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/HashStoreClient.java

@@ -11,8 +11,8 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
 import java.util.Properties;
 import java.sql.Connection;
@@ -21,7 +21,6 @@
 import java.sql.Statement;
 
 import org.dataone.hashstore.filehashstore.FileHashStoreUtility;
-
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
 import org.apache.commons.cli.DefaultParser;
@@ -35,8 +34,8 @@
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 
 /**
- * HashStoreClient is a command line interface that allows a developer to create a new HashStore or
- * interact directly with an existing HashStore. See 'README.md' for usage examples.
+ * HashStoreClient is a development tool used to create a new HashStore or interact directly with
+ * an existing HashStore through the command line. See 'README.md' for usage examples.
  */
 public class HashStoreClient {
     private static HashStore hashStore;
@@ -142,13 +141,6 @@ public static void main(String[] args) throws Exception {
                     String hexDigest = hashStore.getHexDigest(pid, algo);
                     System.out.println(hexDigest);
 
-                } else if (cmd.hasOption("findobject")) {
-                    String pid = cmd.getOptionValue("pid");
-                    FileHashStoreUtility.ensureNotNull(pid, "-pid", "HashStoreClient");
-
-                    String cid = hashStore.findObject(pid);
-                    System.out.println(cid);
-
                 } else if (cmd.hasOption("storeobject")) {
                     System.out.println("Storing object");
                     String pid = cmd.getOptionValue("pid");
@@ -181,7 +173,7 @@ public static void main(String[] args) throws Exception {
                     );
                     pidObjStream.close();
                     System.out.println("Object Info for pid (" + pid + "):");
-                    System.out.println(objInfo.getHexDigests());
+                    System.out.println(objInfo.hexDigests());
 
                 } else if (cmd.hasOption("storemetadata")) {
                     String pid = cmd.getOptionValue("pid");
@@ -230,6 +222,7 @@ public static void main(String[] args) throws Exception {
                 } else if (cmd.hasOption("deleteobject")) {
                     String pid = cmd.getOptionValue("pid");
                     FileHashStoreUtility.ensureNotNull(pid, "-pid", "HashStoreClient");
+
                     hashStore.deleteObject(pid);
                     System.out.println("Object for pid (" + pid + ") has been deleted.");
 
@@ -282,10 +275,6 @@ private static Options addHashStoreClientOptions() {
             "getchecksum", "client_getchecksum", false,
             "Flag to get the hex digest of a data object in a HashStore."
         );
-        options.addOption(
-            "findobject", "client_findobject", false,
-            "Flag to get the hex digest of a data object in a HashStore."
-        );
         options.addOption(
             "storeobject", "client_storeobject", false, "Flag to store objs to a HashStore."
         );
@@ -351,6 +340,7 @@ private static Options addHashStoreClientOptions() {
         options.addOption(
             "dfs", "delfromhs", false, "(knbvm) Test flag to delete objs from a HashStore"
         );
+        options.addOption("hsr", "hsservicerequest", false, "Dev option to test threading.");
         return options;
     }
 
@@ -502,7 +492,7 @@ private static void testWithKnbvm(
 
             // For each row, get guid, docid, rev, checksum and checksum_algorithm
             // and create a List to loop over
-            List<Map<String, String>> resultObjList = new ArrayList<>();
+            Collection<Map<String, String>> resultObjList = new ArrayList<>();
             while (resultSet.next()) {
                 String guid = resultSet.getString("guid");
                 String docid = resultSet.getString("docid");
@@ -576,7 +566,7 @@ private static void testWithKnbvm(
      * @param resultObjList List containing items with the following properties: 'pid', 'path',
      *                      'algorithm', 'checksum'
      */
-    private static void storeObjsWithChecksumFromDb(List<Map<String, String>> resultObjList) {
+    private static void storeObjsWithChecksumFromDb(Collection<Map<String, String>> resultObjList) {
         resultObjList.parallelStream().forEach(item -> {
             String guid = null;
             try {
@@ -587,7 +577,7 @@ private static void storeObjsWithChecksumFromDb(List<Map<String, String>> result
 
                 // Store object
                 System.out.println("Storing object for guid: " + guid);
-                hashStore.storeObject(objStream, guid, checksum, algorithm);
+                hashStore.storeObject(objStream, guid, null, checksum, algorithm, -1);
 
             } catch (PidRefsFileExistsException poee) {
                 String errMsg = "Unexpected Error: " + poee.fillInStackTrace();
@@ -633,7 +623,7 @@ private static void storeObjsWithChecksumFromDb(List<Map<String, String>> result
      * @param resultObjList List containing items with the following properties: 'pid', 'algorithm',
      *                      'checksum'
      */
-    private static void retrieveAndValidateObjs(List<Map<String, String>> resultObjList) {
+    private static void retrieveAndValidateObjs(Collection<Map<String, String>> resultObjList) {
         resultObjList.parallelStream().forEach(item -> {
             String guid = null;
             try {
@@ -693,7 +683,7 @@ private static void retrieveAndValidateObjs(List<Map<String, String>> resultObjL
      * 
      * @param resultObjList List containing items with the following property: 'pid'
      */
-    private static void deleteObjectsFromStore(List<Map<String, String>> resultObjList) {
+    private static void deleteObjectsFromStore(Collection<Map<String, String>> resultObjList) {
         resultObjList.parallelStream().forEach(item -> {
             String guid = null;
             try {
@@ -737,7 +727,7 @@ private static void deleteObjectsFromStore(List<Map<String, String>> resultObjLi
      * @param resultObjList List containing items that have the following properties: 'pid', 'path'
      *                      and 'namespace'
      */
-    private static void storeMetadataFromDb(List<Map<String, String>> resultObjList) {
+    private static void storeMetadataFromDb(Collection<Map<String, String>> resultObjList) {
         resultObjList.parallelStream().forEach(item -> {
             String guid = null;
             try {
@@ -783,7 +773,7 @@ private static void storeMetadataFromDb(List<Map<String, String>> resultObjList)
      * @param resultObjList List containing items with the following properties: 'pid', 'namespace',
      *                      'algorithm', 'checksum'
      */
-    private static void retrieveAndValidateMetadata(List<Map<String, String>> resultObjList) {
+    private static void retrieveAndValidateMetadata(Collection<Map<String, String>> resultObjList) {
         resultObjList.parallelStream().forEach(item -> {
             String guid = null;
             try {
@@ -848,7 +838,7 @@ private static void retrieveAndValidateMetadata(List<Map<String, String>> result
      * 
      * @param resultObjList List containing items with the following property: 'pid'
      */
-    private static void deleteMetadataFromStore(List<Map<String, String>> resultObjList) {
+    private static void deleteMetadataFromStore(Collection<Map<String, String>> resultObjList) {
         resultObjList.parallelStream().forEach(item -> {
             String guid = null;
             try {

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

@@ -53,33 +53,32 @@ public static HashStore getHashStore(String classPackage, Properties storeProper
 
         } catch (ClassNotFoundException cnfe) {
             String errMsg = "HashStoreFactory - Unable to find 'FileHashStore' classPackage: "
-                + classPackage + " - " + cnfe.fillInStackTrace();
+                + classPackage + " - " + cnfe.getCause();
             logHashStore.error(errMsg);
             throw new HashStoreFactoryException(errMsg);
 
         } catch (NoSuchMethodException nsme) {
             String errMsg = "HashStoreFactory - Constructor not found for 'FileHashStore': "
-                + classPackage + " - " + nsme.fillInStackTrace();
+                + 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();
+                        .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);
+    }
+
+}
+