Update to CZ version

images/openspecimen/Dockerfile

@@ -1,34 +1,68 @@
 # OpenSpecimen Tomcat Container
-# 
-# VERSION 0.0.2 
-#
 
-# 0.0.1 : initial creation of image with java version 1.8.0_72-b15 (766.4 MB)
-# 0.0.2 : use existing build for tomcat and autobuild gradle container
+FROM debian:jessie
+ARG DEBIAN_FRONTEND=noninteractive
+ARG VERSION="v6.2.x"
 
-FROM tomcat:9.0-jre8
+RUN apt-get update \
+    && apt-get install -y software-properties-common apt-utils wget gnupg \
+    apt-transport-https ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
 
-MAINTAINER Suyesh Amatya <[email protected]>
+# Setup JDK
+RUN wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add - \
+    && add-apt-repository --yes https://adoptopenjdk.jfrog.io/adoptopenjdk/deb/ \
+    && apt-get update \
+    && apt install -y adoptopenjdk-8-hotspot
 
-RUN apt-get update \
-    && rm -r $CATALINA_HOME/webapps/ROOT \
-    && rm -r $CATALINA_HOME/webapps/docs \
-    && rm -r $CATALINA_HOME/webapps/examples \
-    && mkdir -p /opt/openspecimen/os-data \
-    && mkdir -p /opt/openspecimen/os-plugins \
-    && ln -s "$CATALINA_HOME" /opt/tomcat \
-    && wget http://central.maven.org/maven2/mysql/mysql-connector-java/5.1.31/mysql-connector-java-5.1.31.jar -O /opt/tomcat/lib/mysql-connector-java-5.1.31.jar
-
-# Add admin/admin user
-ADD configs/tomcat-users.xml /opt/tomcat/conf/tomcat-users.xml
-# Add data source configuration for MySQL root user (username="root" password="openspecimen")
-ADD configs/context.xml /opt/tomcat/conf/context.xml
-ADD configs/openspecimen.properties /opt/tomcat/conf/openspecimen.properties
-# ADD openspecimen war file build with the gradle container with default values
-ADD openspecimen.war /opt/dist/openspecimen.war
-
-ADD scripts /opt/scripts
-WORKDIR /opt/scripts
-RUN chmod a+x *.sh
-
-ENTRYPOINT ["/opt/scripts/entrypoint.sh"]
+# Setup tomcat and dependencies
+RUN apt-get install -y build-essential libpng-dev \
+    && mkdir /opt/tomcat/ \
+    && useradd -r -m -U -d /opt/tomcat -s /bin/false tomcat \
+    && wget https://www-eu.apache.org/dist/tomcat/tomcat-9/v9.0.27/bin/apache-tomcat-9.0.27.tar.gz -P /tmp/ \
+    && tar xf /tmp/apache-tomcat-9*.tar.gz -C /opt/tomcat \
+    && ln -s /opt/tomcat/apache-tomcat-9.0.27 /opt/tomcat/latest \
+    && sh -c 'chmod +x /opt/tomcat/latest/bin/*.sh' \
+    && chown -R tomcat:tomcat /opt/tomcat/apache-tomcat-9.0.27
+
+ENV GRADLE_HOME="/opt/gradle/gradle-2.0"
+ENV PATH="${GRADLE_HOME}/bin:${PATH}"
+
+# Setup build tools
+RUN wget http://services.gradle.org/distributions/gradle-2.0-bin.zip -P /tmp \
+    && apt-get install -y unzip curl git \
+    && unzip -d /opt/gradle /tmp/gradle-*.zip \
+    && curl -sL https://deb.nodesource.com/setup_10.x | bash - \
+    && apt-get install -y nodejs \
+    && curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.34.0/install.sh | bash \
+    && cd /tmp \
+    && git clone https://github.com/krishagni/openspecimen.git -b $VERSION \
+    && rm /tmp/openspecimen/build.properties \
+    && rm /opt/tomcat/latest/conf/context.xml \
+    && cd openspecimen/www/ \
+    && npm install --loglevel=error \
+    && npm install --loglevel=error -g grunt gulp-cli bower \
+    && npm audit fix \
+    && bower install --allow-root \
+    && apt remove -y unzip curl \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy config files
+ADD configs/build.properties /tmp/openspecimen/
+ADD configs/context.xml /opt/tomcat/latest/conf/
+ADD configs/openspecimen.properties /opt/tomcat/latest/conf/
+
+# Build WAR file
+RUN cd /tmp/openspecimen \
+    && gradle build \
+    && cp build/libs/openspecimen.war /opt/tomcat/latest/webapps/ \
+    && mkdir -p /opt/tomcat/latest/OpenSpecimen/plugins \
+    && chown tomcat:tomcat /opt/tomcat/latest/conf/openspecimen.properties \
+    && chown tomcat:tomcat /opt/tomcat/latest/conf/context.xml \
+    && wget https://repo1.maven.org/maven2/mysql/mysql-connector-java/8.0.18/mysql-connector-java-8.0.18.jar -P /opt/tomcat/latest/lib/ \
+    && rm -rf /tmp/openspecimen \
+    && apt remove -y git
+
+RUN echo 'export PS1="[\u@openspecimen:\w]# "' >> /root/.bashrc
+
+ENTRYPOINT ["/bin/sh"]

