Merge branch 'release/UV_Core_v3.0.0'

Author: tomas-knap

.travis.yml

@@ -1,3 +1,9 @@
 ## UnifiedViews Core travis build file
 
 language: java
+
+jdk:
+  - oraclejdk8
+
+install: 
+  - mvn clean install -B -V

backend/conf/config.sample.properties

@@ -99,6 +99,14 @@ database.rdf.platform = localRDF
 #database.rdf.password = dba
 # }
 
+# or GraphDB {
+# database.rdf.platform = graphdb
+# database.rdf.url = http://localhost:7200/repositories/uv
+# database.rdf.user = admin
+# database.rdf.password = admin
+# }
+
+
 # Administrator contact email for sending reports and failure notifications 
 email.enabled = false
 email.admin = admin@example.com

backend/pom.xml

@@ -4,11 +4,11 @@
     <parent>
         <groupId>eu.unifiedviews</groupId>
         <artifactId>uv-core</artifactId>
-        <version>2.3.2</version>
+        <version>3.0.0</version>
 	<relativePath>../pom.xml</relativePath>
     </parent>
     <artifactId>backend</artifactId>
-    <version>2.3.2</version>
+    <version>3.0.0</version>
     <packaging>jar</packaging>
     <name>backend</name>
     <description />
@@ -69,6 +69,17 @@
             <artifactId>jetty-server</artifactId>
             <version>${jetty.server.version}</version>
         </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+            <version>2.8.3</version>
+        </dependency>
+        <dependency>
+            <groupId>com.microsoft.sqlserver</groupId>
+            <artifactId>sqljdbc4</artifactId>
+            <version>4.0</version>
+            <type>jar</type>
+        </dependency>
     </dependencies>
 
     <build>
@@ -86,46 +97,42 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>2.4</version>
+                <version>3.0.2</version>
                 <configuration>
                     <archive>
                         <manifest>
                             <addClasspath>true</addClasspath>
                             <mainClass>cz.cuni.mff.xrg.odcs.backend.AppEntry</mainClass>
                             <classpathPrefix>lib/</classpathPrefix>
-                            <classpathLayoutType>custom</classpathLayoutType>
-                            <customClasspathLayout>$${artifact.artifactId}-$${artifact.version}$${dashClassifier?}-$${artifact.extension}/</customClasspathLayout>
-
-                        </manifest>
-                    </archive>
-                </configuration>
+                            <!-- so that manifest does not contain e.g. commons-app-3.0.0-20170503.092434-10.jar but rather commons-app-3.0.0-SNAPSHOT -->
+                            <useUniqueVersions>false</useUniqueVersions>
+                </manifest>
+            </archive>
+        </configuration>
+    </plugin>
+
+    <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-dependency-plugin</artifactId>
+        <version>3.0.0</version>
+        <executions>
+            <execution>
+                <id>copy-dependencies</id>
+                <phase>package</phase>
+                <goals>
+                    <goal>copy-dependencies</goal>
+                </goals>
+                <configuration>
+                    <outputDirectory>${project.build.directory}/lib</outputDirectory>
+                    <!-- the two lines below tell Maven not to include
+                        test scoped dependencies -->
+                            <includeScope>runtime</includeScope>
+                            <excludeScope>provided</excludeScope>
+                        </configuration>
+                    </execution>
+                </executions>
             </plugin>
 
-        <plugin>
-            <groupId>org.apache.maven.plugins</groupId>
-            <artifactId>maven-dependency-plugin</artifactId>
-            <version>2.9</version>
-            <executions>
-                <execution>
-                    <!-- Dependencies are not just copied, but also unpacked - this is a workaround to solve the eclipselink lazy loading issue, see https://github.com/UnifiedViews/Core/pull/555: 
-                     the eclipselink core packages are signed which causes the backend to fail on start because on backend packaging it copies all the dependencies which somehow messes up the signatures. 
-                     The solution proposed in the web is to  filter the *.SF and *.RSA files from META-INF to remove the signature information when preparing the jar -->
-                    <id>unpack-dependencies</id>
-                    <phase>package</phase>
-                    <goals>
-                        <goal>unpack-dependencies</goal>
-                    </goals>
-                    <configuration>
-                        <excludes>**\/*.SF,**\/*.DSA,**\/*.RSA</excludes>
-                        <outputDirectory>${project.build.directory}/lib</outputDirectory>
-                        <includeScope>runtime</includeScope>
-                        <excludeScope>provided</excludeScope>
-                        <useSubDirectoryPerArtifact>true</useSubDirectoryPerArtifact>
-                    </configuration>
-                </execution>
-            </executions>
-        </plugin>
-
         </plugins>
 
