From 741db8438b6d104d3243bab07ce3e6c3bff8b1c8 Mon Sep 17 00:00:00 2001
From: Andrew Thrasher <adthrasher@gmail.com>
Date: Mon, 4 May 2026 13:13:03 -0400
Subject: [PATCH 1/3] fix: broken category filtering

---
 dx_app/src/t-SNE.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dx_app/src/t-SNE.sh b/dx_app/src/t-SNE.sh
index 9df5acc..5c5d472 100755
--- a/dx_app/src/t-SNE.sh
+++ b/dx_app/src/t-SNE.sh
@@ -272,7 +272,6 @@ main() {
       # Lookup normalized long disease name by disease code
       disease_name=$(get_disease_name_for_disease "$disease_code" "$all_colors")
 
-      category=$(get_category "$j")
       if [[ "$category" == "Hematologic Malignancy" ]]
       then
          category="Blood Cancer"

From 74f5f32d26eb61503164f7f36c025e5b46a45b56 Mon Sep 17 00:00:00 2001
From: Andrew Thrasher <adthrasher@gmail.com>
Date: Mon, 4 May 2026 13:13:34 -0400
Subject: [PATCH 2/3] chore: gracefully detect empty sample set

---
 dx_app/src/t-SNE.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/dx_app/src/t-SNE.sh b/dx_app/src/t-SNE.sh
index 5c5d472..961b003 100755
--- a/dx_app/src/t-SNE.sh
+++ b/dx_app/src/t-SNE.sh
@@ -289,7 +289,13 @@ main() {
       fi
    done
 
-   # Turn the metadata entries into and array, then nest everything under the "properties" key
+   if [ ! -e "tmp_metadata.json" ]
+   then
+      echo "{\"error\": {\"type\": \"AppError\", \"message\": \"No reference samples passed filtering criteria.\"}}" > job_error.json
+      exit 1
+   fi
+
+   # Turn the metadata entries into an array, then nest everything under the "properties" key
    jq --slurp "flatten" tmp_metadata.json | jq '[.[] | {"properties": .}]' > filtered_metadata.json
 
    # Handle Dana Farber PDX samples

From 89535c9e5e96e18d8a86410e7ffe7303f6d3ab4a Mon Sep 17 00:00:00 2001
From: Andrew Thrasher <adthrasher@gmail.com>
Date: Tue, 5 May 2026 09:39:40 -0400
Subject: [PATCH 3/3] chore: bump ubuntu version

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 4a40735..529a59f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:20.04 AS builder
+FROM ubuntu:24.04 AS builder
 
 RUN apt-get update \
     && apt-get upgrade -y \