images/openspecimen/configs/build.properties

@@ -0,0 +1,12 @@
+app_home=/opt/tomcat/apache-tomcat-9.0.27/
+app_data_dir=/opt/tomcat/apache-tomcat-9.0.27/os-data/
+datasource_jndi=jdbc/openspecimen
+datasource_type=fresh
+database_host=localhost
+database_port=3306
+database_name=openspecimen
+database_username=dbuser
+database_password=testpw
+plugin_dir=/opt/tomcat/apache-tomcat-9.0.27/OpenSpecimen/plugins/
+show_sql=true
+deployment_type = fresh

images/openspecimen/configs/context.xml

@@ -1,14 +1,12 @@
-<?xml version='1.0' encoding='utf-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
 <!--
   Licensed to the Apache Software Foundation (ASF) under one or more
   contributor license agreements.  See the NOTICE file distributed with
   this work for additional information regarding copyright ownership.
   The ASF licenses this file to You under the Apache License, Version 2.0
   (the "License"); you may not use this file except in compliance with
   the License.  You may obtain a copy of the License at
-
       http://www.apache.org/licenses/LICENSE-2.0
-
   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -18,30 +16,19 @@
 <!-- The contents of this file will be loaded for each web application -->
 <Context>
 
-    <!-- Default set of monitored resources -->
+    <!-- Default set of monitored resources. If one of these changes, the    -->
+    <!-- web application will be reloaded.                                   -->
     <WatchedResource>WEB-INF/web.xml</WatchedResource>
+    <WatchedResource>WEB-INF/tomcat-web.xml</WatchedResource>
+    <WatchedResource>${catalina.base}/conf/web.xml</WatchedResource>
+
+
+    <Resource name="jdbc/openspecimen" driverClassName="com.mysql.cj.jdbc.Driver" url="jdbc:mysql://localhost:3306/openspecimen" auth="Container" maxActive="100" password="testpw" maxWait="10000" username="dbuser" maxIdle="30" type="javax.sql.DataSource"/>
+
+    <Environment name="config/openspecimen" value="/opt/tomcat/apache-tomcat-9.0.27/conf/openspecimen.properties" type="java.lang.String"/>
 
     <!-- Uncomment this to disable session persistence across Tomcat restarts -->
     <!--
     <Manager pathname="" />
     -->
-
-    <!-- Uncomment this to enable Comet connection tacking (provides events
-         on session expiration as well as webapp lifecycle) -->
-    <!--
-    <Valve className="org.apache.catalina.valves.CometConnectionManagerValve" />
-    -->
-
-      <Resource name="jdbc/openspecimen" auth="Container" type="javax.sql.DataSource"
-      	maxActive="100" maxIdle="30" maxWait="10000"
-      	username="§§username" password="§§password" driverClassName="§§useddatabasedriver"
-      	url="jdbc:§§useddatabasetype://§§host:§§port/§§database" 
-		testOnBorrow="true" validationQuery="select 1 from dual" />
-
-	  <Environment
-		  name="config/openspecimen"
-		  value="$TOMCAT_DIR/conf/openspecimen.properties"
-		  type="java.lang.String"/>
-
-
 </Context>

images/openspecimen/configs/openspecimen.properties

@@ -24,18 +24,18 @@ database.type=mysql
 datasource.type=fresh
 
 # Absolute path where Tomcat is installed
-tomcat.dir=/usr/local/tomcat
+tomcat.dir=/opt/tomcat/latest
 
 # Absolute path to OpenSpecimen data directory.
 # Best practice: Create a folder in parallel to 'tomcat.dir' with 
 # the name "openspecimen/data"
-app.data_dir=/opt/openspecimen/os-data
+app.data_dir=/opt/tomcat/latest/OpenSpecimen
 
 # Absolute path to OpenSpecimen data directory.
 # Best practice: Create a folder in parallel to 'tomcat.dir' with 
 # the name "openspecimen/plugins"
-plugin.dir=/opt/openspecimen/os-plugins
+plugin.dir=/opt/tomcat/latest/OpenSpecimen/plugins
 
 # Optional. Absolute path of the customised logging configuration file.
 # The configuration file should follow log4j configuration rules.
-app.log_conf=
+app.log_conf=