From b050c9fb993866484ca60367d200d6724febfe6a Mon Sep 17 00:00:00 2001
From: Gcolon021 <34667267+Gcolon021@users.noreply.github.com>
Date: Wed, 29 Nov 2023 11:20:36 -0500
Subject: [PATCH 1/3] [ALS-5422] Add persistence.xml to visualization resource
 (#161)

The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''.
---
 .../src/main/resources/META-INF/persistence.xml            | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 pic-sure-resources/pic-sure-visualization-resource/src/main/resources/META-INF/persistence.xml

diff --git a/pic-sure-resources/pic-sure-visualization-resource/src/main/resources/META-INF/persistence.xml b/pic-sure-resources/pic-sure-visualization-resource/src/main/resources/META-INF/persistence.xml
new file mode 100644
index 00000000..307ff002
--- /dev/null
+++ b/pic-sure-resources/pic-sure-visualization-resource/src/main/resources/META-INF/persistence.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<persistence version="2.1"
+             xmlns="http://xmlns.jcp.org/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+             xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/persistence http://xmlns.jcp.org/xml/ns/persistence/persistence_2_1.xsd">
+    <persistence-unit name="picsure">
+    </persistence-unit>
+</persistence>

From 3e4fb95a5c178e69a822dc9a151951a55e707133 Mon Sep 17 00:00:00 2001
From: Luke Sikina <lucas.skina@gmail.com>
Date: Thu, 7 Dec 2023 11:23:09 -0500
Subject: [PATCH 2/3] [ALS-0000] Fix aggregate resource

- Very confused as to how this was working before
---
 .../hms/dbmi/avillach/AggregateDataSharingResourceRS.java      | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRS.java b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRS.java
index 46c5a89e..60b62b5c 100644
--- a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRS.java
+++ b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/src/main/java/edu/harvard/hms/dbmi/avillach/AggregateDataSharingResourceRS.java
@@ -228,7 +228,8 @@ public Response querySync(QueryRequest queryRequest) {
 
             Set<String> allowedResultTypes = Set.of(
                     "COUNT", "CROSS_COUNT", "INFO_COLUMN_LISTING", "OBSERVATION_COUNT",
-                    "OBSERVATION_CROSS_COUNT", "CATEGORICAL_CROSS_COUNT", "CONTINUOUS_CROSS_COUNT"
+                    "OBSERVATION_CROSS_COUNT", "CATEGORICAL_CROSS_COUNT", "CONTINUOUS_CROSS_COUNT",
+                    "VARIANT_COUNT_FOR_QUERY", "AGGREGATE_VCF_EXCERPT", "VCF_EXCERPT"
             );
 
             if (!allowedResultTypes.contains(expectedResultType)) {

From 0f908f3fcf71479cf9d3a2b87b197efc3c5afabd Mon Sep 17 00:00:00 2001
From: Gcolon021 <34667267+Gcolon021@users.noreply.github.com>
Date: Fri, 8 Dec 2023 16:13:20 -0500
Subject: [PATCH 3/3] [ALS-5422] Add persistence.xml to visualization resource
 (#161) (#162) (#163)

The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''.