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fix: handle multiple JSON arrays #38

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Sep 9, 2024
+3 −2
Merged

fix: handle multiple JSON arrays #38

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2 changes: 1 addition & 1 deletion dx_app/resources/stjude/bin/bulk_describe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ def bulk_describe_with_id(file_links: List[str], proj_id: str) -> List:
file_links: list of file ids (strings)
proj_id: project id where described items is found
Returns:
list of dictionary containing file infomation
list of dictionary containing file information
"""

payload = {
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3 changes: 2 additions & 1 deletion dx_app/src/t-SNE.sh
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Expand Up @@ -150,7 +150,8 @@ main() {
# Get metadata in parallel for reference data
echo "Getting metadata for all samples"
json=$(echo $ids | xargs python3 /stjude/bin/bulk_describe.py -p $DX_PROJECT_CONTEXT_ID --ids )
echo $json > metadata.json
# Pass through jq because bulk_describe can produce multiple json arrays.
echo $json | jq --slurp "flatten" > metadata.json

# Prepare filters
excluded_types='germline|cell line'
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