♻️ refactor(log-service): Refactor server and log service for docker …

…packaging.

docker/docker-compose.yml

@@ -2,32 +2,31 @@ version: '3.9'
 services:
   tofhir-log-server:
     image: srdc/tofhir-log-server:latest
-    container_name: tofhir-log
-    hostname: tofhir-log
-    environment:
-      - APP_CONF_FILE=/tofhir/conf/log-service.conf
+    container_name: tofhir-log-server
+    hostname: tofhir-log-server
     ports:
       - "8086:8086"
     networks:
       - tofhir-network
     volumes:
-      - './data-ingestion-suite:/tofhir/conf'
-      - './tofhir-docker-logs:/tofhir/logs'
+      - './tofhir-docker-logs:/usr/local/tofhir/logs'
   tofhir-server:
     image: srdc/tofhir-server:latest
     container_name: tofhir
     hostname: tofhir
     environment:
-      - LOG_SERVER_BASE_URL=http://tofhir-log:8086
+      - 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=/tofhir/conf/application.conf
+      - APP_CONF_FILE=/usr/local/tofhir/conf/docker/tofhir-server.conf
+      - CONTEXT_PATH=conf
     ports:
       - "8085:8085"
     networks:
       - tofhir-network
     volumes:
-      - './data-ingestion-suite:/tofhir/conf'
-      - './tofhir-docker-logs:/tofhir/logs'
+      - './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
@@ -39,5 +38,3 @@ networks:
   tofhir-network:
     name: onfhir-network
     external: true
-volumes:
-  fhirdb: {}

docker/engine/Dockerfile-addJar

@@ -4,7 +4,7 @@ ENV TOFHIR_HOME /usr/local/tofhir
 RUN mkdir -p "$TOFHIR_HOME"
 WORKDIR $TOFHIR_HOME
 
-COPY ./tofhir-engine/target/tofhir-standalone.jar .
+COPY ./tofhir-engine/target/tofhir-engine-standalone.jar .
 COPY ./docker/engine/docker-entrypoint.sh .
 RUN chmod +x docker-entrypoint.sh
 

docker/engine/Dockerfile-buildJar

@@ -17,7 +17,7 @@ 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/engine/docker-entrypoint.sh .
 RUN chmod +x 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

@@ -1,14 +1,11 @@
 FROM openjdk:11-jre-slim
 
-# Create folders
-RUN mkdir -p /tofhir
-WORKDIR /tofhir
+ENV TOFHIR_HOME /usr/local/tofhir
+RUN mkdir -p "$TOFHIR_HOME"
+WORKDIR $TOFHIR_HOME
 
-# Add Files
 COPY ./tofhir-log-server/target/tofhir-log-server-standalone.jar .
 COPY ./docker/log-server/docker-entrypoint.sh .
-COPY ./tofhir-log-server/src/main/resources/logback.xml .
+RUN chmod +x docker-entrypoint.sh
 
-RUN chmod +x /tofhir/docker-entrypoint.sh
-
-ENTRYPOINT ["/tofhir/docker-entrypoint.sh"]
+ENTRYPOINT ["./docker-entrypoint.sh"]

docker/log-server/build.sh

@@ -1,4 +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 -t srdc/tofhir-log-server:1.0 .
+docker build -f docker/log-server/Dockerfile -t srdc/tofhir-log-server:latest .
 

docker/log-server/docker-entrypoint.sh

@@ -1,15 +1,42 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
-JAVA_CMD="java -jar "
+JAVA_CMD="java -Xms256m -Xmx3g -jar "
 
 # Configure application.conf path
 if [ ! -z "$APP_CONF_FILE" ]; then
-    JAVA_CMD+="-Dconfig.file=$APP_CONF_FILE "
+  JAVA_CMD+="-Dconfig.file=$APP_CONF_FILE "
 fi
 
-# Finally, tell which jar to run
-JAVA_CMD+="/tofhir/tofhir-log-server-standalone.jar"
+# 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
 
-echo "Running command: $JAVA_CMD"
+# Delay the execution for this amount of seconds
+if [ ! -z "$DELAY_EXECUTION" ]; then
+  sleep $DELAY_EXECUTION
+fi
+
+# Finally, tell which jar to run
+JAVA_CMD+="tofhir-log-server-standalone.jar"
 
-eval $JAVA_CMD
+eval $JAVA_CMD "$@"

docker/server/Dockerfile

@@ -1,14 +1,11 @@
 FROM openjdk:11-jre-slim
 
-# Create folders
-RUN mkdir -p /tofhir
-WORKDIR /tofhir
+ENV TOFHIR_HOME /usr/local/tofhir
+RUN mkdir -p "$TOFHIR_HOME"
+WORKDIR $TOFHIR_HOME
 
-# Add Files
 COPY ./tofhir-server/target/tofhir-server-standalone.jar .
 COPY ./docker/server/docker-entrypoint.sh .
-COPY ./tofhir-server/src/main/resources/logback.xml .
+RUN chmod +x docker-entrypoint.sh
 
-RUN chmod +x /tofhir/docker-entrypoint.sh
-
-ENTRYPOINT ["/tofhir/docker-entrypoint.sh"]
+ENTRYPOINT ["./docker-entrypoint.sh"]

docker/server/build.sh

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

docker/server/docker-entrypoint.sh

@@ -1,23 +1,84 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
-JAVA_CMD="java -jar "
+JAVA_CMD="java -Xms256m -Xmx3g -jar "
 
