Concept fix

.github/workflows/main.yml

@@ -0,0 +1,51 @@
+name: Build Docker Image
+
+on:
+  pull_request:
+    branches: [main,test]
+  release:
+    types: [published]
+  push:
+    branches: [main,test]
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}    
+
+jobs:
+  build-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Publish Docker Image
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          platforms: linux/amd64
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=inline,ref=user/app:buildcache
+          cache-to: type=inline,ref=user/app:buildcache,mode=max

.project

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>oshr</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+	</buildSpec>
+	<natures>
+	</natures>
+</projectDescription>

Dockerfile

@@ -3,43 +3,10 @@
 #
 #
 
-FROM uwitech/ohie-base
-
-
-# Install dependencies
-RUN apt-get update && \
-apt-get install -y software-properties-common
-RUN add-apt-repository ppa:openjdk-r/ppa && \
-apt-get update && \
-apt-get install -y git build-essential curl wget software-properties-common openjdk-7-jre mysql-client
-
-# Install Tomcat
-ENV CATALINA_HOME /usr/local/tomcat
-ENV PATH $CATALINA_HOME/bin:$PATH
-RUN mkdir -p "$CATALINA_HOME" && \
-  mkdir /var/log/xdslog && \
-  chmod 777 /var/log/xdslog
-
-WORKDIR $CATALINA_HOME
-
-ENV GPG_KEYS 05AB33110949707C93A279E3D3EFE6B686867BA6 07E48665A34DCAFAE522E5E6266191C37C037D42 47309207D818FFD8DCD3F83F1931D684307A10A5 541FBE7D8F78B25E055DDEE13C370389288584E7 61B832AC2F1C5A90F0F9B00A1C506407564C17A3 713DA88BE50911535FE716F5208B0AB1D63011C7 79F7026C690BAA50B92CD8B66A3AD3F4F22C4FED 9BA44C2621385CB966EBA586F72C284D731FABEE A27677289986DB50844682F8ACB77FC2E86E29AC A9C5DF4D22E99998D9875A5110C01C5A2F6059E7 DCFD35E0BF8CA7344752DE8B6FB21E8933C60243 F3A04C595DB5B6A5F1ECA43E3B7BBB100D811BBE F7DA48BB64BCB84ECBA7EE6935CD23C10D498E23
-RUN set -ex; \
-	for key in $GPG_KEYS; do \
-		gpg --keyserver hkp://ha.pool.sks-keyservers.net --recv-keys "$key" || gpg --keyserver hkp://pgp.mit.edu --recv-keys "$key"; \
-	done
-
-ENV TOMCATVER 7.0.73
-
-ENV TOMCAT_TGZ_URL http://archive.apache.org/dist/tomcat/tomcat-7/v${TOMCATVER}/bin/apache-tomcat-${TOMCATVER}.tar.gz
-
-RUN set -x \
-    && curl -fSL "$TOMCAT_TGZ_URL" -o tomcat7.tar.gz \
-    && curl -fSL "$TOMCAT_TGZ_URL.asc" -o tomcat7.tar.gz.asc \
-    && gpg --verify tomcat7.tar.gz.asc \
-    && tar -xvf tomcat7.tar.gz --strip-components=1 \
-    && rm bin/*.bat \
-    && rm tomcat7.tar.gz*
+FROM tomcat:8.5-jdk8-adoptopenjdk-hotspot
 
+# Install MySQL client
+RUN apt-get update && apt-get install -y git build-essential curl wget mysql-client
 
 # Install dockerize
 ENV DOCKERIZE_VERSION v0.2.0
@@ -63,18 +30,16 @@ RUN curl -L ${OPENMRS_PLATFORM_URL} \
 ADD modules/webservices.rest-2.12.omod ${TEMP_MODULES}/webservices.rest-2.12.omod
 ADD modules/uiframework-omod-3.4.omod ${TEMP_MODULES}/uiframework-omod-3.4.omod
 
-ADD modules/shr-atna-1.0.1-SNAPSHOT.omod ${TEMP_MODULES}/shr-atna-1.0.1-SNAPSHOT.omod
-ADD modules/shr-contenthandler-3.0.1-SNAPSHOT.omod ${TEMP_MODULES}/shr-contenthandler-3.0.1-SNAPSHOT.omod
-ADD modules/xds-b-repository-1.1.1-SNAPSHOT.omod ${TEMP_MODULES}/xds-b-repository-1.1.1-SNAPSHOT.omod
-ADD modules/shr-cdahandler-1.0.1-SNAPSHOT.omod ${TEMP_MODULES}/shr-cdahandler-1.0.1-SNAPSHOT.omod
+ADD modules/shr-atna-1.1.0.omod ${TEMP_MODULES}/shr-atna-1.1.0.omod
+ADD modules/shr-contenthandler-3.1.0.omod ${TEMP_MODULES}/shr-contenthandler-3.1.0.omod
+ADD modules/xds-b-repository-1.1.2.omod ${TEMP_MODULES}/xds-b-repository-1.1.2.omod
+ADD modules/shr-cdahandler-1.1.0.omod ${TEMP_MODULES}/shr-cdahandler-1.1.0.omod
 ADD modules/shr-odd-0.5.1.omod ${TEMP_MODULES}/shr-odd-0.5.1.omod
 ADD modules/openhie-client-0.1-SNAPSHOT.omod ${TEMP_MODULES}/openhie-client-0.1-SNAPSHOT.omod
 ADD modules/exportccd-1.0.0-SNAPSHOT.omod ${TEMP_MODULES}/exportccd-1.0.0-SNAPSHOT.omod
 
