Merge pull request #17 from diging/develop

Prepare Release
diging · Apr 20, 2017 · b8d9790 · b8d9790
2 parents 6d7f273 + e2e5c25
commit b8d9790
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Showing 20 changed files with 232 additions and 18 deletions.
diff --git a/nepomuk/.classpath b/nepomuk/.classpath
@@ -23,11 +23,6 @@
 			<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v8.0">
-		<attributes>
-			<attribute name="owner.project.facets" value="jst.web"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

diff --git a/nepomuk/.gitignore b/nepomuk/.gitignore
@@ -1,3 +1,4 @@
 /.settings/
 /target/
 /target/
+/buildNumber.properties
diff --git a/nepomuk/pom.xml b/nepomuk/pom.xml
@@ -13,8 +13,9 @@
         <org.slf4j-version>1.7.5</org.slf4j-version>
         <org.springframework-version>4.3.1.RELEASE</org.springframework-version>
         <spring-security-version>4.1.3.RELEASE</spring-security-version>
-        <geco.requests.version>0.2.1-SNAPSHOT</geco.requests.version>
-        <geco.util.version>0.4.1</geco.util.version>
+        <geco.requests.version>0.5</geco.requests.version>
+        <geco.util.version>0.4.2</geco.util.version>
+        <buildNumber></buildNumber>
 
         <admin.password>$2a$04$NXKVTx9XrpEST6CLn/ps7eP8YsK3t.5A/mvAoYpg.X8QqgOKtc1za</admin.password>
         <nepomuk.base.url>http://localhost:8082/nepomuk/</nepomuk.base.url>
@@ -393,6 +394,61 @@
                     <path>/${tomcat.app}</path>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.eclipse.m2e</groupId>
+                <artifactId>lifecycle-mapping</artifactId>
+                <version>1.0.0</version>
+                <configuration>
+                    <lifecycleMappingMetadata>
+                        <pluginExecutions>
+                            <pluginExecution>
+                                <pluginExecutionFilter>
+                                    <groupId>org.codehaus.mojo</groupId>
+                                    <artifactId>buildnumber-maven-plugin</artifactId>
+                                    <versionRange>[0,)</versionRange>
+                                    <goals>
+                                        <goal>create</goal>
+                                    </goals>
+                                </pluginExecutionFilter>
+                                <action>
+                                    <execute>
+                                        <runOnConfiguration>true</runOnConfiguration>
+                                        <runOnIncremental>true</runOnIncremental>
+                                    </execute>
+                                </action>
+                            </pluginExecution>
+                        </pluginExecutions>
+                    </lifecycleMappingMetadata>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>buildnumber-maven-plugin</artifactId>
+                <version>1.4</version>
+                <executions>
+                    <execution>
+                        <phase>validate</phase>
+                        <goals>
+                            <goal>create</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <configuration>
+                    <doCheck>false</doCheck>
+                    <doUpdate>false</doUpdate>
+                    <revisionOnScmFailure></revisionOnScmFailure>
+                    <items>
+                        <item>buildNumber\d*</item>
+                        <item>timestamp</item>
+                    </items>
+                    <format>${geco.nepomuk.version}-{0} ({1,date,yyyy-MM-dd HH:mm:ss})</format>
+                </configuration>
+            </plugin>
         </plugins>
     </build>
+
+    <scm>
+        <connection>scm:svn:http://none</connection>
+        <url>scm:svn:https://none</url>
+    </scm>
 </project>
diff --git a/nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/domain/IFile.java b/nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/domain/IFile.java
@@ -49,4 +49,8 @@ public interface IFile extends IStorableObject {
 
     public abstract String getContentType();
 
+    public abstract void setGilesFileId(String gilesFileId);
+
+    public abstract String getGilesFileId();
+
 }
diff --git a/nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/domain/impl/File.java b/nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/domain/impl/File.java
@@ -1,5 +1,6 @@
 package edu.asu.diging.gilesecosystem.nepomuk.core.domain.impl;
 
+import javax.jdo.annotations.Index;
 import javax.persistence.Entity;
 import javax.persistence.Id;
 
