Merge pull request #32 from diging/develop

Prepare release

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,24 @@
+# Guidelines for Pull Requests
+
+If you haven't yet read our code review guidelines, please do so, You can find them [here](https://diging.atlassian.net/wiki/spaces/DIGING/pages/2256076801/Code+Review+Guidelines).
+
+Please confirm the following by adding an x for each item (turn `[ ]` into `[x]`).
+
+- [ ] I have removed all code style changes that are not necessary (e.g. changing blanks across the whole file that don’t need to be changed, adding empty lines in parts other than your own code)
+- [ ] I am not making any changes to files that don’t have any effect (e.g. imports added that don’t need to be added)
+- [ ] I do not have any sysout statements in my code or commented out code that isn’t needed anymore
+- [ ] I am not reformatting any files in the wrong format or without cause. 
+- [ ] I am not changing file encoding or line endings to something else than UTF-8, LF
+- [ ] My pull request does not show an insane amount of files being changed although my ticket only requires a few files being changed
+- [ ] I have added Javadoc/documentation where appropriate
+- [ ] I have added test cases where appropriate
+- [ ] I have explained any part of my code/implementation decisions that is not be self-explanatory
+
+## Please provide a brief description of your ticket 
+(you can copy the ticket if it hasn't changed) 
+
+<!-- ...Put description here... -->
+
+## Anything else the reviewer needs to know?
+
+<!-- ... describe here ... -->

checkstyle.xml

@@ -0,0 +1,64 @@
+<?xml version="1.0"?>
+<!DOCTYPE module PUBLIC
+          "-//Puppy Crawl//DTD Check Configuration 1.3//EN"
+          "http://checkstyle.sourceforge.net/dtds/configuration_1_3.dtd">
+
+<!--
+    Checkstyle is highly configurable. Be sure to read the documentation at http://checkstyle.sf.net 
+ -->
+
+<module name = "Checker">
+    <property name="charset" value="UTF-8"/>
+    <property name="severity" value="warning"/>
+    <property name="fileExtensions" value="java, properties, xml"/>
+    <module name="TreeWalker">
+        <module name="OuterTypeFilename"/>
+        <module name="IllegalTokenText">
+            <property name="tokens" value="STRING_LITERAL, CHAR_LITERAL"/>
+            <property name="format" value="\\u00(09|0(a|A)|0(c|C)|0(d|D)|22|27|5(C|c))|\\(0(10|11|12|14|15|42|47)|134)"/>
+            <property name="message" value="Consider using special escape sequence instead of octal value or Unicode escaped value."/>
+        </module>
+        <module name="AvoidEscapedUnicodeCharacters">
+            <property name="allowEscapesForControlCharacters" value="true"/>
+            <property name="allowByTailComment" value="true"/>
+            <property name="allowNonPrintableEscapes" value="true"/>
+        </module>
+        <module name="OneTopLevelClass"/>
+        <module name="NoLineWrap"/>
+        <module name="EmptyBlock">
+            <property name="option" value="TEXT"/>
+            <property name="tokens" value="LITERAL_TRY, LITERAL_FINALLY, LITERAL_IF, LITERAL_ELSE, LITERAL_SWITCH"/>
+        </module>
+        <module name="OneStatementPerLine"/>
+        <module name="MissingSwitchDefault"/>
+        <module name="NoFinalizer"/>
+        <module name="OverloadMethodsDeclarationOrder"/>
+        <module name="EmptyCatchBlock">
+            <property name="exceptionVariableName" value="expected|ignore"/>
+        </module>
+        <module name="UpperEll"/>
+
+        <!-- Rules from Sun's Java Style  -->
+        <module name="IllegalImport"/>
+        <module name="EmptyStatement"/>
+        <module name="EqualsHashCode"/>
+        <module name="SimplifyBooleanReturn"/>
+        <module name="TodoComment">
+            <property name="format" value="(TODO)|(FIXME)"/>
+            <message key="todo.match" value="Resolve unexpected comment."/>
+        </module>
+
+        <!-- Custom  -->
+        <module name="DefaultComesLast">
+            <property name="skipIfLastAndSharedWithCase" value="true"/>
+        </module>
+        <module name="Indentation">
+            <property name="basicOffset" value="4"/>
+            <property name="braceAdjustment" value="0"/>
+            <property name="caseIndent" value="4"/>
+            <property name="throwsIndent" value="4"/>
+            <property name="lineWrappingIndentation" value="4"/>
+            <property name="arrayInitIndent" value="4"/>
+        </module>
+    </module>
+</module>

