From 2dc5d21f09429f82846aa3ea46fa33590c46ba76 Mon Sep 17 00:00:00 2001
From: GeorgeC <gcolon021@gmail.com>
Date: Wed, 4 Dec 2024 11:54:43 -0500
Subject: [PATCH] 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.
---
 .../hpds/data/phenotype/ColumnMeta.java       |  3 +--
 docker/pic-sure-hpds-etl/Dockerfile           |  1 +
 etl/pom.xml                                   | 20 +++++++++++++++++++
 .../hpds/etl/phenotype/LoadingStore.java      |  2 +-
 4 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java
index 3243a9db..681102a4 100644
--- a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java
+++ b/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;
diff --git a/docker/pic-sure-hpds-etl/Dockerfile b/docker/pic-sure-hpds-etl/Dockerfile
index a0aea075..b375fc13 100644
--- a/docker/pic-sure-hpds-etl/Dockerfile
+++ b/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 .
diff --git a/etl/pom.xml b/etl/pom.xml
index b388883e..c218d06a 100644
--- a/etl/pom.xml
+++ b/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>
diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java
index 91c8d605..2373e80e 100644
--- a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java
+++ b/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);