@@ -9,19 +10,19 @@
 @Entity
 public class File implements IFile {
 
-    private String uploadId;
-    private String filename;
-    private String username;
-    private String documentId;
-    @Id
-    private String id;
+    @Index private String uploadId;
+    @Index private String filename;
+    @Index private String username;
+    @Index private String documentId;
+    @Id @Index private String id;
     private String uploadDate;
     private String processedDate;
     private long size;
     private String filepath; 
     private FileType fileType;
     private String contentType;
-
+    @Index private String gilesFileId;
+
     public File() {
     }
 
@@ -181,5 +182,15 @@ public String getContentType() {
     public void setContentType(String contentType) {
         this.contentType = contentType;
     }
+
+    @Override
+    public String getGilesFileId() {
+        return gilesFileId;
+    }
+
+    @Override
+    public void setGilesFileId(String gilesFileId) {
+        this.gilesFileId = gilesFileId;
+    }
 
 }
diff --git a/...in/java/edu/asu/diging/gilesecosystem/nepomuk/core/exception/NoUniqueResultException.java b/...in/java/edu/asu/diging/gilesecosystem/nepomuk/core/exception/NoUniqueResultException.java
@@ -0,0 +1,36 @@
+package edu.asu.diging.gilesecosystem.nepomuk.core.exception;
+
+public class NoUniqueResultException extends Exception {
+
+    /**
+     * 
+     */
+    private static final long serialVersionUID = -3769968277605578574L;
+
+    public NoUniqueResultException() {
+        super();
+        // TODO Auto-generated constructor stub
+    }
+
+    public NoUniqueResultException(String message, Throwable cause,
+            boolean enableSuppression, boolean writableStackTrace) {
+        super(message, cause, enableSuppression, writableStackTrace);
+        // TODO Auto-generated constructor stub
+    }
+
+    public NoUniqueResultException(String message, Throwable cause) {
+        super(message, cause);
+        // TODO Auto-generated constructor stub
+    }
+
+    public NoUniqueResultException(String message) {
+        super(message);
+        // TODO Auto-generated constructor stub
+    }
+
+    public NoUniqueResultException(Throwable cause) {
+        super(cause);
+        // TODO Auto-generated constructor stub
+    }
+
+}
diff --git a/.../src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/IFilesDatabaseClient.java b/.../src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/IFilesDatabaseClient.java
@@ -2,7 +2,11 @@
 
 import java.util.List;
 
+import javax.persistence.TypedQuery;
+
 import edu.asu.diging.gilesecosystem.nepomuk.core.domain.IFile;
+import edu.asu.diging.gilesecosystem.nepomuk.core.domain.impl.File;
+import edu.asu.diging.gilesecosystem.nepomuk.core.exception.NoUniqueResultException;
 import edu.asu.diging.gilesecosystem.nepomuk.core.exception.UnstorableObjectException;
 import edu.asu.diging.gilesecosystem.nepomuk.core.store.IDatabaseClient;
 
@@ -20,4 +24,7 @@ public interface IFilesDatabaseClient extends IDatabaseClient<IFile> {
 
     public List<IFile> getFilesByProperty(String propName, String propValue);
 
+    public abstract IFile getFile(String uploadId, String documentId, String filename)
+            throws NoUniqueResultException;
+
 }
diff --git a/nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/IFilesManager.java b/nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/IFilesManager.java
@@ -3,6 +3,7 @@
 import java.util.List;
 
 import edu.asu.diging.gilesecosystem.nepomuk.core.domain.IFile;
+import edu.asu.diging.gilesecosystem.nepomuk.core.exception.NoUniqueResultException;
 import edu.asu.diging.gilesecosystem.nepomuk.core.exception.UnstorableObjectException;
 
 public interface IFilesManager {
@@ -29,4 +30,7 @@ public interface IFilesManager {
     public abstract String getRelativePathOfFile(IFile file);
 
     public abstract byte[] getFileContent(IFile file);
+
+    public abstract IFile getFile(String uploadId, String documentId, String filename)
+            throws NoUniqueResultException;
 }
diff --git a/.../main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/impl/FilesDatabaseClient.java b/.../main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/impl/FilesDatabaseClient.java
@@ -6,12 +6,14 @@
 import javax.annotation.PreDestroy;
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
+import javax.persistence.TypedQuery;
 
 import org.springframework.stereotype.Component;
 import org.springframework.transaction.annotation.Transactional;
 
