#!/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 $autotests"
echo "" > "$autotests"
for i in $(ls *xml |grep -v macros)
do
b=$(basename "$i" .xml)
get_tests2 "$b" >> "$autotests"
done
echo "" >> "$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 "$1" ]]; then
echo "" > macros_discarded_auto.xml
for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
do
echo "" >> macros_discarded_auto.xml
xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml
echo "" >> 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