Merge pull request #213 from EGA-archive/bugfix/EE-2415

Bugfix/EE-2415

.gitignore

@@ -46,3 +46,5 @@ __pycache__
 
 # Personal files
 personal
+local_run
+config-map

ega-data-api-dataedge/src/main/java/eu/elixir/ega/ebi/dataedge/rest/FileController.java

@@ -22,7 +22,9 @@ import eu.elixir.ega.ebi.commons.shared.service.AuthenticationService;
 import lombok.extern.slf4j.Slf4j;
 import eu.elixir.ega.ebi.dataedge.service.FileService;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableBeanFactory;
 import org.springframework.cloud.client.discovery.EnableDiscoveryClient;
+import org.springframework.context.annotation.Scope;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.security.core.Authentication;
@@ -39,6 +41,7 @@ import static org.springframework.web.bind.annotation.RequestMethod.*;
  * @author asenf
  */
 @RestController
+@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
 @EnableDiscoveryClient
 @Slf4j
 @RequestMapping("/files")

ega-data-api-dataedge/src/main/java/eu/elixir/ega/ebi/dataedge/service/internal/RemoteFileServiceImpl.java

@@ -56,9 +56,11 @@ import okhttp3.OkHttpClient;
 import org.apache.commons.lang.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.beans.factory.config.ConfigurableBeanFactory;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.cloud.client.discovery.EnableDiscoveryClient;
 import org.springframework.cloud.client.loadbalancer.LoadBalancerClient;
+import org.springframework.context.annotation.Scope;
 import org.springframework.http.HttpMethod;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
@@ -89,6 +91,7 @@ import static eu.elixir.ega.ebi.commons.config.Constants.RES_SERVICE;
 import static org.apache.catalina.connector.OutputBuffer.DEFAULT_BUFFER_SIZE;
 
 @Service
+@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
 @EnableDiscoveryClient
 @Slf4j
 public class RemoteFileServiceImpl implements FileService {

ega-data-api-res/pom.xml

@@ -21,6 +21,12 @@
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-aop</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>log4j-over-slf4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.springframework.cloud</groupId>
@@ -37,7 +43,7 @@
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-actuator</artifactId>
-        </dependency>		
+        </dependency>
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-context-support</artifactId>
@@ -154,12 +160,20 @@
             <groupId>com.github.uio-bmi</groupId>
             <artifactId>crypt4gh</artifactId>
             <version>v1.2.1</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-jdk14</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>io.minio</groupId>
             <artifactId>minio</artifactId>
             <version>5.0.1</version>
         </dependency>
+
+
 		<dependency>
 			<groupId>uk.ac.ebi.ega</groupId>
 			<artifactId>fire-v3-core</artifactId>
@@ -171,7 +185,7 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
-		
+
         <!-- Test -->
         <dependency>
             <groupId>org.springframework.boot</groupId>

ega-data-api-res/src/main/java/eu/elixir/ega/ebi/reencryptionmvc/rest/FileController.java

@@ -24,7 +24,9 @@ import htsjdk.samtools.seekablestream.ebi.BufferedBackgroundInputStream;
 import lombok.extern.slf4j.Slf4j;
 
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableBeanFactory;
 import org.springframework.cloud.client.discovery.EnableDiscoveryClient;
+import org.springframework.context.annotation.Scope;
 import org.springframework.web.bind.annotation.*;
 
 import javax.servlet.ServletContext;
@@ -46,6 +48,7 @@ import java.util.stream.StreamSupport;
  * @author asenf
  */
 @RestController
+@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
 @EnableDiscoveryClient
 @Slf4j
 @RequestMapping("/file")

