Merge pull request #58 from DataONEorg/feature-57-deleteobj-refactor

Feature-57: `deleteObject` Refactor

.github/workflows/maven.yml

@@ -21,10 +21,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up JDK 11
+    - name: Set up JDK 17
       uses: actions/setup-java@v3
       with:
-        java-version: '11'
+        java-version: '17'
         distribution: 'temurin'
         cache: maven
     - name: Build with Maven

pom.xml

@@ -59,7 +59,7 @@
     <dependency>
       <groupId>org.postgresql</groupId>
       <artifactId>postgresql</artifactId>
-      <version>42.4.3</version>
+      <version>42.7.2</version>
     </dependency>
   </dependencies>
 
@@ -71,8 +71,8 @@
           <artifactId>maven-compiler-plugin</artifactId>
           <version>3.8.1</version>
           <configuration>
-              <source>8</source>
-              <target>8</target>
+              <source>17</source>
+              <target>17</target>
           </configuration>
         </plugin>
         <plugin>
@@ -86,6 +86,8 @@
                   <goal>shade</goal>
               </goals>
               <configuration>
+                <outputFile>${basedir}/target/${project.name}-${project.version}-shaded.jar</outputFile>
+                <outputDirectory>${basedir}</outputDirectory>
                 <transformers>
                   <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                     <manifestEntries>

src/main/java/org/dataone/hashstore/HashStoreFactory.java

@@ -18,12 +18,11 @@ public class HashStoreFactory {
 
     /**
      * Factory method to generate a HashStore
-     * 
+     *
      * @param classPackage    String of the package name, ex.
      *                        "org.dataone.hashstore.filehashstore.FileHashStore"
      * @param storeProperties Properties object with the following keys: storePath, storeDepth,
      *                        storeWidth, storeAlgorithm, storeMetadataNamespace
-     * 
      * @return HashStore instance ready to store objects and metadata
      * @throws HashStoreFactoryException When HashStore failÏs to initialize due to permissions or
      *                                   class-related issues
@@ -52,34 +51,35 @@ public static HashStore getHashStore(String classPackage, Properties storeProper
             hashstore = (HashStore) constructor.newInstance(storeProperties);
 
         } catch (ClassNotFoundException cnfe) {
-            String errMsg = "HashStoreFactory - Unable to find 'FileHashStore' classPackage: "
-                + classPackage + " - " + cnfe.fillInStackTrace();
+            String errMsg =
+                "HashStoreFactory - Unable to find 'FileHashStore' classPackage: " + classPackage
+                    + " - " + cnfe.getCause();
             logHashStore.error(errMsg);
             throw new HashStoreFactoryException(errMsg);
 
         } catch (NoSuchMethodException nsme) {
-            String errMsg = "HashStoreFactory - Constructor not found for 'FileHashStore': "
-                + classPackage + " - " + nsme.fillInStackTrace();
+            String errMsg =
+                "HashStoreFactory - Constructor not found for 'FileHashStore': " + classPackage
+                    + " - " + nsme.getCause();
             logHashStore.error(errMsg);
             throw new HashStoreFactoryException(errMsg);
 
         } catch (IllegalAccessException iae) {
             String errMsg =
                 "HashStoreFactory - Executing method does not have access to the definition of"
-                    + " the specified class , field, method or constructor. " + iae
-                        .fillInStackTrace();
+                    + " the specified class , field, method or constructor. " + iae.getCause();
             logHashStore.error(errMsg);
             throw new HashStoreFactoryException(errMsg);
 
         } catch (InstantiationException ie) {
             String errMsg = "HashStoreFactory - Error instantiating 'FileHashStore'"
-                + "(likely related to `.newInstance()`): " + ie.fillInStackTrace();
+                + "(likely related to `.newInstance()`): " + ie.getCause();
             logHashStore.error(errMsg);
             throw new HashStoreFactoryException(errMsg);
 
         } catch (InvocationTargetException ite) {
-            String errMsg = "HashStoreFactory - Error creating 'FileHashStore' instance: " + ite
-                .fillInStackTrace();
+            String errMsg =
+                "HashStoreFactory - Error creating 'FileHashStore' instance: " + ite.getCause();
             logHashStore.error(errMsg);
             throw new HashStoreFactoryException(errMsg);
 

src/main/java/org/dataone/hashstore/ObjectMetadata.java

@@ -3,54 +3,10 @@
 import java.util.Map;
 
 /**
- * ObjectMetadata is a class that models a unique identifier for an object in the HashStore. It
- * encapsulates information about a file's content identifier (cid), size, and associated hash
- * digest values. By using ObjectMetadata objects, client code can easily obtain metadata of a store
- * object in HashStore without needing to know the underlying file system details.
+ * ObjectMetadata is a record that that contains metadata about an object in the HashStore. It
+ * encapsulates information about a file's authority-based/persistent identifier (pid), content
+ * identifier (cid), size, and associated hash digest values.
  */
-public class ObjectMetadata {
-    private final String cid;
-    private final long size;
-    private final Map<String, String> hexDigests;
+public record ObjectMetadata(String pid, String cid, long size, Map<String, String> hexDigests) {
 