 

backend/src/main/java/cz/cuni/mff/xrg/odcs/backend/AppEntry.java

@@ -5,8 +5,8 @@
 import ch.qos.logback.classic.encoder.PatternLayoutEncoder;
 import ch.qos.logback.classic.filter.ThresholdFilter;
 import ch.qos.logback.core.rolling.RollingFileAppender;
-import ch.qos.logback.core.rolling.SizeAndTimeBasedFNATP;
-import ch.qos.logback.core.rolling.TimeBasedRollingPolicy;
+import ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy;
+import ch.qos.logback.core.util.FileSize;
 import cz.cuni.mff.xrg.odcs.backend.auxiliaries.AppLock;
 import cz.cuni.mff.xrg.odcs.backend.auxiliaries.DatabaseInitializer;
 import cz.cuni.mff.xrg.odcs.backend.communication.EmbeddedHttpServer;
@@ -15,6 +15,7 @@
 import cz.cuni.mff.xrg.odcs.backend.logback.SqlAppender;
 import cz.cuni.mff.xrg.odcs.commons.app.conf.AppConfig;
 import cz.cuni.mff.xrg.odcs.commons.app.conf.ConfigProperty;
+import cz.cuni.mff.xrg.odcs.commons.app.conf.MissingConfigPropertyException;
 import cz.cuni.mff.xrg.odcs.commons.app.execution.log.Log;
 import cz.cuni.mff.xrg.odcs.commons.app.facade.ModuleFacade;
 import org.h2.store.fs.FileUtils;
@@ -54,39 +55,25 @@ public class AppEntry {
     private EmbeddedHttpServer httpProbeServer;
 
     private RollingFileAppender createAppender(LoggerContext loggerContext,
-            String logDirectory, String logFile, int logHistory) {
+            String logDirectory, String logFile, int logHistory, String logMaxSize) {
         final RollingFileAppender rfAppender = new RollingFileAppender();
         rfAppender.setContext(loggerContext);
         rfAppender.setFile(logDirectory + logFile + ".log");
         {
-            TimeBasedRollingPolicy rollingPolicy = new TimeBasedRollingPolicy();
+            SizeAndTimeBasedRollingPolicy rollingPolicy = new SizeAndTimeBasedRollingPolicy();
             rollingPolicy.setContext(loggerContext);
             // rolling policies need to know their parent
             // it's one of the rare cases, where a sub-component knows about its parent
             rollingPolicy.setParent(rfAppender);
             rollingPolicy.setFileNamePattern(logDirectory + logFile + ".%d{yyyy-MM-dd}.%i.log");
-            //rollingPolicy.setTimeBasedFileNamingAndTriggeringPolicy(timeBasedTriggeringPolicy);
             rollingPolicy.setMaxHistory(logHistory);
+            rollingPolicy.setTotalSizeCap(FileSize.valueOf(logMaxSize));
+            rollingPolicy.setMaxFileSize(FileSize.valueOf("10MB"));
 
             rfAppender.setRollingPolicy(rollingPolicy);
 
-            SizeAndTimeBasedFNATP triggeringPolicy;
-            {
-                // triger for name changing	
-                triggeringPolicy = new SizeAndTimeBasedFNATP();
-                triggeringPolicy.setMaxFileSize("10MB");
-                triggeringPolicy.setTimeBasedRollingPolicy(rollingPolicy);
-                rfAppender.setTriggeringPolicy(triggeringPolicy);
-            }
-
-            rollingPolicy.setTimeBasedFileNamingAndTriggeringPolicy(triggeringPolicy);
             rollingPolicy.start();
 
-            {
-                // we need TimeBasedRollingPolicy to have the 
-                // FileNamePattern pattern initialized which is done in rollingPolicy.start();
-                triggeringPolicy.start();
-            }
         }
         PatternLayoutEncoder encoder = new PatternLayoutEncoder();
         encoder.setContext(loggerContext);
@@ -112,11 +99,13 @@ private void initLogbackAppender() {
                 logDirectory = logDirectory + File.separator;
             }
         } catch (Exception e) {
+            //not logging exception, default value is used in this case
         }
 
         try {
             logHistory = appConfig.getInteger(ConfigProperty.BACKEND_LOG_KEEP);
         } catch (Exception e) {
+            //not logging exception, default value is used in this case
         }
 
