use tmp files

.github/workflows/chebi.yml

@@ -180,14 +180,32 @@ jobs:
           added=$(grep '^+CHEBI' "$output_file" | sed 's/-//g') || true
           # retrieve removed lines
           removed=$(grep '^-' "$output_file" | sed 's/-//g') || true
-          # retrieve withdrawn IDs
-          withdrawn=$(echo "$added" | grep 'Entry Withdrawn') || true
+          # Create temporary files
+          tmp_added=$(mktemp)
+          tmp_withdrawn=$(mktemp)
+          tmp_removed=$(mktemp)
 
+          # Write the content of the added variable to the temporary file
+          echo "$added" > "$tmp_added"
+
+          # Retrieve matches and store them in another temporary file
+          grep 'Entry Withdrawn' "$tmp_added" > "$tmp_withdrawn" || true
+
+          # Append matches to the removed variable
           if [ -n "$removed" ]; then
-            removed="${removed}"$'\n'"${withdrawn}"
+            echo -e "$removed\n$(cat $tmp_withdrawn)" > "$tmp_removed"
           else
-            removed="${withdrawn}"
+            cat "$tmp_withdrawn" > "$tmp_removed"
           fi
+
+          # Remove matching lines from the added variable
+          sed '/Entry Withdrawn/d' "$tmp_added" > "$tmp_added.tmp" && mv "$tmp_added.tmp" "$tmp_added"
+
+          # Read the updated content back into the variables
+          added=$(cat "$tmp_added")
+          removed=$(cat "$tmp_removed")                 
+          # Clean up temporary files
+          rm "$tmp_added" "$tmp_withdrawn" "$tmp_removed"
           added=$(echo "$added" | sed '/Entry Withdrawn/d')
           added_filtered=$(comm -23 <(sort <<< "$added") <(sort <<< "$removed"))
           removed_filtered=$(comm -23 <(sort <<< "$removed") <(sort <<< "$added"))