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Add basic test on -h for all the commands

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This commit is contained in:
Eric Coissac
2025-03-08 16:28:06 +01:00
parent 65bd29b955
commit 78caabd2fd
34 changed files with 2872 additions and 3 deletions
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109
obitests/obitools/obiannotate/test.sh Executable file
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@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obiannotate
CMD=obiannotate
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obiclean/test.sh Executable file
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@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obiclean
CMD=obiclean
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obicleandb/test.sh Executable file
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@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obicleandb
CMD=obicleandb
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obicomplement/test.sh Executable file
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@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obicomplement
CMD=obicomplement
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obiconsensus/test.sh Executable file
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@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obiconsensus
CMD=obiconsensus
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obiconvert/test.sh Executable file
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@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obiconvert
CMD=obiconvert
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

19
obitests/obitools/obicount/test.sh
View File

@ -5,6 +5,7 @@
# #
TEST_NAME=obicount TEST_NAME=obicount
CMD=obicount
###### ######
# #
@ -15,6 +16,7 @@ TEST_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
OBITOOLS_DIR="${TEST_DIR/obitest*/}build" OBITOOLS_DIR="${TEST_DIR/obitest*/}build"
export PATH="${OBITOOLS_DIR}:${PATH}" export PATH="${OBITOOLS_DIR}:${PATH}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
TMPDIR="$(mktemp -d)" TMPDIR="$(mktemp -d)"
ntest=0 ntest=0
@ -38,9 +40,14 @@ cleanup() {
if [ $failed -gt 0 ]; then if [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed" log "$TEST_NAME tests failed"
log
log
exit 1 exit 1
fi fi
log
log
exit 0 exit 0
} }
@ -79,6 +86,18 @@ log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
#### ####
###################################################################### ######################################################################
((ntest++))
if $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
((ntest++)) ((ntest++))
if obicount "${TEST_DIR}/wolf_F.fasta.gz" \ if obicount "${TEST_DIR}/wolf_F.fasta.gz" \
> "${TMPDIR}/wolf_F.fasta_count.csv" > "${TMPDIR}/wolf_F.fasta_count.csv"

109
obitests/obitools/obicsv/test.sh Executable file
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@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obicsv
CMD=obicsv
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obidemerge/test.sh Executable file
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@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obidemerge
CMD=obidemerge
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obidistribute/test.sh Executable file
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@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obidistribute
CMD=obidistribute
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obigrep/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obigrep
CMD=obigrep
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obijoin/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obijoin
CMD=obijoin
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obikmermatch/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obikmermatch
CMD=obikmermatch
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obikmersimcount/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obikmersimcount
CMD=obikmersimcount
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obilandmark/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obilandmark
CMD=obilandmark
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obimatrix/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obimatrix
CMD=obimatrix
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obimicrosat/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obimicrosat
CMD=obimicrosat
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obimultiplex/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obimultiplex
CMD=obimultiplex
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

18
obitests/obitools/obiparing/test.sh → obitests/obitools/obipairing/test.sh
View File

@ -4,7 +4,8 @@
# Here give the name of the test serie # Here give the name of the test serie
# #
TEST_NAME=obiparing TEST_NAME=obipairing
CMD=obipairing
###### ######
# #
@ -15,6 +16,7 @@ TEST_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
OBITOOLS_DIR="${TEST_DIR/obitest*/}build" OBITOOLS_DIR="${TEST_DIR/obitest*/}build"
export PATH="${OBITOOLS_DIR}:${PATH}" export PATH="${OBITOOLS_DIR}:${PATH}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
TMPDIR="$(mktemp -d)" TMPDIR="$(mktemp -d)"
ntest=0 ntest=0
@ -38,9 +40,13 @@ cleanup() {
if [ $failed -gt 0 ]; then if [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed" log "$TEST_NAME tests failed"
log
log
exit 1 exit 1
fi fi
log
log
exit 0 exit 0
} }
@ -79,6 +85,16 @@ log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
#### ####
###################################################################### ######################################################################
((ntest++))
if $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
((ntest++)) ((ntest++))
if obipairing -F "${TEST_DIR}/wolf_F.fastq.gz" \ if obipairing -F "${TEST_DIR}/wolf_F.fastq.gz" \
-R "${TEST_DIR}/wolf_R.fastq.gz" \ -R "${TEST_DIR}/wolf_R.fastq.gz" \

0
obitests/obitools/obiparing/wolf_F.fastq.gz → obitests/obitools/obipairing/wolf_F.fastq.gz
View File

0
obitests/obitools/obiparing/wolf_R.fastq.gz → obitests/obitools/obipairing/wolf_R.fastq.gz
View File

0
obitests/obitools/obiparing/wolf_paired_alignment.csv.gz → obitests/obitools/obipairing/wolf_paired_alignment.csv.gz
View File

0
obitests/obitools/obiparing/wolf_paired_join.csv.gz → obitests/obitools/obipairing/wolf_paired_join.csv.gz
View File

109
obitests/obitools/obipcr/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obipcr
CMD=obipcr
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obirefidx/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obirefidx
CMD=obirefidx
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obiscript/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obiscript
CMD=obiscript
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obisplit/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obisplit
CMD=obisplit
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obisummary/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obisummary
CMD=obisummary
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obitag/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obitag
CMD=obitag
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obitagpcr/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obipcr
CMD=obipcr
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obitaxonomy/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obitaxonomy
CMD=obitaxonomy
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

109
obitests/obitools/obiuniq/test.sh Executable file
View File

@ -0,0 +1,109 @@
#!/bin/bash
#
# Here give the name of the test serie
#
TEST_NAME=obiuniq
CMD=obiuniq
######
#
# 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}"
MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
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 [ $failed -gt 0 ]; then
log "$TEST_NAME tests failed"
log
log
exit 1
fi
log
log
exit 0
}
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 "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
######################################################################
####
#### 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 $CMD -h > "${TMPDIR}/help.txt" 2>&1
then
log "$MCMD: printing help OK"
((success++))
else
log "$MCMD: printing help failed"
((failed++))
fi
#########################################
#
# At the end of the tests
# the cleanup function is called
#
#########################################
cleanup

2
pkg/obioptions/options.go
View File

@ -76,7 +76,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
if options.Called("help") { if options.Called("help") {
fmt.Fprint(os.Stderr, options.Help()) fmt.Fprint(os.Stderr, options.Help())
os.Exit(1) os.Exit(0)
} }
if options.Called("version") { if options.Called("version") {

2
pkg/obioptions/version.go
View File

@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be // corresponds to the last commit, and not the one when the file will be
// commited // commited
var _Commit = "b18c9b7" var _Commit = "65bd29b"
var _Version = "Release 4.4.0" var _Version = "Release 4.4.0"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.