nepomuk/pom.xml

@@ -13,10 +13,10 @@
         <org.slf4j-version>1.7.5</org.slf4j-version>
         <org.springframework-version>4.3.2.RELEASE</org.springframework-version>
         <spring-security-version>4.1.3.RELEASE</spring-security-version>
-        <geco.requests.version>0.10</geco.requests.version>
-        <geco.util.version>0.4.3</geco.util.version>
+        <geco.requests.version>0.16</geco.requests.version>
+        <geco.util.version>0.6</geco.util.version>
         <geco.september.util.version>0.3</geco.september.util.version>
-        <geco.kafka-util.version>0.1</geco.kafka-util.version>
+        <geco.kafka-util.version>0.2</geco.kafka-util.version>
         <buildNumber></buildNumber>
 
         <admin.password>$2a$04$NXKVTx9XrpEST6CLn/ps7eP8YsK3t.5A/mvAoYpg.X8QqgOKtc1za</admin.password>
@@ -60,16 +60,15 @@
     </repositories>
 
     <dependencies>
-
         <!-- Giles Ecosystem -->
         <dependency>
             <groupId>edu.asu.diging</groupId>
             <artifactId>giles-eco-requests</artifactId>
             <version>${geco.requests.version}</version>
         </dependency>
         <dependency>
-            <groupId>edu.asu.diging.giles-eco</groupId>
-            <artifactId>util</artifactId>
+            <groupId>edu.asu.diging</groupId>
+            <artifactId>giles-eco-util</artifactId>
             <version>${geco.util.version}</version>
         </dependency>
         <dependency>
@@ -78,8 +77,8 @@
             <version>${geco.september.util.version}</version>
         </dependency>
         <dependency>
-        	<groupId>edu.asu.diging.giles-eco</groupId>
-        	<artifactId>kafka-util</artifactId>
+        	<groupId>edu.asu.diging</groupId>
+        	<artifactId>giles-eco-kafka-util</artifactId>
         	<version>${geco.kafka-util.version}</version>
         </dependency>
 
@@ -408,7 +407,26 @@
             <artifactId>curator-framework</artifactId>
             <version>2.12.0</version>
         </dependency>
+
+        <!-- API, java.xml.bind module -->
+        <dependency>
+            <groupId>jakarta.xml.bind</groupId>
+            <artifactId>jakarta.xml.bind-api</artifactId>
+            <version>2.3.2</version>
+        </dependency>
+
+        <!-- Runtime, com.sun.xml.bind module -->
+        <dependency>
+            <groupId>org.glassfish.jaxb</groupId>
+            <artifactId>jaxb-runtime</artifactId>
+            <version>2.3.2</version>
+        </dependency>
 
+        <dependency>
+            <groupId>javax.xml.bind</groupId>
+            <artifactId>jaxb-api</artifactId>
+            <version>2.4.0-b180830.0359</version>
+        </dependency>
 
     </dependencies>
 
@@ -429,7 +447,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-war-plugin</artifactId>
-                <version>2.6</version>
+                <version>3.3.2</version>
                 <configuration>
                     <webResources>
                         <resource>
@@ -462,8 +480,8 @@
             <plugin>
                 <artifactId>maven-compiler-plugin</artifactId>
                 <configuration>
-                    <source>1.8</source>
-                    <target>1.8</target>
+                    <source>11</source>
+                    <target>11</target>
                 </configuration>
             </plugin>
             <plugin>
@@ -531,7 +549,7 @@
     </build>
 
