From 33fb44edb657a5608ee1de197ab9307f1c3a7bf2 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 16:33:10 +0200
Subject: [PATCH] create temporary directory and clean up on exit

---
 src/agat/agat_sp_add_start_and_stop/test.sh | 28 +++++++++++++--------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/src/agat/agat_sp_add_start_and_stop/test.sh b/src/agat/agat_sp_add_start_and_stop/test.sh
index 824a3006..0c8f3676 100644
--- a/src/agat/agat_sp_add_start_and_stop/test.sh
+++ b/src/agat/agat_sp_add_start_and_stop/test.sh
@@ -6,52 +6,58 @@ set -eo pipefail
 ## VIASH END
 
 test_dir="${meta_resources_dir}/test_data"
-out_dir="${meta_resources_dir}/out_data"
+
+# create temporary directory and clean up on exit
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+ [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
 
 echo "> Run $meta_name with test data and ni flag"
 "$meta_executable" \
   --gff "$test_dir/agat_sp_add_start_and_stop.gff" \
   --fasta "$test_dir/1.fa" \
-  --output "$out_dir/output.gff" \
+  --output "$TMPDIR/output.gff" \
   --ni 
     
 echo ">> Checking output"
-[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
 
 echo ">> Check if output is empty"
-[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
 
 echo ">> Check if output matches expected output"
-diff "$out_dir/output.gff" "$test_dir/agat_sp_add_start_and_stop_1.gff"
+diff "$TMPDIR/output.gff" "$test_dir/agat_sp_add_start_and_stop_1.gff"
 if [ $? -ne 0 ]; then
   echo "Output file output.gff does not match expected output"
   exit 1
 fi
 
-rm -f "$out_dir/output.gff"
+rm -f "$TMPDIR/output.gff"
 
 echo "> Run $meta_name with test data and ni flag"
 "$meta_executable" \
   --gff "$test_dir/agat_sp_add_start_and_stop.gff" \
   --fasta "$test_dir/1.fa" \
-  --output "$out_dir/output.gff" \
+  --output "$TMPDIR/output.gff" \
   --ni \
   --extend
 
   
 echo ">> Checking output"
-[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
 
 echo ">> Check if output is empty"
-[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
 
 echo ">> Check if output matches expected output"
-diff "$out_dir/output.gff" "$test_dir/agat_sp_add_start_and_stop_2.gff"
+diff "$TMPDIR/output.gff" "$test_dir/agat_sp_add_start_and_stop_2.gff"
 if [ $? -ne 0 ]; then
   echo "Output file output.gff does not match expected output"
   exit 1
 fi
 
-rm -f "$out_dir/output.gff"
+rm -f "$TMPDIR/output.gff"
 
 echo "> Test successful"
\ No newline at end of file