From 9f1724e783e71d74dde97ff777dec583adb98af8 Mon Sep 17 00:00:00 2001
From: Gcolon021 <34667267+Gcolon021@users.noreply.github.com>
Date: Mon, 18 Sep 2023 10:00:25 -0400
Subject: [PATCH 1/2] [ALS-4980] Update PicSureService to match contract with
 PIC-SURe API

---
 .../dbmi/avillach/hpds/service/PicSureService.java   | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java b/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java
index 58b81399..12287521 100644
--- a/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java
+++ b/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java
@@ -225,8 +225,8 @@ private QueryStatus convertToQueryStatus(AsyncResult entity) {
 	@Path("/query/{resourceQueryId}/result")
 	@Produces(MediaType.TEXT_PLAIN_VALUE)
 	@Override
-	public Response queryResult(@PathParam("resourceQueryId") String queryId, QueryRequest resultRequest) {
-		AsyncResult result = queryService.getResultFor(queryId);
+	public Response queryResult(@PathParam("resourceQueryId") UUID queryId, QueryRequest resultRequest) {
+		AsyncResult result = queryService.getResultFor(queryId.toString());
 		if (result == null) {
 			// This happens sometimes when users immediately request the status for a query
 			// before it can be initialized. We wait a bit and try again before throwing an
@@ -237,7 +237,7 @@ public Response queryResult(@PathParam("resourceQueryId") String queryId, QueryR
 				return Response.status(500).build();
 			}
 
-			result = queryService.getResultFor(queryId);
+			result = queryService.getResultFor(queryId.toString());
 			if (result == null) {
 				return Response.status(404).build();
 			}
@@ -253,8 +253,8 @@ public Response queryResult(@PathParam("resourceQueryId") String queryId, QueryR
 	@POST
 	@Path("/query/{resourceQueryId}/status")
 	@Override
-	public QueryStatus queryStatus(@PathParam("resourceQueryId") String queryId, QueryRequest request) {
-		return convertToQueryStatus(queryService.getStatusFor(queryId));
+	public QueryStatus queryStatus(@PathParam("resourceQueryId") UUID queryId, QueryRequest request) {
+		return convertToQueryStatus(queryService.getStatusFor(queryId.toString()));
 	}
 
 	@POST
@@ -328,7 +328,7 @@ private Response _querySync(QueryRequest resultRequest) throws IOException {
 			QueryStatus status = query(resultRequest);
 			while (status.getResourceStatus().equalsIgnoreCase("RUNNING")
 					|| status.getResourceStatus().equalsIgnoreCase("PENDING")) {
-				status = queryStatus(status.getResourceResultId(), null);
+				status = queryStatus(UUID.fromString(status.getResourceResultId()), null);
 			}
 			log.info(status.toString());
 

From d84499aa0bac7495e60ea2a290b007e1afb9f9b5 Mon Sep 17 00:00:00 2001
From: ramari16 <ramari16@gmail.com>
Date: Fri, 22 Sep 2023 14:11:39 -0400
Subject: [PATCH 2/2] [ALS-5052] Update to use docker tomcat image (#82)

---
 docker/pic-sure-hpds/Dockerfile | 13 ++--------
 war/pom.xml                     | 46 +++++----------------------------
 2 files changed, 8 insertions(+), 51 deletions(-)

diff --git a/docker/pic-sure-hpds/Dockerfile b/docker/pic-sure-hpds/Dockerfile
index 0b38a4de..1d1f395f 100644
--- a/docker/pic-sure-hpds/Dockerfile
+++ b/docker/pic-sure-hpds/Dockerfile
@@ -1,11 +1,2 @@
-FROM docker.io/alpine:3.16
-
-RUN apk add --no-cache --purge -uU bash &&     rm -rf /var/cache/apk/* /tmp/*
-
-RUN apk add --no-cache --purge -uU curl wget unzip
-
-RUN apk add --no-cache --purge openjdk11
-
-ADD hpds-war-1.0-SNAPSHOT-war-exec.jar /hpds.jar
-
-EXPOSE 8080
+FROM tomcat:9-jre11-openjdk-slim
+ADD hpds-war-1.0-SNAPSHOT.war /usr/local/tomcat/webapps/ROOT.war
\ No newline at end of file
diff --git a/war/pom.xml b/war/pom.xml
index e71e6efa..93c90038 100644
--- a/war/pom.xml
+++ b/war/pom.xml
@@ -20,30 +20,6 @@
 	<build>
 		<pluginManagement>
 			<plugins>
-				<plugin>
-					<groupId>org.apache.tomcat.maven</groupId>
-					<artifactId>tomcat7-maven-plugin</artifactId>
-					<version>2.0</version>
-					<executions>
-						<execution>
-							<id>default-cli</id>
-							<goals>
-								<goal>run</goal>
-							</goals>
-							<configuration>
-								<port>13000</port>
-								<path>/jaxrs-service</path>
-								<useSeparateTomcatClassLoader>true</useSeparateTomcatClassLoader>
-								<jpda>true</jpda>
-								<systemProperties>
-									<JAVA_OPTS>-Xms256m -Xmx512m</JAVA_OPTS>
-								</systemProperties>
-							</configuration>
-						</execution>
-					</executions>
-					<configuration>
-					</configuration>
-				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-compiler-plugin</artifactId>
@@ -90,22 +66,12 @@
 				</executions>
 			</plugin>
 			<plugin>
-				<groupId>org.apache.tomcat.maven</groupId>
-				<artifactId>tomcat7-maven-plugin</artifactId>
-				<executions>
-					<execution>
-						<id>tomcat-run</id>
-						<goals>
-							<goal>exec-war-only</goal>
-						</goals>
-						<phase>package</phase>
-						<configuration>
-							<attachArtifact>true</attachArtifact>
-							<buildDirectory>../docker/pic-sure-hpds</buildDirectory>
-							<path>/</path>
-						</configuration>
-					</execution>
-				</executions>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-war-plugin</artifactId>
+				<version>3.3.1</version>
+				<configuration>
+					<outputDirectory>docker/pic-sure-hpds</outputDirectory>
+				</configuration>
 			</plugin>
 		</plugins>
 	</build>