struct logs with gz rotation

build.gradle

@@ -51,6 +51,7 @@ dependencies {
     implementation 'org.xerial:sqlite-jdbc:3.8.11.2'
     implementation 'com.vladmihalcea:hibernate-types-52:2.14.0'
     implementation 'org.ga4gh:ga4gh-starter-kit-common:0.5.6'
+    implementation 'net.logstash.logback:logstash-logback-encoder:7.0.1'
 
     testCompileOnly 'org.projectlombok:lombok:1.18.22'
 	testAnnotationProcessor 'org.projectlombok:lombok:1.18.22'

src/main/java/org/ga4gh/testbed/api/app/TestbedApiSpringConfig.java

@@ -1,16 +1,13 @@
 package org.ga4gh.testbed.api.app;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
+import ch.qos.logback.classic.Logger;
 import org.apache.catalina.connector.Connector;
 import org.apache.commons.cli.Options;
 import org.ga4gh.starterkit.common.config.DatabaseProps;
 import org.ga4gh.starterkit.common.config.ServerProps;
 import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
 import org.ga4gh.starterkit.common.util.CliYamlConfigLoader;
 import org.ga4gh.starterkit.common.util.DeepObjectMerger;
-import org.ga4gh.starterkit.common.util.logging.LoggingUtil;
 import org.ga4gh.starterkit.common.util.webserver.AdminEndpointsConnector;
 import org.ga4gh.starterkit.common.util.webserver.AdminEndpointsFilter;
 import org.ga4gh.starterkit.common.util.webserver.CorsFilterBuilder;
@@ -30,6 +27,7 @@
 import org.ga4gh.testbed.api.model.TestbedTest;
 import org.ga4gh.testbed.api.model.TestbedVersion;
 import org.ga4gh.testbed.api.utils.hibernate.TestbedApiHibernateUtil;
+import org.ga4gh.testbed.api.utils.logging.TestbedLoggingUtil;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
@@ -42,6 +40,9 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Scope;
 import org.springframework.web.filter.CorsFilter;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
 
 @Configuration
 @ConfigurationProperties
@@ -148,8 +149,13 @@ public DatabaseProps getDatabaseProps(
      * ****************************** */
 
     @Bean
-    public LoggingUtil loggingUtil() {
-        return new LoggingUtil();
+    public TestbedLoggingUtil testbedloggingUtil() {
+        return new TestbedLoggingUtil();
+    }
+
+    @Bean
+    public Logger getLogger(@Autowired TestbedLoggingUtil testbedLoggingUtil) {
+        return testbedLoggingUtil.getLogger();
     }
 
     /* ******************************
@@ -181,4 +187,4 @@ public TestbedApiHibernateUtil getHibernateUtil(
         hibernateUtil.setDatabaseProps(databaseProps);
         return hibernateUtil;
     }
-}
+}

