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Fix whitespace in test script and add merge consistency tests

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This commit fixes minor whitespace issues in the test script and adds new tests to ensure merge attribute consistency between in-memory and on-disk paths.

- Removed trailing spaces in log messages
- Added tests for merge consistency between in-memory and on-disk paths
- These tests catch a bug where shared classifier in on-disk dereplication path caused incorrect merged attributes
This commit is contained in:
Eric Coissac
2026-02-08 18:08:13 +01:00
parent 1a28d5ed64
commit 08490420a2
1 changed files with 64 additions and 11 deletions
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75
obitests/obitools/obiuniq/test.sh
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@@ -39,7 +39,7 @@ cleanup() {
rm -rf "$TMPDIR" # Suppress the temporary directory
if [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log "$TEST_NAME tests failed"
log
log
exit 1
@@ -55,10 +55,10 @@ log() {
echo -e "[$TEST_NAME @ $(date)] $*" 1>&2
}
log "Testing $TEST_NAME..."
log "Test directory is $TEST_DIR"
log "obitools directory is $OBITOOLS_DIR"
log "Temporary directory is $TMPDIR"
log "Testing $TEST_NAME..."
log "Test directory is $TEST_DIR"
log "obitools directory is $OBITOOLS_DIR"
log "Temporary directory is $TMPDIR"
log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
@@ -89,12 +89,12 @@ log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
((ntest++))
if $CMD -h > "${TMPDIR}/help.txt" 2>&1
if $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
log "$MCMD: printing help failed"
((failed++))
fi
@@ -102,7 +102,7 @@ fi
if obiuniq "${TEST_DIR}/touniq.fasta" \
> "${TMPDIR}/touniq_u.fasta"
then
log "OBIUniq simple: running OK"
log "OBIUniq simple: running OK"
((success++))
else
log "OBIUniq simple: running failed"
@@ -134,7 +134,7 @@ fi
if obiuniq -c a "${TEST_DIR}/touniq.fasta" \
> "${TMPDIR}/touniq_u_a.fasta"
then
log "OBIUniq one category: running OK"
log "OBIUniq one category: running OK"
((success++))
else
log "OBIUniq one category: running failed"
@@ -167,7 +167,7 @@ fi
if obiuniq -c a -c b "${TEST_DIR}/touniq.fasta" \
> "${TMPDIR}/touniq_u_a_b.fasta"
then
log "OBIUniq two categories: running OK"
log "OBIUniq two categories: running OK"
((success++))
else
log "OBIUniq two categories: running failed"
@@ -195,6 +195,59 @@ else
((failed++))
fi
##
## Test merge attributes consistency between in-memory and on-disk paths
## This test catches the bug where the shared classifier in the on-disk
## dereplication path caused incorrect merged attributes.
##
((ntest++))
if obiuniq -m a -m b --in-memory \
"${TEST_DIR}/touniq.fasta" \
> "${TMPDIR}/touniq_u_merge_mem.fasta" 2>/dev/null
then
log "OBIUniq merge in-memory: running OK"
((success++))
else
log "OBIUniq merge in-memory: running failed"
((failed++))
fi
((ntest++))
if obiuniq -m a -m b --chunk-count 4 \
"${TEST_DIR}/touniq.fasta" \
> "${TMPDIR}/touniq_u_merge_disk.fasta" 2>/dev/null
then
log "OBIUniq merge on-disk: running OK"
((success++))
else
log "OBIUniq merge on-disk: running failed"
((failed++))
fi
# Extract sorted annotations (JSON attributes) from both outputs
# to compare merge results independently of sequence ordering
grep '^>' "${TMPDIR}/touniq_u_merge_mem.fasta" \
| sed 's/^>seq[0-9]* //' \
| sort \
> "${TMPDIR}/touniq_u_merge_mem.json"
grep '^>' "${TMPDIR}/touniq_u_merge_disk.fasta" \
| sed 's/^>seq[0-9]* //' \
| sort \
> "${TMPDIR}/touniq_u_merge_disk.json"
((ntest++))
if diff "${TMPDIR}/touniq_u_merge_mem.json" \
"${TMPDIR}/touniq_u_merge_disk.json" > /dev/null
then
log "OBIUniq merge on-disk vs in-memory: result OK"
((success++))
else
log "OBIUniq merge on-disk vs in-memory: result failed"
((failed++))
fi
#########################################
#
# At the end of the tests