Merge pull request #1138 from MPDL-Innovations/develop

Input for release 3.3
imeji-community · Mar 1, 2016 · 4173222 · 4173222
2 parents d57a6fe + a10241b
commit 4173222
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Showing 314 changed files with 5,993 additions and 5,121 deletions.
diff --git a/pom.xml b/pom.xml
@@ -93,8 +93,8 @@
 	</mailingLists>
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<maven.compiler.source>1.7</maven.compiler.source>
-		<maven.compiler.target>1.7</maven.compiler.target>
+		<maven.compiler.source>1.8</maven.compiler.source>
+		<maven.compiler.target>1.8</maven.compiler.target>
 		<!-- Setting this property so that generated project uses correct version 
 			of richfaces. -->
 		<org.richfaces.bom.version>4.3.7.Final</org.richfaces.bom.version>
@@ -193,7 +193,7 @@
 				<artifactId>maven-compiler-plugin</artifactId>
 				<version>3.0</version>
 			</plugin>
-			<plugin>
+			 <plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>buildnumber-maven-plugin</artifactId>
 				<version>1.4</version>
@@ -322,6 +322,16 @@
 			<artifactId>commons-lang3</artifactId>
 			<version>3.3.2</version>
 		</dependency>
+		<dependency>
+		  <groupId>commons-codec</groupId>
+		  <artifactId>commons-codec</artifactId>
+		  <version>1.9</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-collections4</artifactId>
+			<version>4.0</version>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.jena</groupId>
 			<artifactId>apache-jena-libs</artifactId>
@@ -425,12 +435,6 @@
 			<artifactId>im4java</artifactId>
 			<version>1.2.0</version>
 		</dependency>
-		<!-- pdf handling -->
-		<dependency>
-			<groupId>org.swinglabs</groupId>
-			<artifactId>pdf-renderer</artifactId>
-			<version>1.0.5</version>
-		</dependency>
 		<!-- image/video hanlding -->
 		<dependency>
 			<groupId>org.openimaj</groupId>
@@ -507,11 +511,6 @@
 			<artifactId>javax.ws.rs-api</artifactId>
 			<version>2.0.1</version>
 		</dependency>
-		<dependency>
-			<groupId>net.java.dev.webdav</groupId>
-			<artifactId>webdav-jaxrs</artifactId>
-			<version>1.2.1</version>
-		</dependency>
 		<dependency>
 			<groupId>org.glassfish.jersey.core</groupId>
 			<artifactId>jersey-client</artifactId>
@@ -588,6 +587,11 @@
 			<artifactId>guava</artifactId>
 			<version>18.0</version>
 		</dependency>
+		<dependency>
+		    <groupId>org.apache.pdfbox</groupId>
+		    <artifactId>pdfbox</artifactId>
+		    <version>1.8.10</version>
+		</dependency>
 	</dependencies>
 	<profiles>
 		<!-- this profile is used by developers -->
@@ -598,7 +602,7 @@
 					encoding Cp1252, i.e. build is platform dependent! -->
 				<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 				<!-- the jdk version to use -->
-				<jdk.version>1.7</jdk.version>
+				<jdk.version>1.8</jdk.version>
 			</properties>
 			<build>
 				<plugins>
@@ -657,7 +661,7 @@
 					encoding Cp1252, i.e. build is platform dependent! -->
 				<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 				<!-- the jdk version to use -->
-				<jdk.version>1.7</jdk.version>
+				<jdk.version>1.8</jdk.version>
 				<project.build.finalName>imeji</project.build.finalName>
 			</properties>
 			<build>

