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PullAndProcessGsAnalysisData.sh fails to process other batches when one batch is incomplete #311

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pneerincx opened this issue May 1, 2024 · 0 comments
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@pneerincx
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The PullAndProcessGsAnalysisData.sh script will skip all other batches if a single batch is incomplete and lacks a "${TMP_ROOT_DIR}/${gsBatch}/${gsBatch}.finished" file to signal that the upload / data transfer was complete.

This is caused by a 2 break statements in this block of code

#
##
### process Analysis data
##
#
readarray -t gsBatches< <(rsync -f"+ */" -f"- *" "${TMP_ROOT_DIR}/" | awk '{if ($5 != "" && $5 != "." && $5 ~/-/){print $5}}')
if [[ "${#gsBatches[@]}" -eq '0' ]]
then
	log4Bash 'WARN' "${LINENO}" "${FUNCNAME:-main}" '0' "No batches found at ${TMP_ROOT_DIR}/"
else
	for gsBatch in "${gsBatches[@]}"
	do
......
done

Should probably be changed into continue statements to skip the incomplete batch and continue with the next item in the for loop instead of exiting the for loop.

Gerbenvandervries added a commit that referenced this issue May 8, 2024
added script that copies nanopore data from prm to tmp + fixing #311
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