updated dependancies for VagrantExample closes #318
diff --git a/extras/vagrantExample/src/main/vagrant/Vagrantfile b/extras/vagrantExample/src/main/vagrant/Vagrantfile
old mode 100644
new mode 100755
index 2b8d310..488457a
--- a/extras/vagrantExample/src/main/vagrant/Vagrantfile
+++ b/extras/vagrantExample/src/main/vagrant/Vagrantfile
@@ -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"
@@ -46,57 +44,40 @@
   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
@@ -110,14 +91,12 @@
     # 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\'
@@ -133,9 +112,7 @@
         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
@@ -145,7 +122,6 @@
     echo "Acquiring and Extracting ..."
     
     function echoerr() { printf "%s\n" "$*" >&2; }
-
     function download {
       ### curl --fail treat http status >= 400 as an error. --location follow redirects status>=300
       curl --silent --show-error --fail --location "$@"
@@ -174,7 +150,6 @@
             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 
@@ -182,15 +157,13 @@
         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
@@ -198,7 +171,6 @@
         download $accumuloUrl \
         | tar -zxC /home/vagrant || exit 103
     fi
-
     echo "Configuring Zookeeper..."
     sudo mkdir --parents /var/zookeeper
     sudo chown vagrant:vagrant /var/zookeeper
@@ -208,15 +180,12 @@
     # 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
@@ -271,7 +240,6 @@
     cat > ${ACCUMULO_HOME}/conf/masters <<EOF
 rya-example-box
 EOF
-
     cat > ${ACCUMULO_HOME}/conf/slaves <<EOF
 rya-example-box
 EOF
@@ -280,97 +248,116 @@
     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
@@ -378,14 +365,10 @@
 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
diff --git a/extras/vagrantExample/src/main/vagrant/readme.md b/extras/vagrantExample/src/main/vagrant/readme.md
index 66afc5b..c21c850 100644
--- a/extras/vagrantExample/src/main/vagrant/readme.md
+++ b/extras/vagrantExample/src/main/vagrant/readme.md
@@ -41,6 +41,18 @@
 

 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

@@ -90,6 +102,11 @@
 

 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

diff --git a/web/web.rya/pom.xml b/web/web.rya/pom.xml
index 54d611a..b7f594f 100644
--- a/web/web.rya/pom.xml
+++ b/web/web.rya/pom.xml
@@ -194,7 +194,7 @@
             </properties>
         </profile>
         <profile>
-            <id>geoindexing</id>
+            <id>mongodb-geo</id>
             <properties>
                 <db.specified>true</db.specified>
                 <database.implementation>mongodb-geo</database.implementation>