 import edu.asu.diging.gilesecosystem.nepomuk.core.domain.IFile;
 import edu.asu.diging.gilesecosystem.nepomuk.core.domain.impl.File;
+import edu.asu.diging.gilesecosystem.nepomuk.core.exception.NoUniqueResultException;
 import edu.asu.diging.gilesecosystem.nepomuk.core.exception.UnstorableObjectException;
 import edu.asu.diging.gilesecosystem.nepomuk.core.files.IFilesDatabaseClient;
 import edu.asu.diging.gilesecosystem.nepomuk.core.store.objectdb.DatabaseClient;
@@ -74,6 +76,21 @@ public IFile getFile(String filename) {
         }
         return files.get(0);
     }
+
+    @Override
+    public IFile getFile(String uploadId, String documentId, String filename) throws NoUniqueResultException {
+        String query = "SELECT t FROM " + File.class.getName()  + " t WHERE t.uploadId = '" + uploadId + "' and t.documentId = '" + documentId + "' and t.filename = '" + filename + "'";
+        TypedQuery<File> docs = em.createQuery(query, File.class);
+
+        List<File> results = docs.getResultList();
+        if (results.size() > 1) {
+            throw new NoUniqueResultException("There are more than one result for file: " + uploadId + ", " + documentId + ", " + filename);
+        }
+        if (results.isEmpty()) {
+            return null;
+        }
+        return results.get(0);
+    }
 
     @Override
     protected String getIdPrefix() {

diff --git a/...muk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/impl/FilesManager.java b/...muk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/impl/FilesManager.java
@@ -9,6 +9,7 @@
 import org.springframework.stereotype.Service;
 
 import edu.asu.diging.gilesecosystem.nepomuk.core.domain.IFile;
+import edu.asu.diging.gilesecosystem.nepomuk.core.exception.NoUniqueResultException;
 import edu.asu.diging.gilesecosystem.nepomuk.core.exception.UnstorableObjectException;
 import edu.asu.diging.gilesecosystem.nepomuk.core.files.IFilesDatabaseClient;
 import edu.asu.diging.gilesecosystem.nepomuk.core.files.IFilesManager;
@@ -71,7 +72,11 @@ public IFile saveFile(IFile file) throws UnstorableObjectException {
         return file;
     }
 
-
+    @Override
+    public IFile getFile(String uploadId, String documentId, String filename) throws NoUniqueResultException {
+        return databaseClient.getFile(uploadId, documentId, filename);
+    }
+
     @Override
     public String getRelativePathOfFile(IFile file) {
         IFileTypeHandler handler = fileHandlerRegistry.getHandler(file

diff --git a/...in/java/edu/asu/diging/gilesecosystem/nepomuk/core/kafka/impl/StorageRequestReceiver.java b/...in/java/edu/asu/diging/gilesecosystem/nepomuk/core/kafka/impl/StorageRequestReceiver.java
@@ -11,6 +11,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import edu.asu.diging.gilesecosystem.nepomuk.core.service.IRequestProcessor;
+import edu.asu.diging.gilesecosystem.nepomuk.core.service.ISystemMessageHandler;
 import edu.asu.diging.gilesecosystem.util.properties.IPropertiesManager;
 import edu.asu.diging.gilesecosystem.requests.IStorageRequest;
 import edu.asu.diging.gilesecosystem.requests.impl.StorageRequest;
@@ -25,6 +26,9 @@ public class StorageRequestReceiver {
 
     @Autowired
     private IPropertiesManager propertiesManager;
+
+    @Autowired
+    private ISystemMessageHandler systemMessageHandler;
 
     @KafkaListener(topics = "${topic_storage_request}")
     public void receiveMessage(String message) {
@@ -34,6 +38,7 @@ public void receiveMessage(String message) {
             request = mapper.readValue(message, StorageRequest.class);
         } catch (IOException e) {
             logger.error("Could not unmarshall request.", e);
+            systemMessageHandler.handleError("Could not unmarshall request.", e);
             // FIXME: handel this case
             return;
         }

diff --git a/...a/edu/asu/diging/gilesecosystem/nepomuk/core/service/apps/impl/RegisteredAppsManager.java b/...a/edu/asu/diging/gilesecosystem/nepomuk/core/service/apps/impl/RegisteredAppsManager.java
@@ -12,6 +12,7 @@
 
