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Fix/type filter #50

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Merged
adthrasher merged 3 commits into from
May 5, 2026
Merged

Fix/type filter #50

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741db84
fix: broken category filtering
adthrasher May 4, 2026
74f5f32
chore: gracefully detect empty sample set
adthrasher May 4, 2026
89535c9
chore: bump ubuntu version
adthrasher May 5, 2026
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM ubuntu:20.04 AS builder
FROM ubuntu:24.04 AS builder

RUN apt-get update \
&& apt-get upgrade -y \
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9 changes: 7 additions & 2 deletions dx_app/src/t-SNE.sh
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Expand Up @@ -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"
Expand All @@ -290,7 +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
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