startall.sh

+#!/bin/bash
+
+## This script will launch the main components for data-api (config, eureka, key, filedatabase)
+## Please run the following components in debug mode: res, data-edge, htsget
+
+
+#Save current dir for future usage
+DIR=$(pwd)
+RUNDIR=$DIR/local_run
+LOG_DIR=$RUNDIR/logs
+
+
+VERSION=1.2.1-SNAPSHOT
+mkdir -p $LOG_DIR
+
+echo "Building project with maven in background..."
+mvn clean install > /dev/null
+echo "Done compiling."
+
+
+#-------------------------------
+echo "Launching config server..."
+
+cd ega-data-api-netflix/ega-data-api-config
+mvn package spring-boot:repackage > /dev/null
+
+cd $DIR
+nohup java -jar ega-data-api-netflix/ega-data-api-config/target/ega-data-api-config-$VERSION.jar > $LOG_DIR/config.logs  2>&1 &
+echo "config: $!" > $RUNDIR/process_ids.txt
+
+
+#-------------------------------
+echo "Launching eureka server..."
+
+cd ega-data-api-netflix/ega-data-api-eureka
+mvn package spring-boot:repackage > /dev/null
+
+cd $DIR
+nohup java -jar ega-data-api-netflix/ega-data-api-eureka/target/ega-data-api-eureka-$VERSION.jar > $LOG_DIR/eureka.logs  2>&1 &
+echo "eureka: $!" >> $RUNDIR/process_ids.txt
+
+
+#-------------------------------
+echo "Launching key server..."
+
+cd ega-data-api-key
+mvn package spring-boot:repackage > /dev/null
+
+cd $DIR
+nohup java -jar ega-data-api-key/target/ega-data-api-key-$VERSION.jar > $LOG_DIR/key.logs  2>&1 &
+echo "key: $!" >> $RUNDIR/process_ids.txt
+
+
+#-------------------------------
+echo "Launching file-database server..."
+
+cd ega-data-api-filedatabase
+mvn package spring-boot:repackage > /dev/null
+
+cd $DIR
+nohup java -jar ega-data-api-filedatabase/target/ega-data-api-filedatabase-$VERSION.jar > $LOG_DIR/file.logs  2>&1 &
+echo "filedatabase: $!" >> $RUNDIR/process_ids.txt
+
+
+#-------------------------------
+echo "Launching res server..."
+
+cd ega-data-api-res
+mvn package spring-boot:repackage > /dev/null
+
+cd $DIR
+nohup java -jar ega-data-api-res/target/ega-data-api-res-$VERSION.jar > $LOG_DIR/res.logs  2>&1 &
+echo "res: $!" >> $RUNDIR/process_ids.txt
+
+
+#-------------------------------
+echo "Launching dataedge server..."
+
+cd ega-data-api-dataedge
+mvn package spring-boot:repackage > /dev/null
+
+cd $DIR
+nohup java -jar ega-data-api-dataedge/target/ega-data-api-dataedge-$VERSION.jar > $LOG_DIR/dataedge.logs  2>&1 &
+echo "dataedge: $!" >> $RUNDIR/process_ids.txt
+
+
+#-------------------------------
+echo "Launching htsget server..."
+
+cd ega-data-api-htsget
+mvn package spring-boot:repackage > /dev/null
+
+cd $DIR
+nohup java -jar ega-data-api-htsget/target/ega-data-api-htsget-$VERSION.jar > $LOG_DIR/htsget.logs  2>&1 &
+echo "htsget: $!" >> $RUNDIR/process_ids.txt
+
+
+#-------------------------------
+echo ""
+echo "All processes started (Name: PID)"
+cat $RUNDIR/process_ids.txt
+
+echo ""
+echo "Logs: $LOG_DIR"
+ls -ltrh $LOG_DIR
+echo ""
+read -n 1 -r -s -p $'Press enter to exit...'
+
+#-------------------------------
+echo "Killing all processes:"
+
+PIDS="$(cat $RUNDIR/process_ids.txt | awk -F' ' '{print $2}' | paste -s -d' ')"
+KILL_COMMAND="kill -9 $PIDS"
+echo "    -> $KILL_COMMAND"
+eval $KILL_COMMAND
+