 # Load DATABASE script file
-RUN curl -L "https://s3.amazonaws.com/openshr/openmrs.sql.gz" \
-         -o openmrs.sql.gz \
-    && gunzip openmrs.sql.gz
+ADD openmrs.sql openmrs.sql
 
 ADD openshr-configuration.sql openshr-configuration.sql
 COPY concepts.sql shrdata.sql* /usr/local/tomcat/
@@ -90,4 +55,5 @@ ADD openmrs-runtime.properties.tmpl "${CATALINA_HOME}/openmrs-runtime.properties
 ADD setenv.sh.tmpl "${CATALINA_HOME}/bin/setenv.sh.tmpl"
 
 # Run openmrs using dockerize
-CMD ["dockerize","-template","/usr/local/tomcat/bin/setenv.sh.tmpl:/usr/local/tomcat/bin/setenv.sh","-template","/usr/local/tomcat/openmrs-runtime.properties.tmpl:/usr/local/tomcat/openmrs-runtime.properties","-wait","tcp://openmrs-mysql-db:3306","-timeout","200s","/root/cmd.sh", "run"]
+ENTRYPOINT dockerize -template /usr/local/tomcat/bin/setenv.sh.tmpl:/usr/local/tomcat/bin/setenv.sh -template /usr/local/tomcat/openmrs-runtime.properties.tmpl:/usr/local/tomcat/openmrs-runtime.properties -wait tcp://$MYSQL_HOST:$MYSQL_PORT -timeout 200s /root/cmd.sh run
+

cmd.sh

@@ -29,29 +29,29 @@ else
 	cp /root/temp/modules/*.omod $OPENMRS_MODULES
 	echo "Modules copied."
 
-	DB=`mysql -u root -p${MYSQL_ROOT_PASSWORD} --skip-column-names -e "SHOW DATABASES LIKE '${OPENMRS_DATABASE}'"`
+	DB=`mysql --ssl-mode=DISABLED -u root -p${MYSQL_ROOT_PASSWORD} --skip-column-names -e "SHOW DATABASES LIKE '${OPENMRS_DATABASE}'"`
 	if [ "$DB" != "${OPENMRS_DATABASE}" ]; then
 		echo "# Init database for OpenMRS #"
 
-		mysql -u root -p${MYSQL_ROOT_PASSWORD} -e "CREATE DATABASE ${OPENMRS_DATABASE};"
+		mysql --ssl-mode=DISABLED -u root -p${MYSQL_ROOT_PASSWORD} -e "CREATE DATABASE ${OPENMRS_DATABASE};"
 
-		mysql -u root -p${MYSQL_ROOT_PASSWORD} -e "GRANT ALL ON openmrs.* to '${MYSQL_USER}'@'%' identified by '${MYSQL_PASSWORD}';"
+		mysql --ssl-mode=DISABLED -u root -p${MYSQL_ROOT_PASSWORD} -e "GRANT ALL ON openmrs.* to '${MYSQL_USER}'@'%' identified by '${MYSQL_PASSWORD}';"
 
 		echo "Create database openmrs from file < openmrs.sql"
-		mysql -u root -p${MYSQL_ROOT_PASSWORD} openmrs < openmrs.sql
+		mysql --ssl-mode=DISABLED  -u root -p${MYSQL_ROOT_PASSWORD} openmrs < openmrs.sql
 
 		echo "Load concepts to openmrs database from file < concepts.sql"
-		mysql -u root -p${MYSQL_ROOT_PASSWORD} openmrs < concepts.sql
+		mysql --ssl-mode=DISABLED -u root -p${MYSQL_ROOT_PASSWORD} openmrs < concepts.sql
 
 		if [ $data_file -eq 1 ]; then
 			echo "Load data to openmrs database from file < shrdata.sql"
-			mysql -u root -p${MYSQL_ROOT_PASSWORD} openmrs < shrdata.sql
+			mysql --ssl-mode=DISABLED -u root -p${MYSQL_ROOT_PASSWORD} openmrs < shrdata.sql
 		else
 			echo "Add shrdata.sql file to this direcatory to load data into SHR database"
 		fi
 
 		echo "Update database openmrs with SHR configuration from file < openshr-configuration.sql"
-		mysql -u root -p${MYSQL_ROOT_PASSWORD} openmrs < openshr-configuration.sql
+		mysql --ssl-mode=DISABLED -u root -p${MYSQL_ROOT_PASSWORD} openmrs < openshr-configuration.sql
 
 		echo "Finish init database"
 		rm openmrs.sql
@@ -64,4 +64,5 @@ fi
 
 
 echo "# Start TOMCAT #"
+export CATALINA_OPTS="$CATALINA_OPTS -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=1048"
 catalina.sh run