diff --git a/src/main/java/de/mpg/imeji/exceptions/InactiveAuthenticationError.java b/src/main/java/de/mpg/imeji/exceptions/InactiveAuthenticationError.java
@@ -0,0 +1,15 @@
+package de.mpg.imeji.exceptions;
+
+/**
+ * Exception for authentication of inactive users
+ * 
+ * @author bastiens
+ *
+ */
+public class InactiveAuthenticationError extends AuthenticationError {
+  private static final long serialVersionUID = 7976153766697083425L;
+
+  public InactiveAuthenticationError(String message) {
+    super(message);
+  }
+}
diff --git a/src/main/java/de/mpg/imeji/exceptions/WorkflowException.java b/src/main/java/de/mpg/imeji/exceptions/WorkflowException.java
@@ -0,0 +1,15 @@
+package de.mpg.imeji.exceptions;
+
+/**
+ * Exception when ann non valid workflow operation is done (for instance: release, discard)
+ * 
+ * @author bastiens
+ *
+ */
+public class WorkflowException extends ImejiException {
+  private static final long serialVersionUID = -5279563970035349584L;
+
+  public WorkflowException(String message) {
+    super(message);
+  }
+}
diff --git a/src/main/java/de/mpg/imeji/logic/Imeji.java b/src/main/java/de/mpg/imeji/logic/Imeji.java
@@ -29,6 +29,7 @@
 import com.hp.hpl.jena.tdb.sys.TDBMaker;
 
 import de.mpg.imeji.exceptions.AlreadyExistsException;
+import de.mpg.imeji.exceptions.ImejiException;
 import de.mpg.imeji.exceptions.NotFoundException;
 import de.mpg.imeji.logic.auth.authorization.AuthorizationPredefinedRoles;
 import de.mpg.imeji.logic.concurrency.locks.LocksSurveyor;
@@ -45,6 +46,7 @@
 import de.mpg.imeji.logic.vo.Space;
 import de.mpg.imeji.logic.vo.Statement;
 import de.mpg.imeji.logic.vo.User;
+import de.mpg.imeji.presentation.beans.ConfigurationBean;
 import de.mpg.imeji.presentation.util.ImejiFactory;
 import de.mpg.imeji.presentation.util.PropertyReader;
 import de.mpg.j2j.annotations.j2jModel;
@@ -57,7 +59,7 @@
  * @version $Revision$ $LastChangedDate$
  */
 public class Imeji {
-  private static final Logger logger = Logger.getLogger(Imeji.class);
+  private static final Logger LOGGER = Logger.getLogger(Imeji.class);
   public static String tdbPath = null;
   public static String collectionModel;
   public static String albumModel;
@@ -71,6 +73,7 @@ public class Imeji {
   public static MetadataProfile defaultMetadataProfile;
   private static final String ADMIN_EMAIL_INIT = "admin@imeji.org";
   private static final String ADMIN_PASSWORD_INIT = "admin";
+  public static ConfigurationBean CONFIG;
   /**
    * Thread to check if locked objects can be unlocked
    */
@@ -90,9 +93,10 @@ public class Imeji {
    * 
    * @throws URISyntaxException
    * @throws IOException
+   * @throws ImejiException
    * 
    */
-  public static void init() throws IOException, URISyntaxException {
+  public static void init() throws IOException, URISyntaxException, ImejiException {
     tdbPath = PropertyReader.getProperty("imeji.tdb.path");
     init(tdbPath);
     ElasticService.start();
@@ -110,34 +114,37 @@ public static void runMigration() throws IOException {
     try {
       in = new FileInputStream(f);
     } catch (FileNotFoundException e) {
-      logger.info("No" + f.getAbsolutePath() + " found, no migration runs");
+      LOGGER.info("No" + f.getAbsolutePath() + " found, no migration runs");
     }
     if (in != null) {
       String migrationRequests = new String(StreamUtils.getBytes(in), "UTF-8");
-      logger.info("Running migration with query: ");
-      logger.info(migrationRequests);
+      LOGGER.info("Running migration with query: ");
+      LOGGER.info(migrationRequests);
       ImejiSPARQL.execUpdate(migrationRequests);
-      logger.info("Migration done!");
+      LOGGER.info("Migration done!");
     }
   }
 
