annotate test-data.sh @ 12:b5ede3ff996c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"

#!/usr/bin/env bash

VERSION=2.5
FILETYPES="filetypes.txt"
CONDAPKG="https://anaconda.org/bioconda/openms/2.5.0/download/linux-64/openms-2.5.0-h463af6b_1.tar.bz2"

# import the magic
. ./generate-foo.sh

# install conda
if [ -z "$tmp" ]; then
	tmp=$(mktemp -d)
	created="yes"
fi

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)
###############################################################################

echo "Clone OpenMS $VERSION sources"
if [[ ! -d $OPENMSGIT ]]; then
	git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
	cd $OPENMSGIT
	git submodule init
	git submodule update
	cd -
else
	cd $OPENMSGIT
		git pull origin release/$VERSION.0
	cd -
fi

echo "Create OpenMS $VERSION conda env"
# TODO currently add lxml (needed by CTDConverter)
# TODO for some reason a to recent openjdk is used
if conda env list | grep "$OPENMSENV"; then
	true
else
	conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION openjdk=8.0.192 ctdopts=1.4 lxml
# chmod -R u-w $OPENMSENV 
fi
###############################################################################
## get the 
## - conda package (for easy access and listing of the OpenMS binaries), 
###############################################################################
echo "Download OpenMS $VERSION package $CONDAPKG"

if [[ ! -d $OPENMSPKG ]]; then
	mkdir $OPENMSPKG
	wget -q -P $OPENMSPKG/ "$CONDAPKG"
	tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/
	rm $OPENMSPKG/"$(basename $CONDAPKG)"
fi

###############################################################################
## Get python libaries for CTD -> Galaxy conversion
## TODO fix to main repo OR conda packkage if PRs are merged 
###############################################################################
echo "Clone CTDConverter"
if [[ ! -d $CTDCONVERTER ]]; then
	#git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
	git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
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 
	wget -q https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML && mv MetaboliteSpectralDB.mzML test-data/
fi
ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv

if [ ! -d test-data/pepnovo_models/ ]; then
	wget http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
	unzip -e PepNovo.20120423.zip -d /tmp/
	mv /tmp/Models test-data/pepnovo_models/
fi
###############################################################################
## generate ctd files using the binaries in the conda package 
###############################################################################
echo "Create CTD files"
conda activate $OPENMSENV
mkdir -p ctd

# TODO because of https://github.com/OpenMS/OpenMS/issues/4641
# this needs to be done from within test-data
cd test-data
for i in $OPENMSPKG/bin/*
do
	b=$(basename $i)
	echo $b
	$b -write_ctd ../ctd/
	sed -i -e 's/²/^2/' ../ctd/$b.ctd
done
cd -
###############################################################################
## fix ini files: OpenMS test data contains ini files with outdated ini files.
## e.g. variables might be in different nodes, outdated variables present, new
## variables missing, ...
## OpenMS tools fix this on the fly (so its no problem for the OpenMS tests)
## but it is for the generation of the tests
## see https://github.com/OpenMS/OpenMS/issues/4462
###############################################################################
echo "Update test INI files"
for ini in test-data/*ini
do
	tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
	bin=$(which $tool)
	if [[ -z $bin ]]; then
          >&2 echo "missing binary to convert $ini"
		  continue
	fi
	cp $ini $ini.backup
	$bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
	if [[ "$?" -ne "0" ]]; then
		>&2 echo "could not convert $ini"
	fi
done

###############################################################################
## create script to create results for the tests and run it
###############################################################################
echo "Create test shell script"

echo -n "" > prepare_test_data.sh
echo 'export COMET_BINARY="comet"' >> prepare_test_data.sh
echo 'export CRUX_BINARY="crux"' >> prepare_test_data.sh
echo 'export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"' >> prepare_test_data.sh
echo 'export FIDO_BINARY="Fido"' >> prepare_test_data.sh
echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh

echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh
echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh
echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh
echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh
echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh
echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh
echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh
echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh
echo 'export SPECTRAST_BINARY="spectrast"' >> prepare_test_data.sh
echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh

prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh

# prepare_test_data > tmp_test_data.sh
# # remove calls not needed for the tools listed in any .list file
# echo LIST $LIST
# if [ ! -z "$LIST" ]; then
# 	REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
# else
# 	REX=".*"
# fi
# echo REX $REX
# cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
# rm tmp_test_data.sh

echo "Execute test shell script"
chmod u+x prepare_test_data.sh
cd ./test-data || exit
../prepare_test_data.sh
cd - || exit


###############################################################################
## create/update test data for the manually generated tests
## - run convert once with the manual tests only and 
## - update test-data (needs to run 2x)
###############################################################################
echo "Execute test shell script for manually curated tests"
chmod u+x prepare_test_data_manual.sh

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

# if [ ! -z "$created" ]; then
# 	echo "Removing temporary directory"
# 	rm -rf "$tmp"
# fi