diff test-data.sh @ 11:12513e823fd0 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data.sh	Wed Sep 09 20:08:15 2020 +0000
@@ -0,0 +1,255 @@
+#!/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="$tmp/CTDConverter"
+
+
+if type conda > /dev/null; then  
+	true
+else
+	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+	bash Miniconda3-latest-Linux-x86_64.sh -b -p "$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)
+###############################################################################
+
+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"
+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
+
+
+# # # 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
+
+# if [ ! -z "$created" ]; then
+# 	echo "Removing temporary directory"
+# 	rm -rf "$tmp"
+# fi