 # Configure application.conf path
 if [ ! -z "$APP_CONF_FILE" ]; then
-    JAVA_CMD+="-Dconfig.file=$APP_CONF_FILE "
+  JAVA_CMD+="-Dconfig.file=$APP_CONF_FILE "
 fi
 
-if [ ! -z "$FHIR_REPO_URL" ]; then
-    JAVA_CMD+="-Dfhir.definitions-fhir-endpoint=$FHIR_REPO_URL "
+# Configure logback configuration file
+if [ ! -z "$LOGBACK_CONF_FILE" ]; then
+  JAVA_CMD+="-Dlogback.configurationFile=$LOGBACK_CONF_FILE "
 fi
 
-if [ ! -z "$LOG_SERVER_BASE_URL" ]; then
-    JAVA_CMD+="-webserver.log-server-base-url=$LOG_SERVER_BASE_URL "
+# 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
 
-# Finally, tell which jar to run
-JAVA_CMD+="/tofhir/tofhir-server-standalone.jar"
+# 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
 
-echo "Running command: $JAVA_CMD"
+# Configure the FHIR endpoint to which this toFHIR can connect to retrieve resource definitions etc.
+if [ ! -z "$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
+eval $JAVA_CMD "$@"

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
    */

tofhir-log-server/src/main/resources/application.conf

@@ -6,7 +6,7 @@ webserver = {
   port = 8086
 
   # Base Uri for server e.g. With this default configuration, the root path of toFHIR server will be http://localhost:8085/tofhir
-  base-uri = tofhir
+  base-uri = tofhir-logs
 
   ssl {
     # Path to the java keystore for enabling ssl for toFHIR server, use null to disable ssl

tofhir-log-server/src/main/scala/io/tofhir/server/endpoint/JobEndpoint.scala

@@ -37,7 +37,6 @@ class JobEndpoint() extends LazyLogging {
     }
   }
 
-
   /**
    * Route to get executions of a mapping job
    * */
@@ -59,6 +58,7 @@ class JobEndpoint() extends LazyLogging {
 
   /**
    * Route to get execution logs of a mapping job execution
+   *
    * @param projectId
    * @param jobId
    * @param executionId

tofhir-log-server/src/main/scala/io/tofhir/server/endpoint/ProjectEndpoint.scala

@@ -15,12 +15,11 @@ class ProjectEndpoint() extends LazyLogging {
 
   def route(request: ToFhirRestCall): Route = {
     pathPrefix(SEGMENT_PROJECTS) {
-      pathPrefix(Segment) { projectId: String =>
-          {
-            request.projectId = Some(projectId)
-            jobEndpoint.route(request)
-          }
-        }
+      pathPrefix(Segment) { projectId: String => {
+        request.projectId = Some(projectId)
+        jobEndpoint.route(request)
+      }
+      }
     }
   }
 }

tofhir-server/src/main/resources/application.conf

@@ -108,8 +108,6 @@ webserver = {
   # Base Uri for server e.g. With this default configuration, the root path of toFHIR server will be http://localhost:8085/tofhir
   base-uri = tofhir
 
-  log-server-base-url = "http://localhost:8086"
-
   ssl {
     # Path to the java keystore for enabling ssl for toFHIR server, use null to disable ssl
     keystore = null
@@ -118,6 +116,11 @@ webserver = {
   }
 }
 
+# The service from where tofhir-server will read the logs.
+log-service = {
+  endpoint = "http://localhost:8086/tofhir-logs"
+}
+
 # Spark configurations
 spark = {
   app.name = "AICCELERATE Data Integration Suite"

tofhir-server/src/main/scala/io/tofhir/server/ToFhirServer.scala

@@ -1,7 +1,7 @@
 package io.tofhir.server
 
 import io.tofhir.engine.config.ToFhirConfig
-import io.tofhir.server.config.WebServerConfig
+import io.tofhir.server.config.{LogServiceConfig, WebServerConfig}
 import io.tofhir.server.endpoint.ToFhirServerEndpoint
 import io.tofhir.server.fhir.FhirDefinitionsConfig
 
@@ -11,7 +11,8 @@ object ToFhirServer {
 
     val webServerConfig = new WebServerConfig(actorSystem.settings.config.getConfig("webserver"))
     val fhirDefinitionsConfig = new FhirDefinitionsConfig(actorSystem.settings.config.getConfig("fhir"))
-    val endpoint = new ToFhirServerEndpoint(ToFhirConfig.engineConfig, webServerConfig, fhirDefinitionsConfig)
+    val logServiceConfig = new LogServiceConfig(actorSystem.settings.config.getConfig("log-service"))
+    val endpoint = new ToFhirServerEndpoint(ToFhirConfig.engineConfig, webServerConfig, fhirDefinitionsConfig, logServiceConfig)
 
     ToFhirHttpServer.start(endpoint.toFHIRRoute, webServerConfig)
   }

tofhir-server/src/main/scala/io/tofhir/server/config/LogServiceConfig.scala

@@ -0,0 +1,10 @@
+package io.tofhir.server.config
+
+import com.typesafe.config.Config
+
+import scala.util.Try
+
+class LogServiceConfig(logServiceConfig: Config) {
+  /** Host name/address to start service on. */
+  lazy val logServiceEndpoint: String = Try(logServiceConfig.getString("endpoint")).getOrElse("http://localhost:8086/tofhir-log")
+}