     <scm>
-        <connection>scm:svn:http://none</connection>
-        <url>scm:svn:https://none</url>
+        <connection>scm:git:http://none</connection>
+        <url>scm:git:https://none</url>
     </scm>
 </project>

nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/config/NepomukKafkaConfig.java

@@ -15,6 +15,7 @@
 import org.springframework.kafka.core.ConsumerFactory;
 import org.springframework.kafka.core.DefaultKafkaConsumerFactory;
 import edu.asu.diging.gilesecosystem.nepomuk.core.service.properties.Properties;
+import edu.asu.diging.gilesecosystem.nepomuk.core.kafka.impl.StorageDeletionRequestReceiver;
 import edu.asu.diging.gilesecosystem.nepomuk.core.kafka.impl.StorageRequestReceiver;
 import edu.asu.diging.gilesecosystem.util.properties.IPropertiesManager;
 
@@ -65,6 +66,11 @@ public ConcurrentKafkaListenerContainerFactory kafkaListenerContainerFactory() {
     public StorageRequestReceiver receiver() {
         return new StorageRequestReceiver();
     }
+
+    @Bean
+    public StorageDeletionRequestReceiver deletionReceiver() {
+        return new StorageDeletionRequestReceiver();
+    }
 
     @Override
     public String getHosts() {

nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/IFileStorageManager.java

@@ -35,5 +35,31 @@ public abstract String getAndCreateStoragePath(String username,
 
     public abstract String getFileFolderPathInBaseFolder(String username, String uploadId,
             String fileId);
+
+    /**
+     * Method to delete a file from storage
+     * 
+     * @param username
+     *            username of user who uploaded an image
+     * @param uploadId
+     *            id of upload a file was part of
+     * @param documentId
+     *            id of document
+     * @param fileId
+     *            id of file
+     * @param deleteEmptyFolders
+     *            if empty folders need to be deleted 
+     * @throws NepomukFileStorageException 
+     */
+    public abstract void deleteFile(String username, String uploadId, String documentId, String fileId) throws NepomukFileStorageException;
 
-}
+    /**
+     * Checks if a file exists at the specified location.
+     * @param username   The username associated with the file.
+     * @param uploadId   The unique identifier for the upload.
+     * @param documentId The identifier for the document.
+     * @param fileName   The name of the file to check.
+     * @return {@code true} if the file exists at the specified location, {@code false} otherwise.
+     */
+    public abstract boolean checkIfFileExists(String username, String uploadId, String documentId, String fileName);
+}

nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/IFilesDatabaseClient.java

@@ -29,4 +29,12 @@ public abstract IFile getFile(String uploadId, String documentId, String filenam
 
     List<String> getUsernames();
 
-}
+    /**
+     * Delete a file given the file ID.
+     * @param fileId 
+     *         ID of the file to be deleted
+     */
+    public abstract void deleteFile(String fileId);
+
+    public abstract List<IFile> getFilesByDocumentId(String documentId);
+}

nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/IFilesManager.java

@@ -35,4 +35,14 @@ public abstract IFile getFile(String uploadId, String documentId, String filenam
             throws NoUniqueResultException;
 
     List<String> getKnownUsernames();
-}
+
+    /**
+     * Delete a file given the file ID.
+     * @param fileId 
+     *         ID of the file to be deleted
+     */
+
+    public abstract void deleteFile(String fileId);
+
+    public abstract List<IFile> getFilesByDocumentId(String documentId);
+}

nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/impl/FileStorageManager.java

@@ -5,6 +5,9 @@
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 
 import org.springframework.stereotype.Service;
 
