mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 21:40:52 +00:00
145 lines
3.6 KiB
Bash
Executable File
145 lines
3.6 KiB
Bash
Executable File
#!/bin/bash
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#
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# Here give the name of the test serie
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#
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TEST_NAME=obiconvert
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CMD=obiconvert
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######
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#
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# Some variable and function definitions: please don't change them
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#
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######
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TEST_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
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if [ -z "$TEST_DIR" ] ; then
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TEST_DIR="."
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fi
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OBITOOLS_DIR="${TEST_DIR/obitest*/}build"
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export PATH="${OBITOOLS_DIR}:${PATH}"
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MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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TMPDIR="$(mktemp -d)"
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ntest=0
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success=0
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failed=0
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cleanup() {
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echo "========================================" 1>&2
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echo "## Results of the $TEST_NAME tests:" 1>&2
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echo 1>&2
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echo "- $ntest tests run" 1>&2
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echo "- $success successfully completed" 1>&2
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echo "- $failed failed tests" 1>&2
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echo 1>&2
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echo "Cleaning up the temporary directory..." 1>&2
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echo 1>&2
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echo "========================================" 1>&2
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rm -rf "$TMPDIR" # Suppress the temporary directory
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if [ $failed -gt 0 ]; then
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log "$TEST_NAME tests failed"
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log
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log
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exit 1
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fi
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log
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log
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exit 0
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}
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log() {
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echo -e "[$TEST_NAME @ $(date)] $*" 1>&2
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}
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log "Testing $TEST_NAME..."
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log "Test directory is $TEST_DIR"
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log "obitools directory is $OBITOOLS_DIR"
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log "Temporary directory is $TMPDIR"
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log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
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######################################################################
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####
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#### Below are the tests
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####
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#### Before each test :
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#### - increment the variable ntest
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####
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#### Run the command as the condition of an if / then /else
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#### - The command must return 0 on success
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#### - The command must return an exit code different from 0 on failure
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#### - The datafiles are stored in the same directory than the test script
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#### - The test script directory is stored in the TEST_DIR variable
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#### - If result files have to be produced they must be stored
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#### in the temporary directory (TMPDIR variable)
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####
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#### then clause is executed on success of the command
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#### - Write a success message using the log function
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#### - increment the variable success
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####
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#### else clause is executed on failure of the command
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#### - Write a failure message using the log function
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#### - increment the variable failed
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####
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######################################################################
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((ntest++))
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if $CMD -h > "${TMPDIR}/help.txt" 2>&1
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then
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log "$MCMD: printing help OK"
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((success++))
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else
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log "$MCMD: printing help failed"
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((failed++))
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fi
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((ntest++))
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if obiconvert -Z "${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
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> "${TMPDIR}/xxx.fasta.gz" && \
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zdiff "${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
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"${TMPDIR}/xxx.fasta.gz"
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then
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log "$MCMD: converting large fasta file to fasta OK"
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((success++))
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else
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log "$MCMD: converting large fasta file to fasta failed"
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((failed++))
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fi
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((ntest++))
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if obiconvert -Z --fastq-output \
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"${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
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> "${TMPDIR}/xxx.fastq.gz" && \
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obiconvert -Z --fasta-output \
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"${TMPDIR}/xxx.fastq.gz" \
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> "${TMPDIR}/yyy.fasta.gz" && \
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zdiff "${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
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"${TMPDIR}/yyy.fasta.gz"
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then
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log "$MCMD: converting large file between fasta and fastq OK"
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((success++))
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else
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log "$MCMD: converting large file between fasta and fastq failed"
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((failed++))
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fi
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#########################################
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#
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# At the end of the tests
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# the cleanup function is called
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#
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#########################################
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cleanup
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