-    /**
-     * Creates a new instance of ObjectMetadata with the given properties.
-     *
-     * @param cid        Unique identifier for the file
-     * @param size       Size of stored file
-     * @param hexDigests A map of hash algorithm names to their hex-encoded digest values for the
-     *                   file
-     */
-    public ObjectMetadata(String cid, long size, Map<String, String> hexDigests) {
-        this.cid = cid;
-        this.size = size;
-        this.hexDigests = hexDigests;
-    }
-
-    /**
-     * Return the cid (content identifier) of the file
-     * 
-     * @return cid
-     */
-    public String getCid() {
-        return cid;
-    }
-
-    /**
-     * Return the size of the file
-     * 
-     * @return size
-     */
-    public long getSize() {
-        return size;
-    }
-
-    /**
-     * Return a map of hex digests (checksums)
-     * 
-     * @return hexDigests
-     */
-    public Map<String, String> getHexDigests() {
-        return hexDigests;
-    }
-}
+}

src/main/java/org/dataone/hashstore/exceptions/CidNotFoundInPidRefsFileException.java

@@ -0,0 +1,12 @@
+package org.dataone.hashstore.exceptions;
+
+/**
+ * Custom exception class for FileHashStore when the expected cid is not found in the pid refs file.
+ */
+public class CidNotFoundInPidRefsFileException extends IllegalArgumentException {
+
+    public CidNotFoundInPidRefsFileException(String message) {
+        super(message);
+    }
+
+}

src/main/java/org/dataone/hashstore/exceptions/HashStoreRefsAlreadyExistException.java

@@ -0,0 +1,14 @@
+package org.dataone.hashstore.exceptions;
+
+import java.nio.file.FileAlreadyExistsException;
+
+/**
+ * Custom exception thrown when called to tag a pid and cid, and reference files already exist
+ */
+public class HashStoreRefsAlreadyExistException extends FileAlreadyExistsException {
+
+    public HashStoreRefsAlreadyExistException(String message) {
+        super(message);
+    }
+
+}

src/main/java/org/dataone/hashstore/exceptions/HashStoreServiceException.java

@@ -0,0 +1,10 @@
+package org.dataone.hashstore.exceptions;
+
+/**
+ * An exception that encapsulates errors from the HashStore Runnable Test Class
+ */
+public class HashStoreServiceException extends Exception {
+    public HashStoreServiceException(String message) {
+        super(message);
+    }
+}

src/main/java/org/dataone/hashstore/exceptions/MissingHexDigestsException.java

@@ -0,0 +1,14 @@
+package org.dataone.hashstore.exceptions;
+
+import java.util.NoSuchElementException;
+
+/**
+ * An exception thrown when hexDigests from a supplied ObjectMetadata object is empty.
+ */
+public class MissingHexDigestsException extends NoSuchElementException {
+
+        public MissingHexDigestsException(String message) {
+            super(message);
+        }
+
+}

src/main/java/org/dataone/hashstore/exceptions/NonMatchingChecksumException.java

@@ -0,0 +1,13 @@
+package org.dataone.hashstore.exceptions;
+
+/**
+ * An exception thrown when a checksum does not match what is expected.
+ */
+
+public class NonMatchingChecksumException extends IllegalArgumentException {
+
+    public NonMatchingChecksumException(String message) {
+        super(message);
+    }
+
+}

src/main/java/org/dataone/hashstore/exceptions/NonMatchingObjSizeException.java

@@ -0,0 +1,14 @@
+package org.dataone.hashstore.exceptions;
+
+/**
+ * An exception thrown when a data object size does not match what is expected.
+ */
+
+public class NonMatchingObjSizeException extends IllegalArgumentException {
+
+    public NonMatchingObjSizeException(String message) {
+        super(message);
+    }
+
+}
+

src/main/java/org/dataone/hashstore/exceptions/OrphanRefsFilesException.java

@@ -0,0 +1,14 @@
+package org.dataone.hashstore.exceptions;
+
+import java.io.IOException;
+
+/**
+ * Custom exception class for FileHashStore when both a pid and cid reference file is found
+ * but object does not exist.
+ */
+public class OrphanRefsFilesException extends IOException {
+    public OrphanRefsFilesException(String message) {
+        super(message);
+    }
+
+}

src/main/java/org/dataone/hashstore/exceptions/PidNotFoundInCidRefsFileException.java

@@ -5,7 +5,7 @@
 /**
  * Custom exception class for FileHashStore when a pid is not found in a cid refs file.
  */
-public class PidNotFoundInCidRefsFileException extends IOException {
+public class PidNotFoundInCidRefsFileException extends IllegalArgumentException {
     public PidNotFoundInCidRefsFileException(String message) {
         super(message);
     }

src/main/java/org/dataone/hashstore/exceptions/PidRefsFileExistsException.java

@@ -3,7 +3,8 @@
 import java.io.IOException;
 
 /**
- * Custom exception class for FileHashStore pidObjects
+ * Custom exception class thrown when a pid refs file already exists (a single pid can only ever
+ * reference one cid)
  */
 public class PidRefsFileExistsException extends IOException {
     public PidRefsFileExistsException(String message) {

src/main/java/org/dataone/hashstore/exceptions/PidRefsFileNotFoundException.java

@@ -0,0 +1,10 @@
+package org.dataone.hashstore.exceptions;
+
+import java.io.FileNotFoundException;
+
+public class PidRefsFileNotFoundException extends FileNotFoundException {
+    public PidRefsFileNotFoundException(String message) {
+        super(message);
+    }
+
+}

src/main/java/org/dataone/hashstore/exceptions/UnsupportedHashAlgorithmException.java

@@ -0,0 +1,13 @@
+package org.dataone.hashstore.exceptions;
+
+/**
+ * An exception thrown when a given algorithm is not supported by FileHashStore java
+ */
+
+public class UnsupportedHashAlgorithmException extends IllegalArgumentException {
+
+    public UnsupportedHashAlgorithmException(String message) {
+        super(message);
+    }
+
+}