Merge pull request #13 from kbase/develop

Develop->master

Author: MrCreosote

RELEASE_NOTES.txt

@@ -4,6 +4,21 @@ OVERVIEW
 -----------------------------------------
 Repo for code shared between Java services.
 
+VERSION: 0.0.16 (Released 6/13/2016)
+--------------------------------------
+
+NEW FEATURES:
+- The JsonServerSyslog class now logs SLF4J messages.
+
+UPDATED FEATURES / MAJOR BUG FIXES:
+- Fixed a bug where the server would stop logging after a syslog daemon
+  restart.
+- removed the UTCDateFormat class (use joda library classes instead).
+- removed UTF8Utils, unused.
+
+ANTICIPATED FUTURE DEVELOPMENTS:
+- None
+
 VERSION: 0.0.15 (Released 1/24/2015)
 --------------------------------------
 

build.xml

@@ -34,7 +34,7 @@
   <fileset dir="${jardir}" id="lib">
     <include name="apache_commons/commons-lang3-3.1.jar"/>
     <include name="junit/junit-4.9.jar"/>
-    <include name="mongo/mongo-java-driver-2.11.2.jar"/>
+    <include name="mongo/mongo-java-driver-2.13.3.jar"/>
     <include name="jackson/jackson-core-2.2.3.jar"/>
     <include name="jackson/jackson-databind-2.2.3.jar"/>
     <include name="jackson/jackson-annotations-2.2.3.jar"/>
@@ -52,9 +52,12 @@
     <include name="apache_commons/http/httpmime-4.3.1.jar"/>
     <include name="apache_commons/commons-logging-1.1.1.jar"/>
     <include name="slf4j/slf4j-api-1.7.7.jar"/>
+    <include name="logback/logback-core-1.1.2.jar"/>
+    <include name="logback/logback-classic-1.1.2.jar"/>
     <include name="apache_commons/velocity-1.7.jar"/>
     <include name="apache_commons/commons-io-2.4.jar"/>
     <include name="javassist/javassist-3.18.2.jar"/>
+    <include name="joda/joda-time-2.2.jar"/>
   </fileset>
 
   <path id="compile.classpath">
@@ -75,7 +78,7 @@
 
   <target name="compile" depends="init, definejarfile" description="compile the source">
     <!-- Compile class files-->
-    <javac destdir="${classes}" includeantruntime="false" target="1.6" source="1.6"
+    <javac destdir="${classes}" includeantruntime="false"
       debug="true" classpathref="compile.classpath">
       <src path="${src}"/>
       <exclude name="us/kbase/common/performance/**"/>
@@ -118,7 +121,7 @@
 
   <target name="test" depends="compile, preparejunitreportdir" description="run tests">
     <echo message="starting ${package} tests"/>
-    <junit failureproperty="test.failed" printsummary="yes">
+    <junit failureproperty="test.failed" printsummary="yes" fork="yes">
       <classpath path="${jarfile}.jar"/>
       <classpath refid="compile.classpath"/>
       <formatter type="plain" usefile="false"/>

src/us/kbase/common/mongo/GetMongoDB.java

@@ -13,6 +13,7 @@
 import com.mongodb.MongoClient;
 import com.mongodb.MongoClientOptions;
 import com.mongodb.MongoException;
+import com.mongodb.MongoTimeoutException;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -35,6 +36,8 @@
  */
 public class GetMongoDB {
 
+	//TODO needs rewrite. 1) Add tests, 2) deprecated methods, 2) replace NFE, 3) auth in constructor, 4) multiple hosts option, 5) logger on/off option 6) retry rewrite for mongo timeouts. 
+	
 	private static Logger getLogger() {
 		return LoggerFactory.getLogger(GetMongoDB.class);
 	}
@@ -96,7 +99,7 @@ public static DB getDB(final String host, final String database)
 	 * @param host the MongoDB host address.
 	 * @param database the database to get.
 	 * @param retryCount - the number of times to retry the MongoDB
-	 * connection, 1 retry / sec. 
+	 * connection, 1 retry / sec, not including the time retrying takes. 
 	 * @param logIntervalCount - how often to log the retries. Logs occur when
 	 * retries % logIntervalCount = 0.
 	 * @return the MongoDB database instance.
@@ -120,9 +123,12 @@ public static DB getDB(final String host, final String database,
 			try {
 				db.getCollectionNames();
 				break;
-			} catch (MongoException.Network men) {
+			} catch (MongoException.Network | MongoTimeoutException e ) {
 				if (retries >= retryCount) {
-					throw (IOException) men.getCause();
+					if (e instanceof MongoException.Network) {
+						throw (IOException) e.getCause();
+					}
+					throw e;
 				}
 				if (retries % logIntervalCount == 0) {
 					getLogger().info(
@@ -165,7 +171,7 @@ public static DB getDB(final String host, final String database,
 	 * @param user the MongoDB user with access to the database.
 	 * @param pwd the MongoDB user's password.
 	 * @param retryCount - the number of times to retry the MongoDB
-	 * connection, 1 retry / sec. 
+	 * connection, 1 retry / sec, not including the time retrying takes. 
 	 * @param logIntervalCount - how often to log the retries. Logs occur when
 	 * retries % logIntervalCount = 0.
 	 * @return the MongoDB database instance.
@@ -191,9 +197,12 @@ public static DB getDB(final String host, final String database,
 			try {
 				db.authenticate(user, pwd.toCharArray());
 				break;
-			} catch (MongoException.Network men) {
+			} catch (MongoException.Network | MongoTimeoutException e) {
 				if (retries >= retryCount) {
-					throw (IOException) men.getCause();
+					if (e instanceof MongoException.Network) {
+						throw (IOException) e.getCause();
+					}
+					throw e;
 				}
 				if (retries % logIntervalCount == 0) {
 					getLogger().info(