diff test-data.sh @ 0:3ebae1b284b9 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data.sh	Fri Jun 14 21:28:32 2024 +0000
@@ -0,0 +1,308 @@
+#!/usr/bin/env bash
+
+# set -x
+
+VERSION=3.1
+FILETYPES="aux/filetypes.txt"
+CONDAPKG="https://anaconda.org/bioconda/openms/3.1.0/download/linux-64/openms-3.1.0-h8964181_1.tar.bz2"
+
+# 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="OpenMS$VERSION-env"
+
+if [ -z "$CTDCONVERTER" ]; then
+    export CTDCONVERTER="$tmp/CTDConverter"
+fi
+
+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 $OPENMSGIT ]]; then
+    if [[ "$created" == "yes" ]]; then
+        GIT_DIR=$(mktemp -d --dry-run)
+        GIT_EXTRA_OPTS="--separate-git-dir=$GIT_DIR"
+    fi
+    git clone -b release/$VERSION.0 --depth 1 --recurse-submodules=THIRDPARTY --shallow-submodules $GIT_EXTRA_OPTS https://github.com/OpenMS/OpenMS.git $OPENMSGIT
+    ## save some space by just keeping the needed binaries
+    find $OPENMSGIT/THIRDPARTY/ -type f -not \( -name maracluster -o -name spectrast \) -delete
+    find $OPENMSGIT/THIRDPARTY/ -empty -type d -delete
+    if [[ "$created" == "yes" ]]; then
+        rm -rf $GIT_DIR
+    fi
+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 --solver libmamba --override-channels --strict-channel-priority --channel conda-forge --channel bioconda -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.5 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/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
+else
+    cd $CTDCONVERTER
+    git pull origin topic/fix-selects2
+    cd -
+fi
+conda activate $OPENMSENV
+cd $CTDCONVERTER
+python -m pip install . --no-deps
+cd -
+conda deactivate
+
+
+# # ###############################################################################
+# # ## 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" ! -name "test-data" ! -name MetaboliteSpectralDB.mzML -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 -nc https://raw.githubusercontent.com/sneumann/OpenMS/master/share/OpenMS/CHEMISTRY/MetaboliteSpectralDB.mzML
+    # wget -nc https://abibuilder.cs.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
+#     mkdir -p /tmp/pepnovo
+#     wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
+#     unzip PepNovo.20120423.zip -d /tmp/pepnovo/
+#     mv /tmp/pepnovo/Models test-data/pepnovo_models/
+#     rm PepNovo.20120423.zip
+#     rm -rf /tmp/pepnovo
+# fi
+###############################################################################
+## generate ctd files using the binaries in the conda package 
+###############################################################################
+echo "Create CTD files"
+conda activate $OPENMSENV
+rm -rf ctd
+mkdir -p ctd
+
+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
+###############################################################################
+## 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
+###############################################################################
+# parse data preparation calls from OpenMS sources for a tool with a given id
+function prepare_test_data {
+#     id=$1
+# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
+
+    OLD_OSW_PARAM=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt |sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' |awk '{printf("%s@NEWLINE@", $0)}' |  sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep OLD_OSW_PARAM | head -n 1 | sed 's/^[^"]\+//; s/)$//; s/"//g')
+    # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
+    cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |
+        sed "s/\${OLD_OSW_PARAM}/$OLD_OSW_PARAM/" |
+        grep -v "\.ini\.json" |
+        sed 's/.ini.json /ini /' | 
+        sed 's/#.*$//'| 
+        sed 's/^\s*//; s/\s*$//' | 
+        grep -v "^$"  | 
+        awk '{printf("%s@NEWLINE@", $0)}' | 
+        sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
+        sed 's/degenerate_cases\///' | 
+        egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | 
+        grep add_test | 
+        egrep "TOPP|UTILS" |
+        sed 's@${DATA_DIR_SHARE}/@@g;'|
+        sed 's@${TMP_RIP_PATH}@./@g'|
+        sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| 
+	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
+    while read line
+    do
+        test_id=$(echo "$line" | sed 's/add_test(//; s/"//g;  s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
+
+        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
+            >&2 echo "    skip failing "$test_id
+            continue
+        fi
+
+        line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
+        # line="$(fix_tmp_files $line)"
+        echo 'echo executing "'$test_id'"'
+        echo "$line > $test_id.stdout 2> $test_id.stderr"
+        echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/    /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"    
+    done
+}
+
+echo "Create test shell script"
+
+echo -n "" > prepare_test_data.sh
+echo 'export COMET_BINARY="comet"' >> prepare_test_data.sh
+echo 'export CRUX_BINARY="crux"' >> prepare_test_data.sh
+echo 'export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"' >> prepare_test_data.sh
+echo 'export FIDO_BINARY="Fido"' >> prepare_test_data.sh
+echo 'export LUCIPHOR_BINARY="$(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-3.5/MSFragger-3.5.jar"'>> prepare_test_data.sh
+echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh
+echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh
+echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh
+echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh
+echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh
+echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh
+echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
+echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh
+echo 'export SAGE_BINARY=sage' >> prepare_test_data.sh
+
+prepare_test_data >> prepare_test_data.sh #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 $(ls ctd/*ctd)
+do
+    b=$(basename "$i" .ctd)
+    ./get_tests.py --id "$b" --cmake "$OPENMSGIT"/src/tests/topp/CMakeLists.txt "$OPENMSGIT"/src/tests/topp/THIRDPARTY/third_party_tests.cmake >> "$autotests"
+    wc -l "$autotests"
+done
+echo "</macros>" >> "$autotests"
+
+# 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 SeedListGenerator
+# TODO reevaluate in >2.8 
+# - https://github.com/OpenMS/OpenMS/pull/5873
+# - https://github.com/OpenMS/OpenMS/pull/5912
+#
+# Furthermore we remove tests for tools without binaries in conda
+# -> MSFragger MaRaClusterAdapter NovorAdapter 
+#
+# not able to specify composite test data  
+# -> SpectraSTSearchAdapter 
+echo "Discard some tests"
+if [[ ! -z "$1" ]]; then
+    echo "" > macros_discarded_auto.xml
+    for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
+    do
+        echo "<xml name=\"manutest_$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 [[ "$created" == "yes" ]]; then
+    echo "Removing temporary directory"
+    rm -rf "$tmp"
+fi