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Add integration tests for hictk fix-mcool. Update unit tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| #!/usr/bin/env bash | ||
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| # Copyright (C) 2023 Roberto Rossini <roberros@uio.no> | ||
| # | ||
| # SPDX-License-Identifier: MIT | ||
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| set -e | ||
| set -o pipefail | ||
| set -u | ||
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| echo "#########################" | ||
| echo "#### hictk fix-mcool ####" | ||
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| # readlink -f is not available on macos... | ||
| function readlink_py { | ||
| set -eu | ||
| python3 -c 'import os, sys; print(os.path.realpath(sys.argv[1]))' "$1" | ||
| } | ||
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| function check_files_exist { | ||
| set -eu | ||
| status=0 | ||
| for f in "$@"; do | ||
| if [ ! -f "$f" ]; then | ||
| 2>&1 echo "Unable to find test file \"$f\"" | ||
| status=1 | ||
| fi | ||
| done | ||
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| return "$status" | ||
| } | ||
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| status=0 | ||
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| if [ $# -ne 1 ]; then | ||
| 2>&1 echo "Usage: $0 path_to_hictk" | ||
| status=1 | ||
| fi | ||
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| hictk_bin="$1" | ||
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| data_dir="$(readlink_py "$(dirname "$0")/../data/")" | ||
| script_dir="$(readlink_py "$(dirname "$0")")" | ||
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| invalid_mcool="$data_dir/cooler/invalid_coolers/corrupted_index.mcool" | ||
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| export PATH="$PATH:$script_dir" | ||
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| if [ $status -ne 0 ]; then | ||
| exit $status | ||
| fi | ||
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| if ! check_files_exist "$invalid_mcool"; then | ||
| exit 1 | ||
| fi | ||
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| outdir="$(mktemp -d -t hictk-tmp-XXXXXXXXXX)" | ||
| trap 'rm -rf -- "$outdir"' EXIT | ||
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| "$hictk_bin" fix-mcool "$invalid_mcool" "$outdir/out.mcool" | ||
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| if ! "$hictk_bin" validate --validate-index "$outdir/out.mcool"; then | ||
| status=1 | ||
| fi | ||
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| if [ "$status" -eq 0 ]; then | ||
| printf '\n### PASS ###\n' | ||
| else | ||
| cat "$outdir/out.txt" | ||
| printf '\n### FAIL ###\n' | ||
| fi | ||
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| exit "$status" |
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