zip ${mavenRepoUrl}org/apache/rya/rya.indexing.example/${RYA_EXAMPLE_VERSION}/${ryaIndexing}.zip || exit 112
fi
sudo mkdir --parents ${ryaIndexing}
sudo unzip -q -o ${ryaIndexing}.zip -d ${ryaIndexing}

# before continuing, wait for tomcat to deploy wars:
waitForDeploy /var/lib/tomcat7/webapps/rdf4j-workbench/WEB-INF/lib/
waitForDeploy /var/lib/tomcat7/webapps/rdf4j-server/WEB-INF/lib/

waitForDeploy /var/lib/tomcat9/webapps/rdf4j-workbench/WEB-INF/lib/
waitForDeploy /var/lib/tomcat9/webapps/rdf4j-server/WEB-INF/lib/
# soft linking the files doesn't seem to work in tomcat, so we copy them instead :(
sudo cp ${ryaIndexing}/dist/lib/* /var/lib/tomcat7/webapps/rdf4j-workbench/WEB-INF/lib/ || exit 113
sudo cp ${ryaIndexing}/dist/lib/* /var/lib/tomcat7/webapps/rdf4j-server/WEB-INF/lib/ || exit 114

# These are older libs that breaks tomcat 7
sudo rm --force /var/lib/tomcat7/webapps/rdf4j-workbench/WEB-INF/lib/servlet-api-2.5.jar
sudo rm --force /var/lib/tomcat7/webapps/rdf4j-workbench/WEB-INF/lib/jsp-api-2.1.jar
sudo rm --force /var/lib/tomcat7/webapps/rdf4j-server/WEB-INF/lib/servlet-api-2.5.jar
sudo rm --force /var/lib/tomcat7/webapps/rdf4j-server/WEB-INF/lib/jsp-api-2.1.jar

sudo chown -R tomcat7:tomcat7 /var/lib/tomcat7/webapps/rdf4j-workbench/WEB-INF/lib/
sudo chown -R tomcat7:tomcat7 /var/lib/tomcat7/webapps/rdf4j-server/WEB-INF/lib/

sudo -u tomcat cp ${ryaIndexing}/dist/lib/* /var/lib/tomcat9/webapps/rdf4j-workbench/WEB-INF/lib/ || exit 113
sudo -u tomcat cp ${ryaIndexing}/dist/lib/* /var/lib/tomcat9/webapps/rdf4j-server/WEB-INF/lib/ || exit 114
# These are older libs that break tomcat and rdf4j that come with Rya above.
sudo rm --force /var/lib/tomcat9/webapps/rdf4j-workbench/WEB-INF/lib/servlet-api-2.5.jar
sudo rm --force /var/lib/tomcat9/webapps/rdf4j-workbench/WEB-INF/lib/jsp-api-2.1.jar
s=/var/lib/tomcat9/webapps/rdf4j-server/WEB-INF/lib/
sudo rm --force $s/servlet-api-2.5.jar $s/lib/jsp-api-2.1.jar
sudo find "$s" -name 'spring-*-3.*.jar' -exec sudo rm --force {} +
sudo rm $s/spring-aop-4.2.1.RELEASE.jar $s/rdf4j-http-server-spring-2.3.1.jar
sudo rm --force $s/slf4j-log4j12-1.7.25.jar $s/slf4j-api-1.7.25.jar $s/jcabi-log-0.14.jar $s/jcl-over-slf4j-1.7.25.jar $s/minlog-1.3.0.jar $s/commons-logging-1.1.1.jar $s/log4j-1.2.16.jar
sudo chown -R tomcat:tomcat /var/lib/tomcat9/webapps/rdf4j-workbench/WEB-INF/lib/
sudo chown -R tomcat:tomcat /var/lib/tomcat9/webapps/rdf4j-server/WEB-INF/lib/
# ----------------------
echo "Downloading and installing new templates for RDF4J WorkBench"
ryaVagrant=rya.vagrant.example-${RYA_EXAMPLE_VERSION}
# Place in the vagrant folder from your dev project: extras/vagrantExample/target/rya.vagrant.example-*.jar
if [[ -s "/vagrant/${ryaVagrant}.jar" ]] ; then
echo "Using found local file: /vagrant/${ryaVagrant}.jar "
cp "/vagrant/${ryaVagrant}.jar" ./
fi
if [[ ! -s ${ryaVagrant}.jar ]] ; then
echo "Downloading ${ryaVagrant}.jar"
download --output ${ryaVagrant}.jar https://www.dropbox.com/s/p07u42et9rui3x7/${ryaVagrant}.jar?raw=1 || exit 120
# TODO: Eventually this version of the Rya distribution will be on maven...and then we can use the following instead
#download --output ${ryaVagrant}.jar ${mavenRepoUrl}org/apache/rya/rya.vagrant.example/${RYA_EXAMPLE_VERSION}/${ryaVagrant}.jar || exit 120
download --output ${ryaVagrant}.jar ${mavenRepoUrl}org/apache/rya/rya.vagrant.example/${RYA_EXAMPLE_VERSION}/${ryaVagrant}.jar || exit 120
fi
sudo mkdir --parents ${ryaVagrant}
sudo unzip -q -o ${ryaVagrant}.jar -d ${ryaVagrant}
sudo cp ${ryaVagrant}/*.xsl /var/lib/tomcat7/webapps/rdf4j-workbench/transformations/
sudo chown tomcat7:tomcat7 /var/lib/tomcat7/webapps/rdf4j-workbench/transformations/*