   /**
    * Initialize a {@link Jena} database according at one path location in filesystem
    * 
    * @param path
+   * @throws ImejiException
+   * @throws URISyntaxException
+   * @throws IOException
    */
-  public static void init(String path) {
+  public static void init(String path) throws IOException, URISyntaxException, ImejiException {
     if (path != null) {
       File f = new File(path);
       if (!f.exists()) {
         f.getParentFile().mkdirs();
       }
       tdbPath = f.getAbsolutePath();
     }
-    logger.info("Initializing Jena dataset (" + tdbPath + ")...");
+    LOGGER.info("Initializing Jena dataset (" + tdbPath + ")...");
     dataset = tdbPath != null ? TDBFactory.createDataset(tdbPath) : TDBFactory.createDataset();
-    logger.info("... dataset done!");
-    logger.info("Initializing Jena models...");
+    LOGGER.info("... dataset done!");
+    LOGGER.info("Initializing Jena models...");
     albumModel = getModelName(Album.class);
     collectionModel = getModelName(CollectionImeji.class);
     imageModel = getModelName(Item.class);
@@ -152,7 +159,8 @@ public static void init(String path) {
     initModel(statementModel);
     initModel(profileModel);
     initModel(spaceModel);
-    logger.info("... models done!");
+    LOGGER.info("... models done!");
+    CONFIG = new ConfigurationBean();
     initadminUser();
     initDefaultMetadataProfile();
   }
@@ -208,22 +216,22 @@ private static void initadminUser() {
         try {
           uc.retrieve(Imeji.adminUser.getEmail());
         } catch (NotFoundException e) {
-          logger.info(
+          LOGGER.info(
               "!!! IMPORTANT !!! Create admin@imeji.org as system administrator with password admin. !!! CHANGE PASSWORD !!!");
           uc.create(Imeji.adminUser, USER_TYPE.ADMIN);
-          logger.info("Created admin user successfully:" + Imeji.adminUser.getEmail());
+          LOGGER.info("Created admin user successfully:" + Imeji.adminUser.getEmail());
         }
       } else {
-        logger.info("Admin user already exists:");
+        LOGGER.info("Admin user already exists:");
         for (User admin : admins) {
-          logger.info(admin.getEmail() + " is admin + (" + admin.getId() + ")");
+          LOGGER.info(admin.getEmail() + " is admin + (" + admin.getId() + ")");
         }
       }
     } catch (AlreadyExistsException e) {
-      logger.warn(Imeji.adminUser.getEmail() + " already exists");
+      LOGGER.warn(Imeji.adminUser.getEmail() + " already exists");
     } catch (Exception e) {
       if (e.getCause() instanceof AlreadyExistsException) {
-        logger.warn(Imeji.adminUser.getEmail() + " already exists");
+        LOGGER.warn(Imeji.adminUser.getEmail() + " already exists");
       } else {
         throw new RuntimeException("Error initializing Admin user! ", e);
       }
@@ -232,50 +240,50 @@ private static void initadminUser() {
 
   private static void initDefaultMetadataProfile() {
     ProfileController pc = new ProfileController();
-    logger.info("Initializing default metadata profile...");
+    LOGGER.info("Initializing default metadata profile...");
     try {
       defaultMetadataProfile = pc.initDefaultMetadataProfile();
     } catch (Exception e) {
-      logger.error("error retrieving/creating default metadata profile: ", e);
+      LOGGER.error("error retrieving/creating default metadata profile: ", e);
     }
     if (defaultMetadataProfile != null) {
-      logger.info("Default metadata profile is set-up to " + defaultMetadataProfile.getId());
+      LOGGER.info("Default metadata profile is set-up to " + defaultMetadataProfile.getId());
     } else {
-      logger.info(
+      LOGGER.info(
           "Checking for default metadata profile is finished: no default metadata profile has been set.");
 
     }
   }
 
   public static void shutdown() {
-    logger.info("Shutting down thread executor...");
+    LOGGER.info("Shutting down thread executor...");
     Imeji.executor.shutdown();
     nightlyExecutor.stop();
-    logger.info("executor shutdown shutdown? " + Imeji.executor.isShutdown());
+    LOGGER.info("executor shutdown shutdown? " + Imeji.executor.isShutdown());
     ElasticService.shutdown();
-    logger.info("Ending LockSurveyor...");
+    LOGGER.info("Ending LockSurveyor...");
     locksSurveyor.terminate();
-    logger.info("...done");
-    logger.info("Closing Jena! TDB...");
+    LOGGER.info("...done");
+    LOGGER.info("Closing Jena! TDB...");
     TDB.sync(Imeji.dataset);
-    logger.info("sync done");
+    LOGGER.info("sync done");
     Imeji.dataset.close();
-    logger.info("dataset closed");
+    LOGGER.info("dataset closed");
     TDB.closedown();
-    logger.info("tdb closed");
+    LOGGER.info("tdb closed");
     TDBMaker.releaseLocation(Location.create(Imeji.tdbPath));
-    logger.info("location released");
-    logger.info("...done!");
+    LOGGER.info("location released");
+    LOGGER.info("...done!");
 
