PR14/15: pic-sure-hpds (8 modules) — adopt parent + BOM (Java 25)

.github/workflows/pic-sure-hpds-test.yml

@@ -0,0 +1,22 @@
+name: pic-sure-hpds tests
+on:
+  pull_request:
+    paths: ['services/pic-sure-hpds/**']
+  push:
+    branches: [main]
+    paths: ['services/pic-sure-hpds/**']
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2
+      - name: Set up JDK 25
+        uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 #v5.2.0
+        with:
+          java-version: '25'
+          distribution: 'temurin'
+          cache: maven
+      - name: Test with Maven
+        run: mvn -B -pl services/pic-sure-hpds/common,services/pic-sure-hpds/data,services/pic-sure-hpds/etl,services/pic-sure-hpds/processing,services/pic-sure-hpds/service,services/pic-sure-hpds/genomic-processor,services/pic-sure-hpds/war,services/pic-sure-hpds/docker -am verify
+        env:
+          GITHUB_TOKEN: ${{ github.token }}

pom.xml

@@ -24,6 +24,7 @@
         <module>services/picsure-dictionary/dictionaryweights</module>
         <module>services/pic-sure-logging</module>
         <module>services/pic-sure-auth-microapp</module>
+        <module>services/pic-sure-hpds</module>
         <!-- pic-sure-legacy is deliberately NOT aggregated: it is quarantined
              (Java 11/javax, own parent pom) and builds independently. -->
     </modules>

services/pic-sure-hpds/common/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<artifactId>pic-sure-hpds</artifactId>
 		<groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
-		<version>3.0.0-SNAPSHOT</version>
+		<version>${revision}</version>
 	</parent>
 
 	<artifactId>common</artifactId>

services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/Crypto.java

@@ -26,89 +26,95 @@
 
 public class Crypto {
 
-	public static final String DEFAULT_KEY_NAME = "DEFAULT";
-
-	// This needs to be set in a static initializer block to be overridable in tests.
-	private static final String DEFAULT_ENCRYPTION_KEY_PATH;
-	static{
-		DEFAULT_ENCRYPTION_KEY_PATH = "/opt/local/hpds/encryption_key";
-	}
-
-	private static final Logger LOGGER = LoggerFactory.getLogger(Crypto.class);
-
-	private static final HashMap<String, byte[]> keys = new HashMap<String, byte[]>();
-
-	public static void loadDefaultKey() {
-		loadKey(DEFAULT_KEY_NAME, DEFAULT_ENCRYPTION_KEY_PATH);
-	}
-
-	public static void loadKey(String keyName, String filePath) {
-		try {
-			setKey(keyName, IOUtils.toString(new FileInputStream(filePath), Charset.forName("UTF-8")).trim().getBytes());
-			LOGGER.info("****LOADED CRYPTO KEY****");	
-		} catch (IOException e) {
-			LOGGER.error("****CRYPTO KEY NOT FOUND****", e);
-		}
-	}
-
-	public static byte[] encryptData(byte[] plaintextBytes) {
-		return encryptData(DEFAULT_KEY_NAME, plaintextBytes);
-	}
-
-	public static byte[] encryptData(String keyName, byte[] plaintextBytes) {
-		byte[] key = keys.get(keyName);
-		SecureRandom secureRandom = new SecureRandom();
-		SecretKey secretKey = new SecretKeySpec(key, "AES");
-		byte[] iv = new byte[12]; //NEVER REUSE THIS IV WITH SAME KEY
-		secureRandom.nextBytes(iv);
-		byte[] cipherText;
-		Cipher cipher;
-		try {
-			cipher = Cipher.getInstance("AES/GCM/NoPadding");
-			GCMParameterSpec parameterSpec = new GCMParameterSpec(128, iv); //128 bit auth tag length
-			cipher.init(Cipher.ENCRYPT_MODE, secretKey, parameterSpec);
-			cipherText = new byte[cipher.getOutputSize(plaintextBytes.length)];
-			cipher.doFinal(plaintextBytes, 0, plaintextBytes.length, cipherText, 0);
-			LOGGER.debug("Length of cipherText : " + cipherText.length);
-			ByteBuffer byteBuffer = ByteBuffer.allocate(4 + iv.length + cipherText.length);
-			byteBuffer.putInt(iv.length);
-			byteBuffer.put(iv);
-			byteBuffer.put(cipherText);
-			byte[] cipherMessage = byteBuffer.array();
-			return cipherMessage;
-		} catch (NoSuchAlgorithmException | NoSuchPaddingException | InvalidKeyException | InvalidAlgorithmParameterException | ShortBufferException | IllegalBlockSizeException | BadPaddingException e) {
-			throw new RuntimeException("Exception while trying to encrypt data : ", e);
-		}
-	}
-
-	public static byte[] decryptData(byte[] encrypted) {
-		return decryptData(DEFAULT_KEY_NAME, encrypted);
-	}
-
-	public static byte[] decryptData(String keyName, byte[] encrypted) {
-		byte[] key = keys.get(keyName);
-		ByteBuffer byteBuffer = ByteBuffer.wrap(encrypted);
-		int ivLength = byteBuffer.getInt();
-		byte[] iv = new byte[ivLength];
-		byteBuffer.get(iv);
-		byte[] cipherText = new byte[byteBuffer.remaining()];
-		byteBuffer.get(cipherText);
-		Cipher cipher;
-		try {
-			cipher = Cipher.getInstance("AES/GCM/NoPadding");
-			cipher.init(Cipher.DECRYPT_MODE, new SecretKeySpec(key, "AES"), new GCMParameterSpec(128, iv));
-			return cipher.doFinal(cipherText);
-		} catch (NoSuchAlgorithmException | NoSuchPaddingException | InvalidKeyException | InvalidAlgorithmParameterException | IllegalBlockSizeException | BadPaddingException e) {
-			throw new RuntimeException("Exception caught trying to decrypt data : " + e, e);
-		}
-	}
-
-	private static void setKey(String keyName, byte[] key) {
-		keys.put(keyName, key);
-	}
-
-	public static boolean hasKey(String keyName) {
-		return keys.containsKey(keyName);
-	}
+    public static final String DEFAULT_KEY_NAME = "DEFAULT";
+
+    // This needs to be set in a static initializer block to be overridable in tests.
+    private static final String DEFAULT_ENCRYPTION_KEY_PATH;
+    static {
+        DEFAULT_ENCRYPTION_KEY_PATH = "/opt/local/hpds/encryption_key";
+    }
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(Crypto.class);
+
+    private static final HashMap<String, byte[]> keys = new HashMap<String, byte[]>();
+
+    public static void loadDefaultKey() {
+        loadKey(DEFAULT_KEY_NAME, DEFAULT_ENCRYPTION_KEY_PATH);
+    }
+
+    public static void loadKey(String keyName, String filePath) {
+        try {
+            setKey(keyName, IOUtils.toString(new FileInputStream(filePath), Charset.forName("UTF-8")).trim().getBytes());
+            LOGGER.info("****LOADED CRYPTO KEY****");
+        } catch (IOException e) {
+            LOGGER.error("****CRYPTO KEY NOT FOUND****", e);
+        }
+    }
+
+    public static byte[] encryptData(byte[] plaintextBytes) {
+        return encryptData(DEFAULT_KEY_NAME, plaintextBytes);
+    }
+
+    public static byte[] encryptData(String keyName, byte[] plaintextBytes) {
+        byte[] key = keys.get(keyName);
+        SecureRandom secureRandom = new SecureRandom();
+        SecretKey secretKey = new SecretKeySpec(key, "AES");
+        byte[] iv = new byte[12]; // NEVER REUSE THIS IV WITH SAME KEY
+        secureRandom.nextBytes(iv);
+        byte[] cipherText;
+        Cipher cipher;
+        try {
+            cipher = Cipher.getInstance("AES/GCM/NoPadding");
+            GCMParameterSpec parameterSpec = new GCMParameterSpec(128, iv); // 128 bit auth tag length
+            cipher.init(Cipher.ENCRYPT_MODE, secretKey, parameterSpec);
+            cipherText = new byte[cipher.getOutputSize(plaintextBytes.length)];
+            cipher.doFinal(plaintextBytes, 0, plaintextBytes.length, cipherText, 0);
+            LOGGER.debug("Length of cipherText : " + cipherText.length);
+            ByteBuffer byteBuffer = ByteBuffer.allocate(4 + iv.length + cipherText.length);
+            byteBuffer.putInt(iv.length);
+            byteBuffer.put(iv);
+            byteBuffer.put(cipherText);
+            byte[] cipherMessage = byteBuffer.array();
+            return cipherMessage;
+        } catch (
+            NoSuchAlgorithmException | NoSuchPaddingException | InvalidKeyException | InvalidAlgorithmParameterException
+            | ShortBufferException | IllegalBlockSizeException | BadPaddingException e
+        ) {
+            throw new RuntimeException("Exception while trying to encrypt data : ", e);
+        }
+    }
+
+    public static byte[] decryptData(byte[] encrypted) {
+        return decryptData(DEFAULT_KEY_NAME, encrypted);
+    }
+
+    public static byte[] decryptData(String keyName, byte[] encrypted) {
+        byte[] key = keys.get(keyName);
+        ByteBuffer byteBuffer = ByteBuffer.wrap(encrypted);
+        int ivLength = byteBuffer.getInt();
+        byte[] iv = new byte[ivLength];
+        byteBuffer.get(iv);
+        byte[] cipherText = new byte[byteBuffer.remaining()];
+        byteBuffer.get(cipherText);
+        Cipher cipher;
+        try {
+            cipher = Cipher.getInstance("AES/GCM/NoPadding");
+            cipher.init(Cipher.DECRYPT_MODE, new SecretKeySpec(key, "AES"), new GCMParameterSpec(128, iv));
+            return cipher.doFinal(cipherText);
+        } catch (
+            NoSuchAlgorithmException | NoSuchPaddingException | InvalidKeyException | InvalidAlgorithmParameterException
+            | IllegalBlockSizeException | BadPaddingException e
+        ) {
+            throw new RuntimeException("Exception caught trying to decrypt data : " + e, e);
+        }
+    }
+
+    private static void setKey(String keyName, byte[] key) {
+        keys.put(keyName, key);
+    }
+
+    public static boolean hasKey(String keyName) {
+        return keys.containsKey(keyName);
+    }
 
