Initial spring boot commit. Needs more testing

client-api/pom.xml

@@ -22,12 +22,7 @@
   </properties>
 
   <dependencies>
-    <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>4.13.1</version>
-      <scope>test</scope>
-    </dependency>
+
   </dependencies>
 
   <build>

common/pom.xml

@@ -22,8 +22,8 @@
 			<artifactId>guava</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-jaxrs</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
 		</dependency>
 	</dependencies>
 </project>

common/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/storage/FileBackedJsonIndexStorage.java

@@ -1,7 +1,7 @@
 package edu.harvard.hms.dbmi.avillach.hpds.storage;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.type.TypeReference;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
 
 import java.io.*;
 import java.util.zip.GZIPInputStream;

common/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/CryptoDefaultKeyTest.java

@@ -1,22 +1,22 @@
 package edu.harvard.hms.dbmi.avillach.hpds.crypto;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+import org.springframework.test.context.event.annotation.BeforeTestClass;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import java.io.File;
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
 
-import org.junit.BeforeClass;
-import org.junit.Ignore;
-import org.junit.Test;
-
-@Ignore // We should rewrite the crypto class to make it more testable, these tests don't work on certain JDKs
+@Disabled // We should rewrite the crypto class to make it more testable, these tests don't work on certain JDKs
 public class CryptoDefaultKeyTest {
 
 	String TEST_MESSAGE = "This is a test.";
 
-	@BeforeClass
+	@BeforeTestClass
 	public static void overrideDefaultKeyLocation() throws IllegalArgumentException, IllegalAccessException {
 	}
 

common/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/CryptoNamedKeyTest.java

@@ -1,20 +1,18 @@
 package edu.harvard.hms.dbmi.avillach.hpds.crypto;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
 import java.io.File;
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
 
 import javax.crypto.AEADBadTagException;
 
-import org.junit.BeforeClass;
-import org.junit.Ignore;
-import org.junit.Test;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+import org.springframework.test.context.event.annotation.BeforeTestClass;
+
+import static org.junit.jupiter.api.Assertions.*;
 
-@Ignore // We should rewrite the crypto class to make it more testable, these tests don't work on certain JDKs
+@Disabled // We should rewrite the crypto class to make it more testable, these tests don't work on certain JDKs
 public class CryptoNamedKeyTest {
 
 	private static final String TEST_NAMED_ENCRYPTIOON_KEY_PATH = "src/test/resources/test_named_encryption_key";
@@ -23,7 +21,7 @@ public class CryptoNamedKeyTest {
 
 	String TEST_NAMED_KEY = "TEST_NAMED_KEY";
 
-	@BeforeClass
+	@BeforeTestClass
 	public static void overrideDefaultKeyLocation() throws IllegalArgumentException, IllegalAccessException, NoSuchFieldException, SecurityException {
 		Field field = Crypto.class.getDeclaredField("DEFAULT_ENCRYPTION_KEY_PATH");
 		field.setAccessible(true);
@@ -45,29 +43,21 @@ public void testNamedKeyEncryptDecrypt() {
 
 	@Test
 	public void testNamedKeyEncryptNotUsingDefaultKey() {
-		Crypto.loadKey(TEST_NAMED_KEY, TEST_NAMED_ENCRYPTIOON_KEY_PATH);
-		byte[] ciphertext = Crypto.encryptData(TEST_NAMED_KEY, TEST_MESSAGE.getBytes());
-		assertTrue(!new String(ciphertext).contentEquals(TEST_MESSAGE));
-		try{
+		assertThrows(AEADBadTagException.class, () -> {
+			Crypto.loadKey(TEST_NAMED_KEY, TEST_NAMED_ENCRYPTIOON_KEY_PATH);
+			byte[] ciphertext = Crypto.encryptData(TEST_NAMED_KEY, TEST_MESSAGE.getBytes());
+			assertFalse(new String(ciphertext).contentEquals(TEST_MESSAGE));
 			Crypto.decryptData(ciphertext);
-		}catch(RuntimeException e) {
-			assertEquals(e.getCause().getClass(), AEADBadTagException.class);
-			return;
-		}
-		fail("Expected AEADBadTagException to be thrown");
+		});
 	}
 
 	@Test
 	public void testNamedKeyDecryptNotUsingDefaultKey() {
-		Crypto.loadKey(TEST_NAMED_KEY, TEST_NAMED_ENCRYPTIOON_KEY_PATH);
-		byte[] ciphertext = Crypto.encryptData(TEST_MESSAGE.getBytes());
-		assertTrue(!new String(ciphertext).contentEquals(TEST_MESSAGE));
-		try{
+		assertThrows(AEADBadTagException.class, () -> {
+			Crypto.loadKey(TEST_NAMED_KEY, TEST_NAMED_ENCRYPTIOON_KEY_PATH);
+			byte[] ciphertext = Crypto.encryptData(TEST_MESSAGE.getBytes());
+			assertTrue(!new String(ciphertext).contentEquals(TEST_MESSAGE));
 			Crypto.decryptData(TEST_NAMED_KEY, ciphertext);
-		}catch(RuntimeException e) {
-			assertEquals(e.getCause().getClass(), AEADBadTagException.class);
-			return;
-		}
-		fail("Expected AEADBadTagException to be thrown");
+		});
 	}
 }

data/pom.xml

@@ -26,12 +26,8 @@
 			<artifactId>commons-csv</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-core-asl</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-mapper-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>edu.harvard.hms.dbmi.avillach</groupId>

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMasks.java

@@ -1,8 +1,9 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.genotype;
 