@@ -49,8 +52,7 @@ public void saveFile(String username, String uploadId, String documentId,
     @Override
     public String getAndCreateStoragePath(String username, String uploadId,
             String documentId) {
-        String path = baseDirectory + File.separator 
-                + getFileFolderPathInBaseFolder(username, uploadId, documentId);
+        String path = getStoragePath(username, uploadId, documentId);
         createDirectory(path);
         return path;
     }
@@ -119,5 +121,42 @@ private boolean createDirectory(String dirPath) {
     public void setFileTypeFolder(String fileTypeFolder) {
         this.fileTypeFolder = fileTypeFolder;
     }
+
+    private String getStoragePath(String username, String uploadId,
+            String documentId) {
+        return baseDirectory + File.separator 
+                + getFileFolderPathInBaseFolder(username, uploadId, documentId);
+    }
+
+    public void deleteFile(String username, String uploadId, String documentId, String fileName) throws NepomukFileStorageException {
+        String originalFilePath = getStoragePath(username, uploadId, documentId);
+        Path path = Paths.get(originalFilePath + File.separator + fileName);
+        try {
+            Files.delete(path);
+        } catch (IOException ex) {
+            throw new NepomukFileStorageException("Could not delete file.", ex);
+        }
+        String documentFolder = getStoragePath(username, uploadId, documentId);
+        File docFolder = new File(documentFolder);
+        if (docFolder.isDirectory() && docFolder.list().length == 0) {
+            // If another process adds a file to the folder just before deletion, we do not want to delete the folder.
+            // The goal is to ensure that the folder remains intact even if new files are added during the deletion process.
+            // Using the File.delete() instead of Files.delete(path) as an exception is not required to be thrown in this scenario.
+            boolean deleted = docFolder.delete();
+            if (deleted) {
+                Path documentFolderPath = Paths.get(documentFolder);
+                Path uploadFolderDirectory = documentFolderPath.getParent();
+                File uploadFolder = new File(uploadFolderDirectory.toString());
+                if (uploadFolder.isDirectory() && uploadFolder.list().length == 0) {
+                    uploadFolder.delete();
+                }
+            }
+        }
+    }
 
+    @Override
+    public boolean checkIfFileExists(String username, String uploadId, String documentId, String fileName) {
+        Path path = Paths.get(getStoragePath(username, uploadId, documentId) + File.separator + fileName);
+        return Files.exists(path);
+    }
 }

nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/impl/FilesDatabaseClient.java

@@ -56,6 +56,13 @@ public List<IFile> getFilesByUploadId(String uploadId) {
         return results;
     }
 
+    @Override
+    public List<IFile> getFilesByDocumentId(String documentId) {
+        List<IFile> results = new ArrayList<IFile>();
+        searchByProperty("documentId", documentId, File.class).forEach(f -> results.add((IFile)f));
+        return results;
+    }
+
     @Override
     public List<IFile> getFilesByUsername(String username) {
         List<IFile> results = new ArrayList<IFile>();
@@ -120,4 +127,9 @@ public List<String> getUsernames() {
         TypedQuery<String> docs = em.createQuery(query, String.class);
         return docs.getResultList();       
     }
+
+    @Override
+    public void deleteFile(String fileId) {
+        em.remove(getById(fileId));
+    }
 }

nepomuk/src/main/java/edu/asu/diging/gilesecosystem/nepomuk/core/files/impl/FilesManager.java

@@ -35,6 +35,11 @@ public class FilesManager implements IFilesManager {
     public List<IFile> getFilesByUploadId(String uploadId) {
         return databaseClient.getFilesByUploadId(uploadId);
     }
+
+    @Override
+    public List<IFile> getFilesByDocumentId(String documentId) {
+        return databaseClient.getFilesByDocumentId(documentId);
+    }
 
     @Override
     public IFile getFile(String id) {
@@ -86,5 +91,9 @@ public String getRelativePathOfFile(IFile file) {
     public List<String> getKnownUsernames() {
         return databaseClient.getUsernames();
     }
-
+
+    @Override
+    public void deleteFile(String fileId) {
+        databaseClient.deleteFile(fileId);
+    }
 }