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Changes to be committed:

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modified:   Makefile
	modified:   obitests/obitools/obicount/test.sh
This commit is contained in:
Eric Coissac
2025-02-19 14:28:49 +01:00
parent 7e90537379
commit 443a9b3ce3
2 changed files with 34 additions and 14 deletions
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6
Makefile
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@ -64,10 +64,8 @@ update-deps:
test:
$(GOTEST) ./...
obitests: obitools
for t in $$(find obitests -name test.sh -print) ; do \
bash $${t} ; \
done
obitests:
@find obitests -name test.sh -exec bash {} \;
man:
make -C doc man

42
obitests/obitools/obicount/test.sh
View File

@ -1,4 +1,4 @@
#!/bin/bash -e
#!/bin/bash
#
# Here give the name of the test serie
@ -34,25 +34,37 @@ cleanup() {
echo "========================================" 1>&2
rm -rf "$TMPDIR" # Suppress the temporary directory
if [ $failed -gt 0 ]; then
exit 1
fi
exit 0
}
log() {
echo "[$TEST_NAME @ $(date)] $*" 1>&2
}
trap cleanup EXIT ERR SIGINT SIGTERM
echo "Testing $TEST_NAME..." 1>&2
log "Testing $TEST_NAME..."
log "Test directory is $TEST_DIR"
log "Temporary directory is $TMPDIR"
#################################################
######################################################################
####
#### Below are the tests
####
#### Before each test :
#### - increment the variable ntest
####
#### Run the command as the condition of a if / then /else
#### Run the command as the condition of an if / then /else
#### - The command must return 0 on success
#### - The command must return an exit code different from 0 on failure
#### - The datafiles are stored in the same directory than the test script
#### - The test script directory is stored in the TEST_DIR variable
#### - If result files have to be produced they must be stored
#### in the temporary directory (TMPDIR variable)
####
#### then clause is executed on success of the command
#### - Write a success message using the log function
@ -62,11 +74,12 @@ echo "Testing $TEST_NAME..." 1>&2
#### - Write a failure message using the log function
#### - increment the variable failed
####
#################################################
######################################################################
((ntest++))
if obicount "${TEST_DIR}/wolf_F.fasta.gz" \
> "${TMPDIR}/wolf_F.fasta_count.csv" ; then
> "${TMPDIR}/wolf_F.fasta_count.csv"
then
log "OBICount: fasta reading OK"
((success++))
else
@ -98,7 +111,7 @@ fi
((ntest++))
if diff "${TMPDIR}/wolf_F.fasta_count.csv" \
"${TMPDIR}/wolf_F.fastq_count.csv" > /dev/null
"${TMPDIR}/wolf_F.fastq_count.csv" > /dev/null
then
log "OBICount: counting on fasta and fastq are identical OK"
((success++))
@ -109,7 +122,7 @@ fi
((ntest++))
if diff "${TMPDIR}/wolf_F.fasta_count.csv" \
"${TMPDIR}/wolf_F.csv_count.csv" > /dev/null
"${TMPDIR}/wolf_F.csv_count.csv" > /dev/null
then
log "OBICount: counting on fasta and csv are identical OK"
((success++))
@ -117,3 +130,12 @@ else
log "OBICount: counting on fasta and csv are different failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup