Merge pull request #108 from srdc/tofhir-log-server

Tofhir log server

docker/docker-compose.yml

@@ -0,0 +1,40 @@
+version: '3.9'
+services:
+  tofhir-log-server:
+    image: srdc/tofhir-log-server:latest
+    container_name: tofhir-log-server
+    hostname: tofhir-log-server
+    ports:
+      - "8086:8086"
+    networks:
+      - tofhir-network
+    volumes:
+      - './tofhir-docker-logs:/usr/local/tofhir/logs'
+  tofhir-server:
+    image: srdc/tofhir-server:latest
+    container_name: tofhir
+    hostname: tofhir
+    environment:
+      - LOG_SERVICE_ENDPOINT=http://tofhir-log-server:8086/tofhir-logs
+      - FHIR_DEFINITIONS_ENDPOINT=http://onfhir:8080/fhir
+      - FHIR_REPO_URL=http://onfhir:8080/fhir
+      - APP_CONF_FILE=/usr/local/tofhir/conf/docker/tofhir-server.conf
+      - CONTEXT_PATH=conf
+    ports:
+      - "8085:8085"
+    networks:
+      - tofhir-network
+    volumes:
+      - './data-integration-suite:/usr/local/tofhir/conf'
+      - './tofhir-docker-logs:/usr/local/tofhir/logs'
+  tofhir-web:
+    image: srdc/tofhir-web:latest
+    container_name: tofhir-web
+    ports:
+      - "8082:80"
+    networks:
+      - tofhir-network
+networks:
+  tofhir-network:
+    name: onfhir-network
+    external: true

docker/Dockerfile-addJar → docker/engine/Dockerfile-addJar

@@ -4,8 +4,8 @@ ENV TOFHIR_HOME /usr/local/tofhir
 RUN mkdir -p "$TOFHIR_HOME"
 WORKDIR $TOFHIR_HOME
 
-COPY ./tofhir-engine/target/tofhir-standalone.jar .
-COPY ./docker/docker-entrypoint.sh .
+COPY ./tofhir-engine/target/tofhir-engine-standalone.jar .
+COPY ./docker/engine/docker-entrypoint.sh .
 RUN chmod +x docker-entrypoint.sh
 
 ENTRYPOINT ["./docker-entrypoint.sh"]

docker/Dockerfile-buildJar → docker/engine/Dockerfile-buildJar

@@ -17,9 +17,9 @@ ENV TOFHIR_HOME /usr/local/tofhir
 RUN mkdir -p "$TOFHIR_HOME"
 WORKDIR $TOFHIR_HOME
 
-COPY --from=builder $TOFHIR_HOME/tofhir-engine/target/tofhir-standalone.jar .
+COPY --from=builder $TOFHIR_HOME/tofhir-engine/target/tofhir-engine-standalone.jar .
 
-COPY docker/docker-entrypoint.sh .
+COPY docker/engine/docker-entrypoint.sh .
 RUN chmod +x docker-entrypoint.sh
 
 ENTRYPOINT ["./docker-entrypoint.sh"]

docker/engine/build.sh

@@ -0,0 +1,4 @@
+# Execute one of the following commands from the project.root.directory (../../)
+
+docker build -f docker/engine/Dockerfile-addJar -t srdc/tofhir:latest -t srdc/tofhir:1.0 .
+docker build -f docker/engine/Dockerfile-buildJar -t srdc/tofhir:latest -t srdc/tofhir:1.0 .

docker/docker-entrypoint.sh → docker/engine/docker-entrypoint.sh

@@ -37,7 +37,7 @@ if [ ! -z "$FHIR_BATCH_SIZE" ]; then
   JAVA_CMD+="-Dtofhir.fhir-writer.batch-group-size=$FHIR_BATCH_SIZE "
 fi
 if [ ! -z "$DB_PATH" ]; then
-  JAVA_CMD+="-Dtofhir.db=$DB_PATH "
+  JAVA_CMD+="-Dtofhir.db-path=$DB_PATH "
 fi
 
 # Delay the execution for this amount of seconds
@@ -46,6 +46,6 @@ if [ ! -z "$DELAY_EXECUTION" ]; then
 fi
 
 # Finally, tell which jar to run
-JAVA_CMD+="tofhir-standalone.jar"
+JAVA_CMD+="tofhir-engine-standalone.jar"
 
 eval $JAVA_CMD "$@"

docker/log-server/Dockerfile

@@ -0,0 +1,11 @@
+FROM openjdk:11-jre-slim
+
+ENV TOFHIR_HOME /usr/local/tofhir
+RUN mkdir -p "$TOFHIR_HOME"
+WORKDIR $TOFHIR_HOME
+
+COPY ./tofhir-log-server/target/tofhir-log-server-standalone.jar .
+COPY ./docker/log-server/docker-entrypoint.sh .
+RUN chmod +x docker-entrypoint.sh
+
+ENTRYPOINT ["./docker-entrypoint.sh"]

docker/log-server/build.sh

@@ -0,0 +1,4 @@
+# Execute one of the following commands from the project.root.directory (../../)
+
+docker build -f docker/log-server/Dockerfile -t srdc/tofhir-log-server:latest .
+

docker/log-server/docker-entrypoint.sh

@@ -0,0 +1,42 @@
+#!/usr/bin/env bash
+
+JAVA_CMD="java -Xms256m -Xmx3g -jar "
+
+# Configure application.conf path
+if [ ! -z "$APP_CONF_FILE" ]; then
+  JAVA_CMD+="-Dconfig.file=$APP_CONF_FILE "
+fi
+
+# Configure logback configuration file
+if [ ! -z "$LOGBACK_CONF_FILE" ]; then
+  JAVA_CMD+="-Dlogback.configurationFile=$LOGBACK_CONF_FILE "
+fi
+
+# Configure Spark
+if [ ! -z "$SPARK_APPNAME" ]; then
+  JAVA_CMD+="-Dspark.app-name=$SPARK_APPNAME "
+fi
+if [ ! -z "$SPARK_MASTER" ]; then
+  JAVA_CMD+="-Dspark.master=$SPARK_MASTER "
+fi
+
+# Configure tofhir-server web server
+if [ ! -z "$WEBSERVER_HOST" ]; then
+  JAVA_CMD+="-Dwebserver.host=$WEBSERVER_HOST "
+fi
+if [ ! -z "$WEBSERVER_PORT" ]; then
+  JAVA_CMD+="-Dwebserver.port=$WEBSERVER_PORT "
+fi
+if [ ! -z "$WEBSERVER_BASEURI" ]; then
+  JAVA_CMD+="-Dwebserver.base-uri=$WEBSERVER_BASEURI "
+fi
+
+# Delay the execution for this amount of seconds
+if [ ! -z "$DELAY_EXECUTION" ]; then
+  sleep $DELAY_EXECUTION
+fi
+
+# Finally, tell which jar to run
+JAVA_CMD+="tofhir-log-server-standalone.jar"
+
+eval $JAVA_CMD "$@"

docker/server/Dockerfile

@@ -0,0 +1,11 @@
+FROM openjdk:11-jre-slim
+
+ENV TOFHIR_HOME /usr/local/tofhir
+RUN mkdir -p "$TOFHIR_HOME"
+WORKDIR $TOFHIR_HOME
+
+COPY ./tofhir-server/target/tofhir-server-standalone.jar .
+COPY ./docker/server/docker-entrypoint.sh .
+RUN chmod +x docker-entrypoint.sh
+
+ENTRYPOINT ["./docker-entrypoint.sh"]

docker/server/build.sh

@@ -0,0 +1,4 @@
+# Execute one of the following commands from the project.root.directory (../../)
+
+docker build -f docker/server/Dockerfile -t srdc/tofhir-server:latest .
+

docker/server/docker-entrypoint.sh

@@ -0,0 +1,84 @@
+#!/usr/bin/env bash
+
+JAVA_CMD="java -Xms256m -Xmx3g -jar "
+
+# Configure application.conf path
+if [ ! -z "$APP_CONF_FILE" ]; then
+  JAVA_CMD+="-Dconfig.file=$APP_CONF_FILE "
+fi
+
+# Configure logback configuration file
+if [ ! -z "$LOGBACK_CONF_FILE" ]; then
+  JAVA_CMD+="-Dlogback.configurationFile=$LOGBACK_CONF_FILE "
+fi
+
+# Configure Spark
+if [ ! -z "$SPARK_APPNAME" ]; then
+  JAVA_CMD+="-Dspark.app-name=$SPARK_APPNAME "
+fi
+if [ ! -z "$SPARK_MASTER" ]; then
+  JAVA_CMD+="-Dspark.master=$SPARK_MASTER "
+fi
+
+# Configure toFHIR mapping-related paths
+if [ ! -z "$CONTEXT_PATH" ]; then
+  JAVA_CMD+="-Dtofhir.context-path=$CONTEXT_PATH "
+fi
+if [ ! -z "$MAPPINGS_FOLDER" ]; then
+  JAVA_CMD+="-Dtofhir.mappings.repository.folder-path=$MAPPINGS_FOLDER "
+fi
+if [ ! -z "$SCHEMAS_FOLDER" ]; then
+  JAVA_CMD+="-Dtofhir.mappings.schemas.repository.folder-path=$SCHEMAS_FOLDER "
+fi
+if [ ! -z "$MAPPING_JOB" ]; then
+  JAVA_CMD+="-Dtofhir.mapping-jobs.initial-job-file-path=$MAPPING_JOB "
+fi
+if [ ! -z "$FHIR_BATCH_SIZE" ]; then
+  JAVA_CMD+="-Dtofhir.fhir-writer.batch-group-size=$FHIR_BATCH_SIZE "
+fi
+if [ ! -z "$DB_PATH" ]; then
+  JAVA_CMD+="-Dtofhir.db-path=$DB_PATH "
+fi
+
+# Configure the FHIR endpoint to which this toFHIR can connect to retrieve resource definitions etc.
+if [ ! -z "$FHIR_DEFINITIONS_ENDPOINT" ]; then
+  JAVA_CMD+="-Dfhir.definitions-fhir-endpoint=$FHIR_DEFINITIONS_ENDPOINT "
+fi
+if [ ! -z "$FHIR_DEFINITIONS_ROOT_URL" ]; then
+  JAVA_CMD+="-Dfhir.definitions-root-urls=$FHIR_DEFINITIONS_ROOT_URL "
+fi
+if [ ! -z "$FHIR_DEFINITIONS_PROFILES_PATH" ]; then
+  JAVA_CMD+="-Dfhir.profiles-path=$FHIR_DEFINITIONS_ROOT_URL "
+fi
+if [ ! -z "$FHIR_DEFINITIONS_VALUESETS_PATH" ]; then
+  JAVA_CMD+="-Dfhir.valuesets-path=$FHIR_DEFINITIONS_VALUESETS_PATH "
+fi
+if [ ! -z "$FHIR_DEFINITIONS_CODESYSTEMS_URL" ]; then
+  JAVA_CMD+="-Dfhir.codesystems-path=$FHIR_DEFINITIONS_CODESYSTEMS_URL "
+fi
+
+# Configure tofhir-server web server
+if [ ! -z "$WEBSERVER_HOST" ]; then
+  JAVA_CMD+="-Dwebserver.host=$WEBSERVER_HOST "
+fi
+if [ ! -z "$WEBSERVER_PORT" ]; then
+  JAVA_CMD+="-Dwebserver.port=$WEBSERVER_PORT "
+fi
+if [ ! -z "$WEBSERVER_BASEURI" ]; then
+  JAVA_CMD+="-Dwebserver.base-uri=$WEBSERVER_BASEURI "
+fi
+
+# Configure log service
+if [ ! -z "$LOG_SERVICE_ENDPOINT" ]; then
+  JAVA_CMD+="-Dlog-service.endpoint=$LOG_SERVICE_ENDPOINT "
+fi
+
+# Delay the execution for this amount of seconds
+if [ ! -z "$DELAY_EXECUTION" ]; then
+  sleep $DELAY_EXECUTION
+fi
+
+# Finally, tell which jar to run
+JAVA_CMD+="tofhir-server-standalone.jar"
+
+eval $JAVA_CMD "$@"

pom.xml

@@ -57,6 +57,7 @@
     <modules>
         <module>tofhir-engine</module>
         <module>tofhir-server</module>
+        <module>tofhir-log-server</module>
         <module>tofhir-common</module>
         <module>tofhir-rxnorm</module>
     </modules>
@@ -356,6 +357,11 @@
                 <artifactId>tofhir-server-common_2.13</artifactId>
                 <version>${project.version}</version>
             </dependency>
+            <dependency>
+                <groupId>io.onfhir</groupId>
+                <artifactId>tofhir-log-server-common_2.13</artifactId>
+                <version>${project.version}</version>
+            </dependency>
             <dependency>
                 <groupId>io.onfhir</groupId>
                 <artifactId>tofhir-engine_2.13</artifactId>

tofhir-engine/pom.xml

@@ -92,7 +92,7 @@
                                 </filter>
                             </filters>
                             <createDependencyReducedPom>false</createDependencyReducedPom>
-                            <finalName>tofhir-standalone</finalName>
+                            <finalName>tofhir-engine-standalone</finalName>
                             <transformers>
                                 <!-- add Main-Class to manifest file -->
                                 <transformer

tofhir-engine/src/main/scala/io/tofhir/engine/ToFhirEngine.scala

@@ -27,6 +27,7 @@ class ToFhirEngine(mappingRepository: Option[IFhirMappingCachedRepository] = Non
 
   //Spark configurations
   private val sparkConf: SparkConf = ToFhirConfig.createSparkConf
+
   val engineConfig: ToFhirEngineConfig = ToFhirConfig.engineConfig
 
   val sparkSession: SparkSession = SparkSession.builder().config(sparkConf).getOrCreate()

tofhir-engine/src/main/scala/io/tofhir/engine/config/ToFhirConfig.scala

@@ -24,6 +24,7 @@ object ToFhirConfig {
   lazy val sparkAppName: String = Try(sparkConfig.getString("app.name")).getOrElse("AICCELERATE Data Integration Suite")
   /** Master url of the Spark cluster */
   lazy val sparkMaster: String = Try(sparkConfig.getString("master")).getOrElse("local[4]")
+
   /**
    * Default configurations for spark
    */