src/main/java/org/ga4gh/testbed/api/utils/logging/TestbedLoggingUtil.java

@@ -0,0 +1,156 @@
+package org.ga4gh.testbed.api.utils.logging;
+
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
+import ch.qos.logback.classic.LoggerContext;
+import ch.qos.logback.classic.spi.ILoggingEvent;
+import ch.qos.logback.core.ConsoleAppender;
+import ch.qos.logback.core.rolling.RollingFileAppender;
+import ch.qos.logback.core.rolling.TimeBasedRollingPolicy;
+import net.logstash.logback.encoder.LogstashEncoder;
+import net.logstash.logback.fieldnames.LogstashFieldNames;
+import org.ga4gh.starterkit.common.config.ServerProps;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import javax.annotation.PostConstruct;
+
+public class TestbedLoggingUtil{
+
+    @Autowired
+    private ServerProps serverProps;
+
+    private boolean configured;
+
+    private Logger logger;
+
+    public TestbedLoggingUtil() {
+        configured = false;
+    }
+
+    @PostConstruct
+    public void buildLogger() {
+        setLogger((Logger) LoggerFactory.getLogger(getClass()));
+
+        LoggerContext loggerContext = logger.getLoggerContext();
+        loggerContext.reset();
+
+        // logback logstash encoder
+        LogstashEncoder logstashEncoder = new LogstashEncoder();
+        logstashEncoder.setIncludeCallerData(true);
+        LogstashFieldNames fieldnames = logstashEncoder.getFieldNames();
+
+        // To ignore the default fields - level value, version and thread fields,
+        // set them as null
+        fieldnames.setLevelValue(null);
+        fieldnames.setVersion(null);
+        fieldnames.setThread(null);
+
+        // rename existing field names
+        fieldnames.setLevel("level");
+        fieldnames.setTimestamp("utc_timestamp");
+        fieldnames.setLogger("logger");
+        fieldnames.setCallerClass("class_name");
+        fieldnames.setCallerMethod("method_name");
+        fieldnames.setCallerFile("file_name");
+        fieldnames.setCallerLine("line_number");
+
+        // set the new fieldnames
+        logstashEncoder.setFieldNames(fieldnames);
+
+        // set the timezone as UTC
+        logstashEncoder.setTimeZone("UTC");
+
+        if (getServerProps().getLogFile() == null) {
+
+            // write logs to console
+            ConsoleAppender<ILoggingEvent> appender = new ConsoleAppender<>();
+            appender.setContext(loggerContext);
+            appender.setName("consoleAppender");
+            appender.setEncoder(logstashEncoder);
+            logstashEncoder.start();
+            appender.start();
+            getLogger().addAppender(appender);
+        } else {
+
+            // write logs to file
+
+            // zip rotate at the start of every day - UTC timezone
+            TimeBasedRollingPolicy<ILoggingEvent> policy = new TimeBasedRollingPolicy<>();
+            policy.setFileNamePattern(("./logs/" + getServerProps().getLogFile()).replace(".log",".%d{yyyy-MM-dd, UTC}.log.gz"));
+
+            // keep history of log files from the past 30 days.
+            policy.setMaxHistory(30);
+            policy.setContext(loggerContext);
+
+            // Add to the appender
+            RollingFileAppender<ILoggingEvent> appender = new RollingFileAppender<>();
+            appender.setContext(loggerContext);
+            appender.setName("rollingFileAppender");
+
+            // add the log files to ./logs directory
+            appender.setFile("./logs/"+getServerProps().getLogFile());
+            appender.setAppend(true);
+            appender.setPrudent(false);
+            appender.setRollingPolicy(policy);
+            appender.setEncoder(logstashEncoder);
+            policy.setParent(appender);
+            policy.start();
+            logstashEncoder.start();
+            appender.start();
+            getLogger().addAppender(appender);
+        }
+        setLogLevel();
+        setConfigured(true);
+    }
+
+    private void setLogLevel() {
+        Level level;
+
+        switch(serverProps.getLogLevel()) {
+            case TRACE:
+                level = Level.TRACE;
+                break;
+            case DEBUG:
+                level = Level.DEBUG;
+                break;
+            case INFO:
+                level = Level.INFO;
+                break;
+            case WARN:
+                level = Level.WARN;
+                break;
+            case ERROR:
+                level = Level.ERROR;
+                break;
+            default:
+                level = Level.DEBUG;
+                break;
+        }
+        getLogger().setLevel(level);
+    }
+
+    public void setServerProps(ServerProps serverProps) {
+        this.serverProps = serverProps;
+    }
+
+    public ServerProps getServerProps() {
+        return serverProps;
+    }
+
+    public void setConfigured(boolean configured) {
+        this.configured = configured;
+    }
+
+    public boolean getConfigured() {
+        return configured;
+    }
+
+    public void setLogger(Logger logger) {
+        this.logger = logger;
+    }
+
+    public Logger getLogger() {
+        return logger;
+    }
+
+}