         // check existance of directory
@@ -132,16 +121,27 @@ private void initLogbackAppender() {
             }
         }
 
+
+        //check if there is any preferred max size for logs
+        String logMaxSize = "1GB";
+        // we try to load values from configuration
+        try {
+            logMaxSize = appConfig.getString(ConfigProperty.BACKEND_LOG_MAX_SIZE);
+            // user set path, ensure that it end's on file separator
+        } catch (MissingConfigPropertyException e) {
+            //not logging exception, default value is used in this case
+        }
+
         // now prepare the logger 
 
         final LoggerContext loggerContext = (LoggerContext) LoggerFactory.getILoggerFactory();
 
         RollingFileAppender allLog = createAppender(loggerContext, logDirectory,
-                "backend", logHistory);
+                "backend", logHistory, logMaxSize);
         allLog.start();
 
         RollingFileAppender errorLog = createAppender(loggerContext, logDirectory,
-                "backend_err", logHistory);
+                "backend_err", logHistory, logMaxSize);
         {
             // add filter
             ThresholdFilter levelFilter = new ThresholdFilter();
@@ -199,7 +199,7 @@ private void run() throws Exception {
         lockKey.append(appConfig.getInteger(ConfigProperty.BACKEND_PORT));
         if (!AppLock.setLock(lockKey.toString())) {
             // another application is already running
-            LOG.info("Another instance of UnifiedViews is probably running.");
+            LOG.warn("Another instance of UnifiedViews is already running on this machine.");
             return;
         }
 

backend/src/main/java/cz/cuni/mff/xrg/odcs/backend/auxiliaries/AppLock.java

@@ -1,18 +1,16 @@
 package cz.cuni.mff.xrg.odcs.backend.auxiliaries;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.io.File;
 import java.io.FileOutputStream;
 import java.nio.channels.FileChannel;
 import java.nio.channels.FileLock;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
- * The Class AppLock taken from
- * http://nerdydevel.blogspot.com/2012/07/run-only-single-java-application-instance.html
- * 
- * @author rumatoest
+ * Ensures that only single instance of UnifiedViews runs on a single machine.
+ * Inspired by: https://github.com/javaplugs/javaplugs/blob/master/src/main/java/com/github/javaplugs/app/AppLock.java
  */
 public class AppLock {
 

backend/src/main/java/cz/cuni/mff/xrg/odcs/backend/auxiliaries/DatabaseInitializer.java

@@ -46,23 +46,23 @@ public void initialize() {
         userRole.setName("User");
 
         User admin = new User();
-        admin.setFullName("John Admin");
+        admin.setFullName("admin");
         admin.setPassword("test");
         admin.setTableRows(20);
         admin.setUsername("admin");
         admin.setEmail(adminEmailAddress);
         admin.addRole(adminRole);
-        admin.setExternalIdentifier("http://www.johnadmin.cz");
+        admin.setExternalIdentifier("admin");
         admin.addRole(userRole);
 
         User user = new User();
-        user.setFullName("John User");
+        user.setFullName("user");
         user.setPassword("test");
         user.setTableRows(20);
         user.setUsername("user");
         user.setEmail(userEmailAddress);
         user.addRole(userRole);
-        user.setExternalIdentifier("http://johnuser.at");
+        user.setExternalIdentifier("user");
 
         UserNotificationRecord userNotificationRecordAdmin = new UserNotificationRecord();
         userNotificationRecordAdmin.setUser(admin);
@@ -93,10 +93,10 @@ public void initialize() {
         //set properties holding version of UV in DB (used by Debian installation to detect the version)
         Property property1 = new Property();
         property1.setKey("UV.Core.version");
-        property1.setValue("002.003.000");
+        property1.setValue("003.000.000");
         Property property2 = new Property();
         property2.setKey("UV.Plugin-DevEnv.version");
-        property2.setValue("002.001.005");
+        property2.setValue("003.000.000");
 
         addNewPermissionToRoles("administrator", adminRole);
         addNewPermissionToRoles("pipeline.delete", true, adminRole, userRole);