mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 08:10:45 +00:00
48138b605c
modified: .github/workflows/obitest.yml modified: Makefile modified: obitests/obitools/obicount/test.sh
142 lines
3.4 KiB
Bash
Executable File
142 lines
3.4 KiB
Bash
Executable File
#!/bin/bash
|
|
|
|
#
|
|
# Here give the name of the test serie
|
|
#
|
|
TEST_NAME=obicount
|
|
|
|
######
|
|
#
|
|
# Some variable and function definitions: please don't change them
|
|
#
|
|
######
|
|
TEST_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
|
|
OBITOOLS_DIR="${TEST_DIR/obitest*/}build"
|
|
export PATH="${OBITOOLS_DIR}:${PATH}"
|
|
|
|
|
|
TMPDIR="$(mktemp -d)"
|
|
ntest=0
|
|
success=0
|
|
failed=0
|
|
|
|
cleanup() {
|
|
echo "========================================" 1>&2
|
|
echo "## Results of the $TEST_NAME tests:" 1>&2
|
|
|
|
echo 1>&2
|
|
echo "- $ntest tests run" 1>&2
|
|
echo "- $success successfully completed" 1>&2
|
|
echo "- $failed failed tests" 1>&2
|
|
echo 1>&2
|
|
echo "Cleaning up the temporary directory..." 1>&2
|
|
echo 1>&2
|
|
echo "========================================" 1>&2
|
|
|
|
rm -rf "$TMPDIR" # Suppress the temporary directory
|
|
|
|
if [ $failed -gt 0 ]; then
|
|
exit 1
|
|
fi
|
|
|
|
exit 0
|
|
}
|
|
|
|
log() {
|
|
echo "[$TEST_NAME @ $(date)] $*" 1>&2
|
|
}
|
|
|
|
log "Testing $TEST_NAME..."
|
|
log "Test directory is $TEST_DIR"
|
|
log "obitools directory is $OBITOOLS_DIR"
|
|
log "Temporary directory is $TMPDIR"
|
|
|
|
######################################################################
|
|
####
|
|
#### Below are the tests
|
|
####
|
|
#### Before each test :
|
|
#### - increment the variable ntest
|
|
####
|
|
#### Run the command as the condition of an if / then /else
|
|
#### - The command must return 0 on success
|
|
#### - The command must return an exit code different from 0 on failure
|
|
#### - The datafiles are stored in the same directory than the test script
|
|
#### - The test script directory is stored in the TEST_DIR variable
|
|
#### - If result files have to be produced they must be stored
|
|
#### in the temporary directory (TMPDIR variable)
|
|
####
|
|
#### then clause is executed on success of the command
|
|
#### - Write a success message using the log function
|
|
#### - increment the variable success
|
|
####
|
|
#### else clause is executed on failure of the command
|
|
#### - Write a failure message using the log function
|
|
#### - increment the variable failed
|
|
####
|
|
######################################################################
|
|
|
|
((ntest++))
|
|
if obicount "${TEST_DIR}/wolf_F.fasta.gz" \
|
|
> "${TMPDIR}/wolf_F.fasta_count.csv"
|
|
then
|
|
log "OBICount: fasta reading OK"
|
|
((success++))
|
|
else
|
|
log "OBICount: fasta reading failed"
|
|
((failed++))
|
|
fi
|
|
|
|
((ntest++))
|
|
if obicount "${TEST_DIR}/wolf_F.fastq.gz" \
|
|
> "${TMPDIR}/wolf_F.fastq_count.csv"
|
|
then
|
|
log "OBICount: fastq reading OK"
|
|
((success++))
|
|
else
|
|
log "OBICount: fastq reading failed"
|
|
((failed++))
|
|
fi
|
|
|
|
((ntest++))
|
|
if obicount "${TEST_DIR}/wolf_F.csv.gz" \
|
|
> "${TMPDIR}/wolf_F.csv_count.csv"
|
|
then
|
|
log "OBICount: csv reading OK"
|
|
((success++))
|
|
else
|
|
log "OBICount: csv reading failed"
|
|
((failed++))
|
|
fi
|
|
|
|
((ntest++))
|
|
if diff "${TMPDIR}/wolf_F.fasta_count.csv" \
|
|
"${TMPDIR}/wolf_F.fastq_count.csv" > /dev/null
|
|
then
|
|
log "OBICount: counting on fasta and fastq are identical OK"
|
|
((success++))
|
|
else
|
|
log "OBICount: counting on fasta and fastq are different failed"
|
|
((failed++))
|
|
fi
|
|
|
|
((ntest++))
|
|
if diff "${TMPDIR}/wolf_F.fasta_count.csv" \
|
|
"${TMPDIR}/wolf_F.csv_count.csv" > /dev/null
|
|
then
|
|
log "OBICount: counting on fasta and csv are identical OK"
|
|
((success++))
|
|
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
|