 }

services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/exception/NotEnoughMemoryException.java

@@ -2,11 +2,13 @@
 
 public class NotEnoughMemoryException extends RuntimeException {
 
-	private static final long serialVersionUID = 2592915631853567560L;
+    private static final long serialVersionUID = 2592915631853567560L;
 
-	public NotEnoughMemoryException() {
-		super("Not enough available heap space to allocate results array."
-				+ "Please reduce ID_BATCH_SIZE or CACHE_SIZE system property or increase the heap available to this application. "
-				+ "This query will be retried up to 3 times.");
-	}
+    public NotEnoughMemoryException() {
+        super(
+            "Not enough available heap space to allocate results array."
+                + "Please reduce ID_BATCH_SIZE or CACHE_SIZE system property or increase the heap available to this application. "
+                + "This query will be retried up to 3 times."
+        );
+    }
 }

services/pic-sure-hpds/common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/exception/ResultSetTooLargeException.java

@@ -1,21 +1,20 @@
 package edu.harvard.hms.dbmi.avillach.hpds.exception;
 
 public class ResultSetTooLargeException extends RuntimeException {
-	/**
-	 * This exception is thrown when a result set would be larger in memory than
-	 * Integer.MAX_INT bytes. This is a JVM limitation... but seriously people...
-	 * 
-	 * You actually don't need that much data on the client side, work with us
-	 * to implement whatever filtering you need.
-	 * 
-	 * @param multiplesOfCapacity The number of pieces to split this result to actually have it work.
-	 */
-	public ResultSetTooLargeException(long multiplesOfCapacity) {
-		super("The result set is too large to handle in one request. "
-				+ "We have a plan to fix this limitation, but for now try "
-				+ "splitting your selected fields array in " + multiplesOfCapacity + " equal pieces "
-				+ "and running " + multiplesOfCapacity + " queries. Additionally, do you actually "
-				+ "need all this data? Do you have the compute resources "
-				+ "to handle processing it?");
-	}
+    /**
+     * This exception is thrown when a result set would be larger in memory than Integer.MAX_INT bytes. This is a JVM limitation... but
+     * seriously people...
+     * 
+     * You actually don't need that much data on the client side, work with us to implement whatever filtering you need.
+     * 
+     * @param multiplesOfCapacity The number of pieces to split this result to actually have it work.
+     */
+    public ResultSetTooLargeException(long multiplesOfCapacity) {
+        super(
+            "The result set is too large to handle in one request. " + "We have a plan to fix this limitation, but for now try "
+                + "splitting your selected fields array in " + multiplesOfCapacity + " equal pieces " + "and running " + multiplesOfCapacity
+                + " queries. Additionally, do you actually " + "need all this data? Do you have the compute resources "
+                + "to handle processing it?"
+        );
+    }
 }