Add CSVLoaderNewSearch jar and refine Java formatting

Added the CSVLoaderNewSearch jar to the Dockerfile and updated the Maven build process in pom.xml to include its packaging. Additionally, cleaned up Java code formatting by removing an unnecessary semicolon and adjusting spacing for consistency. These changes enhance the ETL process and maintain code readability.

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

@@ -2,14 +2,13 @@
 
 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;
 
 
 @JsonInclude(JsonInclude.Include.NON_NULL)
-public class ColumnMeta implements Serializable{
+public class ColumnMeta implements Serializable {
 
 	private static final long serialVersionUID = -124111104912063811L;
 	private String name;

docker/pic-sure-hpds-etl/Dockerfile

@@ -7,6 +7,7 @@ RUN apk add --no-cache --purge -uU curl wget unzip gnupg openssl
 ADD create_key.sh .
 ADD SQLLoader-jar-with-dependencies.jar .
 ADD CSVLoader-jar-with-dependencies.jar .
+ADD CSVLoaderNewSearch-jar-with-dependencies.jar .
 ADD CSVDumper-jar-with-dependencies.jar .
 ADD VCFLocalLoader-jar-with-dependencies.jar .
 ADD VariantMetadataLoader-jar-with-dependencies.jar .

etl/pom.xml

@@ -130,6 +130,26 @@
 							<goal>single</goal>
 						</goals>
 					</execution>
+					<execution>
+						<id>buildCSVLoaderNewSearch</id>
+						<configuration>
+							<archive>
+								<manifest>
+									<mainClass>edu.harvard.hms.dbmi.avillach.hpds.etl.phenotype.CSVLoaderNewSearch</mainClass>
+								</manifest>
+							</archive>
+							<outputDirectory>${project.basedir}/../docker/pic-sure-hpds-etl</outputDirectory>
+							<descriptorRefs>
+								<descriptorRef>jar-with-dependencies</descriptorRef>
+							</descriptorRefs>
+							<classifier>CSVLoaderNewSearch</classifier>
+							<finalName>CSVLoaderNewSearch</finalName>
+						</configuration>
+						<phase>package</phase>
+						<goals>
+							<goal>single</goal>
+						</goals>
+					</execution>
 					<execution>
 						<id>buildCSVLoader</id>
 						<configuration>

etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java

@@ -161,7 +161,7 @@ public void dumpStats() {
 	 */
 	public void dumpStatsAndColumnMeta(String hpdsDirectory) {
 		try (ObjectInputStream objectInputStream =
-					 new ObjectInputStream(new GZIPInputStream(new FileInputStream(hpdsDirectory + "columnMeta.javabin")));){
+					 new ObjectInputStream(new GZIPInputStream(new FileInputStream(hpdsDirectory + "columnMeta.javabin")))){
 			TreeMap<String, ColumnMeta> metastore = (TreeMap<String, ColumnMeta>) objectInputStream.readObject();
 			try(BufferedWriter writer = Files.newBufferedWriter(Paths.get(hpdsDirectory + "columnMeta.csv"), StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING)) {
 				CSVPrinter printer = new CSVPrinter(writer, CSVFormat.DEFAULT);