comparison test-data.sh @ 5:531935403142 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"

4:69489bd3426b

export OPENMSGIT="$tmp/OpenMS$VERSION.0-git"
export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/"
export OPENMSENV="$tmp/OpenMS$VERSION-env"
export CTDCONVERTER="$tmp/CTDConverter"


if type conda > /dev/null; then  
	true
else
	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
	bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
	source "$tmp/miniconda/bin/activate"
fi
eval "$(conda shell.bash hook)"

if [[ -z "$1" ]]; then
	autotests="/dev/null"
else
	autotests="$1"
fi

###############################################################################
## get 
## - conda environment (for executing the binaries) and 
## - the git clone of OpenMS (for generating the tests)

else
	cd $CTDCONVERTER
	git pull origin topic/cdata
	cd -
fi
export PYTHONPATH=$(pwd)/CTDopts

###############################################################################
## copy all the test data files to test-data
## most of it (outputs) will be overwritten later, but its needed for
## prepare_test_data
###############################################################################
echo "Get test data"
cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then 

cd ./test-data || exit
../prepare_test_data_manual.sh
cd - || exit


# # # exit

###############################################################################
## auto generate tests
###############################################################################

echo "Write test macros to "$autotests
echo "<macros>" > $autotests
for i in $(ls *xml |grep -v macros)
do
	b=$(basename "$i" .xml)
	get_tests2 "$b" >> $autotests 
done
echo "</macros>" >> $autotests

echo "Create test data links"
link_tmp_files

# tests for tools using output_prefix parameters can not be auto generated
# hence we output the tests for manual curation in macros_test.xml
# and remove them from the autotests
if [[ ! -z "$1" ]]; then
	echo "" > macros_discarded_auto.xml
	for i in OpenSwathFileSplitter IDRipper MzMLSplitter
	do
		echo "<xml name=\"manutest_$i\">" >>  macros_discarded_auto.xml
		xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >>  macros_discarded_auto.xml
		echo "</xml>"  >>  macros_discarded_auto.xml
		xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
		mv tmp macros_autotest.xml
	done
	>&2 "discarded autogenerated macros for curation in macros_discarded_auto.xml"
fi
conda deactivate

## remove broken symlinks in test-data
find test-data/ -xtype l -delete

5:531935403142

export OPENMSGIT="$tmp/OpenMS$VERSION.0-git"
export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/"
export OPENMSENV="$tmp/OpenMS$VERSION-env"
export CTDCONVERTER="$tmp/CTDConverter"

if [[ -z "$1" ]]; then
	autotests="/dev/null"
else
	autotests="$1"
fi

if type conda > /dev/null; then  
	true
else
	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
	bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
	source "$tmp/miniconda/bin/activate"
fi
eval "$(conda shell.bash hook)"


###############################################################################
## get 
## - conda environment (for executing the binaries) and 
## - the git clone of OpenMS (for generating the tests)

else
	cd $CTDCONVERTER
	git pull origin topic/cdata
	cd -
fi
# export PYTHONPATH=$(pwd)/CTDopts

###############################################################################
## copy all the test data files to test-data
## most of it (outputs) will be overwritten later, but its needed for
## prepare_test_data
###############################################################################
echo "Get test data"
find test-data -type f,l,d ! -name "*fa"  ! -name "*loc" -delete

cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then 

cd ./test-data || exit
../prepare_test_data_manual.sh
cd - || exit


###############################################################################
## auto generate tests
###############################################################################
echo "Write test macros to $autotests"
echo "<macros>" > "$autotests"
for i in $(ls *xml |grep -v macros)
do
	b=$(basename "$i" .xml)
	get_tests2 "$b" >> "$autotests"
done
echo "</macros>" >> "$autotests"

echo "Create test data links"
link_tmp_files

# tests for tools using output_prefix parameters can not be auto generated
# hence we output the tests for manual curation in macros_test.xml
# and remove them from the autotests
# -> OpenSwathFileSplitter IDRipper MzMLSplitter
#
# Furthermore we remove tests for tools without binaries in conda
# -> MSFragger MaRaClusterAdapter NovorAdapter 
#
# not able to specify composite test data  
# -> SpectraSTSearchAdapter 
if [[ ! -z "$1" ]]; then
	echo "" > macros_discarded_auto.xml
	for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
	do
		echo "<xml name=\"manutest_$i\">" >>  macros_discarded_auto.xml
		xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >>  macros_discarded_auto.xml
		echo "</xml>"  >>  macros_discarded_auto.xml
		xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
		mv tmp macros_autotest.xml
	done
	>&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"
fi
conda deactivate

## remove broken symlinks in test-data
find test-data/ -xtype l -delete