#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.99f01bf4" && echo "/cromwell_root/tmp.99f01bf4")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
outb0727dba="${tmpDir}/out.$$" errb0727dba="${tmpDir}/err.$$"
mkfifo "$outb0727dba" "$errb0727dba"
trap 'rm "$outb0727dba" "$errb0727dba"' EXIT
tee '/cromwell_root/stdout' < "$outb0727dba" &
tee '/cromwell_root/stderr' < "$errb0727dba" >&2 &
(
cd /cromwell_root


		set -euo pipefail
		python <<CODE
NULL_SENTINEL = "GDAC_FC_NULL"

filepaths = 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with open("datapathsfile.tsv", "w") as fout:
	for filepath in filepaths:
		if not filepath.endswith(NULL_SENTINEL):
			fout.write("NA\t" + filepath + "\n")
CODE

		if [ ! -s datapathsfile.tsv ] ; then
			echo "No files to merge, exiting" 1>&2
			exit 1
		fi

		/src/merge_data_files.py \
			column \
			1 \
			CPTAC3-LUAD-TP.clin.merged.txt \
			datapathsfile.tsv

		if true
			then zip -r aggregate_data . -x \
				"fc-[a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9]/*" \
				lost+found/\* \
				broad-institute-gdac/\* \
				"tmp.[a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9]/*" \
				exec.sh
		fi
)  > "$outb0727dba" 2> "$errb0727dba"
echo $? > /cromwell_root/rc.tmp
(
# add a .file in every empty directory to facilitate directory delocalization on the cloud
cd /cromwell_root
find . -type d -exec sh -c '[ -z "$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \;
)
(
cd /cromwell_root
sync


)
mv /cromwell_root/rc.tmp /cromwell_root/rc