waitForDeploy /var/lib/tomcat9/webapps/rdf4j-workbench/transformations
sudo -u tomcat cp ${ryaVagrant}/*.xsl /var/lib/tomcat9/webapps/rdf4j-workbench/transformations/
sudo chown tomcat:tomcat /var/lib/tomcat9/webapps/rdf4j-workbench/transformations/*
# ----------------------
echo "Deploying Rya Web"
ryaWar=web.rya-${RYA_EXAMPLE_VERSION}.war
# Place in the vagrant folder from your dev project: web/web.rya/target/web.rya.war rename to add version.
if [[ -s "/vagrant/${ryaWar}" ]] ; then
echo "Using found local file: /vagrant/${ryaWar} "
cp "/vagrant/${ryaWar}" ./
fi
if [[ ! -s ${ryaWar} ]] ; then
echo "Downloading ${ryaWar}"
download https://www.dropbox.com/s/jrmgfey8ch1vrd6/${ryaWar}?raw=1 --output ${ryaWar} || exit 121
# TODO: Eventually this version of the Rya distribution will be on maven...and then we can use the following instead
#download ${mavenRepoUrl}org/apache/rya/web.rya/${RYA_EXAMPLE_VERSION}/${ryaWar} --output ${ryaWar} || exit 121
###download https://www.dropbox.com/s/jrmgfey8ch1vrd6/${ryaWar}?raw=1 --output ${ryaWar} || exit 121
download ${mavenRepoUrl}org/apache/rya/web.rya/${RYA_EXAMPLE_VERSION}/${ryaWar} --output ${ryaWar} || exit 121
fi
sudo cp ${ryaWar} /var/lib/tomcat7/webapps/web.rya.war
# remove this so we can wait for it to be recreated.
sudo rm -rf /var/lib/tomcat9/webapps/web.rya/WEB-INF/classes
sudo -u tomcat cp ${ryaWar} /var/lib/tomcat9/webapps/web.rya.war
# Wait for the war to deploy
waitForDeploy /var/lib/tomcat7/webapps/web.rya/WEB-INF/classes/

# These are older libs that breaks tomcat 7
sudo rm --force /var/lib/tomcat7/webapps/web.rya/WEB-INF/lib/servlet-api-2.5*.jar
sudo rm --force /var/lib/tomcat7/webapps/web.rya/WEB-INF/lib/jsp-api-2.1.jar

waitForDeploy /var/lib/tomcat9/webapps/web.rya/WEB-INF/classes/
# These are older libs that break tomcat
sudo rm --force /var/lib/tomcat9/webapps/web.rya/WEB-INF/lib/servlet-api-2.5*.jar
sudo rm --force /var/lib/tomcat9/webapps/web.rya/WEB-INF/lib/jsp-api-2.1.jar
echo "Modify Rya Web Config"
cat > /var/lib/tomcat7/webapps/web.rya/WEB-INF/classes/environment.properties <<EOF
sudo chmod -R a+rwX /var/lib/tomcat9/webapps/web.rya/
cat > /var/lib/tomcat9/webapps/web.rya/WEB-INF/classes/environment.properties <<EOF
instance.name=dev
instance.zk=localhost:2181
instance.username=root
instance.password=root
rya.tableprefix=rya_
rya.displayqueryplan=true
EOF

echo "Rya web deployed at http://rya-example-box:8080/web.rya/sparqlQuery.jsp"

# restart tomcat
sudo -E service tomcat7 restart

systemctl restart tomcat9 || exit $?
echo "Finished and ready to use!"
echo "You can re-apply these settings without losing data by running the command 'vagrant provision'"
SHELL

end
17 changes: 17 additions & 0 deletions extras/vagrantExample/src/main/vagrant/readme.md
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,18 @@ Once Vagrant is installed, starting up the Rya-Example-Box is fairly straightfor

1. Download the [Rya-Example-Box Vagrantfile] to the custom directory. Note that it must be named `Vagrantfile` with no extension.

1. Optionally, if you downloaded and built Rya, copy built Rya libraries from your project into the custom directory. If not, Vagrant will attempt to download from the public repository when building the VM. The following files can be copied or linked (ln -s file destination).

extras/indexingExample/target/rya.indexing.example-*-distribution.zip
extras/vagrantExample/target/rya.vagrant.example-*.jar
web/web.rya/target/web.rya.war

The last one must be renamed to include the version, for example: web.rya-4.0.1.war

1. Modify the Vagrantfile so the RYA_EXAMPLE_VERSION matches the version in your files or in the public repository. It may already match the current version, but verify it since it is a pre-release guess. This is around line 56. For example:

export RYA_EXAMPLE_VERSION=4.0.1

1. Open a DOS prompt (Windows) or Terminal (Mac/Linux), change to the custom directory, and issue the command `vagrant up`. Note that it may take up to 30 minutes to download, install, and configure Rya and all of the components.

### Verification
Expand Down Expand Up @@ -90,6 +102,11 @@ RDF4J Workbench requires a set of "transformations" for listing Rya in the RDF4J

If these files do note exists, open the vagrant file and look for the line `echo "Downloading Rya"`. Try working through those commands manually on your Vagrant VM.

#### java.io.FileNotFoundException: class path resource [environment.properties] cannot be opened because it does not exist
This file is missing:
/var/lib/tomcat9/webapps/web.rya/WEB-INF/classes/environment.properties
It is created by the Vagrantfile. It may be overwritten if the webapp is redeployed. Run `vagrant up --provision` .

#### Other useful commands

Below is a list of other useful commands on the VMs
Expand Down
2 changes: 1 addition & 1 deletion web/web.rya/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -194,7 +194,7 @@ under the License.
</properties>
</profile>
<profile>
<id>geoindexing</id>
<id>mongodb-geo</id>
<properties>
<db.specified>true</db.specified>
<database.implementation>mongodb-geo</database.implementation>
Expand Down