fix: handle multiple JSON arrays

stjudecloud · Sep 9, 2024 · ca532f1 · ca532f1
1 parent 9dd3d85
commit ca532f1
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/dx_app/resources/stjude/bin/bulk_describe.py b/dx_app/resources/stjude/bin/bulk_describe.py
@@ -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 = {

diff --git a/dx_app/src/t-SNE.sh b/dx_app/src/t-SNE.sh
@@ -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'