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fix: clone command in test_trtools.sh testing script #214

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merged 4 commits into from
Feb 21, 2024
Merged

fix: clone command in test_trtools.sh testing script #214

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c759bb8
try to resolve failing bioconda tests
aryarm Feb 19, 2024
37c75bb
ensure test_trtools.sh can be run with a dev install but explain the …
aryarm Feb 20, 2024
43aa80c
Update local files warning in test_trtools.sh
LiterallyUniqueLogin Feb 21, 2024
81b0e7d
Update trtools/testsupport/test_trtools.sh
LiterallyUniqueLogin Feb 21, 2024
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14 changes: 8 additions & 6 deletions test/cmdline_tests.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -25,13 +25,15 @@ if [ $# -eq 0 ]; then
# use default example location
EXDATADIR="example-files"
BEAGLEDIR="trtools/testsupport/sample_vcfs/beagle"
elif (( $# != 2 )) ; then
echo "usage: cmdline_tests.sh {example_dir} {beagle_dir}" 2>&1
echo "Expected 2 arguments but recieved $#" 2>&1
BEAGLESCRIPT="scripts/trtools_prep_beagle_vcf.sh"
elif (( $# != 3 )) ; then
echo "usage: cmdline_tests.sh {example_dir} {beagle_dir} {beagle_script}" 2>&1
echo "Expected 3 arguments but recieved $#" 2>&1
exit 1
else
EXDATADIR=$1
BEAGLEDIR=$2
BEAGLESCRIPT=$3
fi

TMPDIR=$(mktemp -d -t tmp-XXXXXXXXXX)
Expand Down Expand Up @@ -220,10 +222,10 @@ prep_beagle_out="$TMPDIR"/test_prep_beagle_vcf.vcf.gz
ref_panel="$BEAGLEDIR"/1kg_snpstr_21_first_100k_first_50_annotated.vcf.gz
imputed_vcf="$BEAGLEDIR"/1kg_snpstr_21_first_100k_second_50_STRs_imputed.vcf.gz

runcmd_fail "trtools_prep_beagle_vcf.sh hipstr nonexistent.vcf.gz $imputed_vcf $prep_beagle_out"
runcmd_fail "trtools_prep_beagle_vcf.sh hipstr $ref_panel nonexistent.vcf.gz $prep_beagle_out"
runcmd_fail "$BEAGLESCRIPT hipstr nonexistent.vcf.gz $imputed_vcf $prep_beagle_out"
runcmd_fail "$BEAGLESCRIPT hipstr $ref_panel nonexistent.vcf.gz $prep_beagle_out"

trtools_prep_beagle_vcf.sh hipstr "$ref_panel" "$imputed_vcf" "$prep_beagle_out"
$BEAGLESCRIPT hipstr "$ref_panel" "$imputed_vcf" "$prep_beagle_out"

if ! [[ -f "$prep_beagle_out" ]] ; then
echo "prep_beagle_vcf test didn't produce output file" >&2
Expand Down
10 changes: 8 additions & 2 deletions trtools/testsupport/test_trtools.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,13 @@

# Run the tests for an installed copy of trtools
# If not already present, megabytes of test data will be downloaded before test running
# Please note that this script tests TRTools against
# test files from a published release and will miss any local changes to those files

# If TRTools was installed normally, this script can be executed by simply running
# 'test_trtools.sh' on the command line.
# Otherwise, if TRTools was installed via poetry, you should run the command
# 'poetry run trtools/testsupport/test_trtools.sh'.
echo "Running test_trtools.sh"

command -v git >/dev/null 2>&1 || { echo >&2 "git is not available, but is required for downloading the test data. Aborting."; exit 1; }
Expand All @@ -15,7 +21,7 @@ if [ ! -d "$TMP" ] ; then
echo "Downloading test data ..."
mkdir $TMP
pushd $TMP
git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git
git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git .
popd
echo "Download done"
else
Expand All @@ -41,4 +47,4 @@ cd "$loc" || exit 1
# run unit tests
python -m pytest . -p trtools.testsupport.dataloader --datadir "$TMP"/trtools/testsupport
# run command line tests
$TMP/test/cmdline_tests.sh $TMP/example-files $TMP/trtools/testsupport/sample_vcfs/beagle
$TMP/test/cmdline_tests.sh $TMP/example-files $TMP/trtools/testsupport/sample_vcfs/beagle $TMP/scripts/trtools_prep_beagle_vcf.sh
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