Merge pull request #40 from safrant/master

Merge Synth into Master - Final

docker/Dockerfile

@@ -19,6 +19,7 @@ RUN wget http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.9-bin.tar.gz
 RUN git clone https://github.com/CBIIT/cananolab
 WORKDIR /tmp/cananolab
 RUN git checkout synthesis
+RUN git pull
 
 ENV PATH=/opt/apache-maven/bin:/opt/apache-ant-1.9.9/bin:$PATH
 ENV JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk
@@ -33,7 +34,6 @@ RUN mkdir -p /local/content/caNanoLab \
 COPY entrypoint/run.sh /usr/bin/
 COPY resources/standalone-full.xml /opt/wildfly-8.2.1.Final/standalone/configuration/standalone-full.xml
 COPY resources/module.xml /opt/wildfly-8.2.1.Final/modules/com/mysql/main
-COPY resources/mysql-connector-java-5.1.26.jar /opt/wildfly-8.2.1.Final/modules/com/mysql/main 
 COPY resources/run.sh /opt/wildfly-8.2.1.Final/bin
 
 EXPOSE 8080 19990

docker/docker-compose.yml

@@ -10,7 +10,7 @@ services:
       - "8080:8080"
       - "19990:19990"
     environment:
-      nano_db: canano-db:3306/canano
+      nano_db: canano-db:3306/canano?enabledTLSProtocols=TLSv1.2&serverTimezone=UTC
       nano_user: root
       nano_password: password
     networks:

docker/resources/run.sh

@@ -9,12 +9,16 @@ ant dist
 cd /usr/local/cananolab/software/cananolab-webapp/target/dist/
 cp /usr/local/cananolab/docker/resources/standalone-full.xml /opt/wildfly-8.2.1.Final/standalone/configuration
 cp caNanoLab.war /local/content/caNanoLab/artifacts
-cd /usr/local/cananolab/software/cananolab-webapp/target/dist/common
-cp bcprov-jdk15on-1.47.jar csmapi-5.2.jar mysql-connector-java-5.1.26.jar caNanoLab_modules.cli caNanoLab_setup.cli caNanoLab_deploy.cli /local/content/caNanoLab/artifacts
+cd /usr/local/cananolab/software/cananolab-webapp/lib/sdk
 
+cp  bcprov-jdk15on-1.66.jar csmapi* mysql-connector-java-8.0.18.jar /local/content/caNanoLab/artifacts
+cd /usr/local/cananolab/software/cananolab-webapp/target/dist/common
+cp caNanoLab_modules.cli caNanoLab_setup.cli caNanoLab_deploy.cli /local/content/caNanoLab/artifacts
 cp wikihelp.properties /local/content/caNanoLab/config
 
 /opt/wildfly-8.2.1.Final/bin/jboss-cli.sh --file=/local/content/caNanoLab/artifacts/caNanoLab_modules.cli
-/opt/wildfly-8.2.1.Final/bin/jboss-cli.sh --file=/local/content/caNanoLab/artifacts/caNanoLab_setup.cli
+
+cp /local/content/caNanoLab/artifacts/caNanoLab.war /opt/wildfly-8.2.1.Final/standalone/deployments
+echo "DEPLOYED"
 cp /local/content/caNanoLab/artifacts/caNanoLab.war /opt/wildfly-8.2.1.Final/standalone/deployments
 echo "DEPLOYED"