-import org.codehaus.jackson.annotate.JsonProperty;
-import org.codehaus.jackson.map.annotate.JsonSerialize;
-import org.codehaus.jackson.map.ser.ToStringSerializer;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+import com.fasterxml.jackson.databind.ser.std.ToStringSerializer;
 
 import java.io.Serializable;
 import java.math.BigInteger;
@@ -174,15 +175,19 @@ public VariantMasks() {
 	}
 
 	@JsonProperty("ho")
-	@JsonSerialize(using = ToStringSerializer.class, include=JsonSerialize.Inclusion.NON_NULL)
+	@JsonInclude(JsonInclude.Include.NON_NULL)
+	@JsonSerialize(using = ToStringSerializer.class)
 	public BigInteger homozygousMask;
 	@JsonProperty("he")
-	@JsonSerialize(using = ToStringSerializer.class, include=JsonSerialize.Inclusion.NON_NULL)
+	@JsonSerialize(using = ToStringSerializer.class)
+	@JsonInclude(JsonInclude.Include.NON_NULL)
 	public BigInteger heterozygousMask;
 	@JsonProperty("hon")
-	@JsonSerialize(using = ToStringSerializer.class, include=JsonSerialize.Inclusion.NON_NULL)
+	@JsonSerialize(using = ToStringSerializer.class)
+	@JsonInclude(JsonInclude.Include.NON_NULL)
 	public BigInteger homozygousNoCallMask;
 	@JsonProperty("hen")
-	@JsonSerialize(using = ToStringSerializer.class, include=JsonSerialize.Inclusion.NON_NULL)
+	@JsonSerialize(using = ToStringSerializer.class)
+	@JsonInclude(JsonInclude.Include.NON_NULL)
 	public BigInteger heterozygousNoCallMask;
 }

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java

@@ -1,12 +1,14 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
 import java.io.Serializable;
 import java.util.List;
 
-import org.codehaus.jackson.annotate.JsonIgnore;
-import org.codehaus.jackson.map.annotate.JsonSerialize;
 
-@JsonSerialize(include=JsonSerialize.Inclusion.NON_NULL)
+@JsonInclude(JsonInclude.Include.NON_NULL)
 public class ColumnMeta implements Serializable{
 
 	private static final long serialVersionUID = -124111104912063811L;

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/storage/FileBackedStorageVariantIndexImpl.java

@@ -1,7 +1,7 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.storage;
 
+import com.fasterxml.jackson.core.type.TypeReference;
 import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJsonIndexStorage;
-import org.codehaus.jackson.type.TypeReference;
 
 import java.io.File;
 import java.io.FileNotFoundException;

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/storage/FileBackedStorageVariantMasksImpl.java

@@ -1,8 +1,8 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.storage;
 
+import com.fasterxml.jackson.core.type.TypeReference;
 import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMasks;
 import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJsonIndexStorage;
-import org.codehaus.jackson.type.TypeReference;
 
 import java.io.File;
 import java.io.FileNotFoundException;

etl/pom.xml

@@ -13,11 +13,6 @@
 
 	<name>etl</name>
 	<dependencies>
-		<dependency>
-    			<groupId>ch.qos.logback</groupId>
-    			<artifactId>logback-core</artifactId>
-    			<version>1.2.9</version>
-		</dependency>
 		<dependency>
     			<groupId>org.apache.commons</groupId>
    	 		<artifactId>commons-compress</artifactId>
@@ -30,19 +25,8 @@
 		</dependency>
 		<dependency>
     			<groupId>com.fasterxml.jackson.core</groupId>
-    			<artifactId>jackson-core</artifactId>
-    			<version>2.10.5</version>
+    			<artifactId>jackson-databind</artifactId>
 		</dependency>
-		<dependency>
-   			 <groupId>com.fasterxml.jackson.core</groupId>
-    			<artifactId>jackson-annotations</artifactId>
-    			<version>2.10.5</version>
-		</dependency>
-		<dependency>
-                        <groupId>com.fasterxml.jackson.core</groupId>
-                        <artifactId>jackson-databind</artifactId>
-                        <version>2.10.5.1</version>
-                </dependency>
 		<dependency>
 			<groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
 			<artifactId>data</artifactId>

etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/NewVCFLoader.java

@@ -9,12 +9,10 @@
 import java.util.zip.GZIPOutputStream;
 
 import edu.harvard.hms.dbmi.avillach.hpds.data.storage.FileBackedStorageVariantMasksImpl;
-import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJavaIndexedStorage;
 import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedJsonIndexStorage;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVParser;
 import org.apache.commons.csv.CSVRecord;
-import org.codehaus.jackson.type.TypeReference;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

etl/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySampleTest.java

@@ -1,24 +1,19 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.genotype;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.ObjectInputStream;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
-import java.util.zip.GZIPInputStream;
 
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
 
 import edu.harvard.hms.dbmi.avillach.hpds.etl.genotype.NewVCFLoader;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.test.context.event.annotation.BeforeTestClass;
+
+import static org.springframework.test.util.AssertionErrors.*;
 
 /**
  * These tests are in the ETL project so that we can read in data from disk each time instead of storing binfiles
@@ -71,7 +66,7 @@ public class BucketIndexBySampleTest {
 	Set<String>  variantSet;
 	List<Integer> patientSet;
 
-	@BeforeClass
+	@BeforeTestClass
 	public static void initializeBinfile() throws Exception {
 		//load variant data
 		NewVCFLoader.main(new String[] {VCF_INDEX_FILE, STORAGE_DIR, MERGED_DIR});	
@@ -83,7 +78,7 @@ public static void initializeBinfile() throws Exception {
 //		bucketIndexBySample.printPatientMasks();
 	}
 
-	@Before
+	@BeforeEach
 	public void setUpTest() {
 		//start with fresh, empty collections
 		variantSet = new HashSet<String>();