 import edu.asu.diging.gilesecosystem.nepomuk.core.apps.IRegisteredApp;
 import edu.asu.diging.gilesecosystem.nepomuk.core.apps.IRegisteredAppDatabaseClient;
+import edu.asu.diging.gilesecosystem.nepomuk.core.service.ISystemMessageHandler;
 import edu.asu.diging.gilesecosystem.nepomuk.core.service.apps.IRegisteredAppManager;
 import edu.asu.diging.gilesecosystem.nepomuk.core.exception.TokenGenerationErrorException;
 import edu.asu.diging.gilesecosystem.util.exceptions.UnstorableObjectException;
@@ -30,6 +31,9 @@ public class RegisteredAppsManager implements IRegisteredAppManager {
     @Autowired
     private ITokenService tokenService;
 
+    @Autowired
+    private ISystemMessageHandler systemMessageHandler;
+
     @Override
     public IRegisteredApp storeApp(IRegisteredApp app) {
 
@@ -40,6 +44,7 @@ public IRegisteredApp storeApp(IRegisteredApp app) {
             databaseClient.store(app);
         } catch (UnstorableObjectException e) {
             logger.error("Could not store app.", e);
+            systemMessageHandler.handleError("Could not store app.", e);
             return null;
         }
         return app;

diff --git a/...java/edu/asu/diging/gilesecosystem/nepomuk/core/service/handlers/AbstractFileHandler.java b/...java/edu/asu/diging/gilesecosystem/nepomuk/core/service/handlers/AbstractFileHandler.java
@@ -19,13 +19,17 @@
 import edu.asu.diging.gilesecosystem.nepomuk.core.files.IFileStorageManager;
 import edu.asu.diging.gilesecosystem.nepomuk.core.files.IFilesManager;
 import edu.asu.diging.gilesecosystem.nepomuk.core.service.IFileTypeHandler;
+import edu.asu.diging.gilesecosystem.nepomuk.core.service.ISystemMessageHandler;
 
 public abstract class AbstractFileHandler implements IFileTypeHandler {
 
     private Logger logger = LoggerFactory.getLogger(getClass());
-    
+
     @Autowired
     private IFilesManager filesManager;
+
+    @Autowired
+    private ISystemMessageHandler systemMessageHandler;
 
     protected byte[] getFileContentFromUrl(URL url) throws IOException {
         URLConnection con = url.openConnection();
@@ -58,12 +62,17 @@ public byte[] getFileContent(IFile file) {
         try {
             return getFileContentFromUrl(fileObject.toURI().toURL());
         } catch (IOException e) {
+            systemMessageHandler.handleError("Could not read file.", e);
             logger.error("Could not read file.", e);
             return null;
         }
     }
 
     public IFile processFile(IFile file, byte[] content) throws NepomukFileStorageException {
+        if (content == null) {
+            logger.warn("File " + file.getGilesFileId() + " does not have any content.");
+            return null;
+        }
 
         Tika tika = new Tika();
         String contentType = tika.detect(content);
@@ -76,6 +85,7 @@ public IFile processFile(IFile file, byte[] content) throws NepomukFileStorageEx
             filesManager.saveFile(file);
         } catch (UnstorableObjectException e) {
             logger.error("Could not store file.", e);
+            systemMessageHandler.handleError("Could not store file.", e);
             return null;
         }
         return file;

diff --git a/...c/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/service/impl/RequestProcessor.java b/...c/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/service/impl/RequestProcessor.java
@@ -81,6 +81,7 @@ public void processRequest(IStorageRequest request) {
         newFile.setUsername(request.getUsername());
         newFile.setFilename(request.getFilename());
         newFile.setFileType(request.getFileType());
+        newFile.setGilesFileId(request.getFileId());
 
         byte[] content = downloadFile(request.getDownloadUrl());
         try {

diff --git a/...in/java/edu/asu/diging/gilesecosystem/nepomuk/core/service/impl/SystemMessageHandler.java b/...in/java/edu/asu/diging/gilesecosystem/nepomuk/core/service/impl/SystemMessageHandler.java
@@ -39,7 +39,7 @@ public class SystemMessageHandler implements ISystemMessageHandler {
     public void setup() {
         requestFactory.config(SystemMessageRequest.class);
     }
-    
+
     /* (non-Javadoc)
      * @see edu.asu.diging.gilesecosystem.nepomuk.core.service.impl.ISystemMessageHandler#handleError(java.lang.Exception)
      */