     // This is a bug of com.hp.hpl.jena.sparql.engine.QueryExecutionBase
     // implementation:
     // AlarmClock is not correctly released, it leads to the memory leaks
     // after tomcat stop
     // see https://github.com/imeji-community/imeji/issues/966!
-    logger.info("Release AlarmClock...");
+    LOGGER.info("Release AlarmClock...");
     AlarmClock alarmClock = AlarmClock.get();
     alarmClock.release();
-    logger.info("done");
+    LOGGER.info("done");
   }
 
   /**

diff --git a/src/main/java/de/mpg/imeji/logic/ImejiNamespaces.java b/src/main/java/de/mpg/imeji/logic/ImejiNamespaces.java
@@ -28,6 +28,7 @@ public class ImejiNamespaces {
   public static final String REGISTRATION_TOKEN = "http://imeji.org/terms/registrationToken";
   public static final String SPACE = "http://imeji.org/terms/space";
   public static final String CHECKSUM = "http://imeji.org/terms/checksum";
+  public static final String STORAGE_ID = "http://imeji.org/terms/storageId";
 
 
   /*

diff --git a/src/main/java/de/mpg/imeji/logic/ImejiTriple.java b/src/main/java/de/mpg/imeji/logic/ImejiTriple.java
@@ -1,6 +1,6 @@
 package de.mpg.imeji.logic;
 
-import de.mpg.imeji.logic.auth.Authorization;
+import de.mpg.imeji.logic.auth.authorization.Authorization;
 
 /**
  * An RDF Triple, which can be Checked by the {@link Authorization}

diff --git a/.../mpg/imeji/logic/auth/Authentication.java → ...c/auth/authentication/Authentication.java b/.../mpg/imeji/logic/auth/Authentication.java → ...c/auth/authentication/Authentication.java
@@ -22,7 +22,7 @@
  * wissenschaftlich-technische Information mbH and Max-Planck- Gesellschaft zur Förderung der
  * Wissenschaft e.V. All rights reserved. Use is subject to license terms.
  */
-package de.mpg.imeji.logic.auth;
+package de.mpg.imeji.logic.auth.authentication;
 
 import de.mpg.imeji.exceptions.AuthenticationError;
 import de.mpg.imeji.logic.vo.User;
@@ -36,6 +36,7 @@
  */
 public interface Authentication {
 
+
   /**
    * Log in a user with a login (email or user name) and password
    * 

diff --git a/...eji/logic/auth/AuthenticationFactory.java → ...authentication/AuthenticationFactory.java b/...eji/logic/auth/AuthenticationFactory.java → ...authentication/AuthenticationFactory.java
@@ -22,12 +22,12 @@
  * wissenschaftlich-technische Information mbH and Max-Planck- Gesellschaft zur Förderung der
  * Wissenschaft e.V. All rights reserved. Use is subject to license terms.
  */
-package de.mpg.imeji.logic.auth;
+package de.mpg.imeji.logic.auth.authentication;
 
 import javax.servlet.http.HttpServletRequest;
 
-import de.mpg.imeji.logic.auth.authentication.HttpAuthentication;
-import de.mpg.imeji.logic.auth.authentication.SimpleAuthentication;
+import de.mpg.imeji.logic.auth.authentication.impl.HttpAuthentication;
+import de.mpg.imeji.logic.auth.authentication.impl.DefaultAuthentication;
 
 /**
  * Factory for Authentication
@@ -37,6 +37,7 @@
  * @version $Revision$ $LastChangedDate$
  */
 public class AuthenticationFactory {
+
   /**
    * Factory with a login and a password
    * 
@@ -45,7 +46,7 @@ public class AuthenticationFactory {
    * @return
    */
   public static Authentication factory(String login, String pwd) {
-    return new SimpleAuthentication(login, pwd);
+    return new DefaultAuthentication(login, pwd);
   }
 
   /**