Mercurial > repos > galaxyp > openms_baselinefilter
view generate-foo.sh @ 15:1936361a3dbb draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 19:43:23 +0000 |
| parents | 2c6de76669fe |
| children | ddbae9eb797e |
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#!/usr/bin/env bash # parse test definitions from OpenMS sources for a tool with a given id function get_tests2 { id=$1 >&2 echo "generate tests for $id" echo '<xml name="autotest_'"$id"'">' # get the tests from the CMakeLists.txt # 1st remove some tests # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399 # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt # - several tools with duplicated input (leads to conflict when linking) # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525 # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) # - some input files are originally in a subdir (degenerated cases/), but not in test-data # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404 # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet) # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002 # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's@${DATA_DIR_SHARE}/@@g' | grep -v 'OpenSwathMzMLFileCacher .*-convert_back' | sed 's/${TMP_RIP_PATH}/""/' | grep -v "MaRaClusterAdapter.*-consensus_out"| grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " | sed 's@degenerate_cases/@@g' | grep -v 'TOPP_SeedListGenerator_3"' | egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' | egrep -v '"TOPP_FeatureFinderIdentification_4"' | sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/') # grep -v 'FileFilter.*-spectra:select_polarity ""' | # grep -v 'MassTraceExtractor_2.ini ' | # grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" | # grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" | # grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" | # grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" | # grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" | # 1st part is a dirty hack to join lines containing a single function call, e.g. # addtest(.... # ....) echo "$CMAKE" | sed 's/#.*//; s/^\s*//; s/\s*$//' | grep -v "^#" | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE" | while read -r line do line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g') # >&2 echo $line test_id=$(echo "$line" | cut -d" " -f 1) tool_id=$(echo "$line" | cut -d" " -f 2) if [[ $test_id =~ _out_?[0-9]? ]]; then >&2 echo " skip $test_id $line" continue fi if [[ ${id,,} != ${tool_id,,} ]]; then >&2 echo " skip $test_id ($id != $tool_id) $line" continue fi #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1) if grep -lq "$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 tes=" <test>\n" line=$(fix_tmp_files "$line") line=$(unique_files "$line") # >&2 echo $line #if there is an ini file then we use this to generate the test #otherwise the ctd file is used #other command line parameters are inserted later into this xml if grep -lq "\-ini" <<<"$line"; then ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/') ini="test-data/$ini" else ini="ctd/$tool_id.ctd" fi cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//') ctdtmp=$(mktemp) #echo python3 fill_ctd_clargs.py --ctd $ini $cli # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli" eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp" # echo $ctdtmp # >&2 cat $ctdtmp testtmp=$(mktemp) python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' rm $ctdtmp $testtmp #> /dev/null #rm $testtmp done echo '</xml>' } #some tests use the same file twice which does not work in planemo tests #hence we create symlinks for each file used twice function unique_files { line=$@ for arg in $@ do if [[ ! -f "test-data/$arg" ]]; then continue fi cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) while [[ $cnt -gt 1 ]]; do new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./") ln -fs $arg test-data/$new_arg line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/") cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) done done echo $line } # options of out_type selects need to be fixed to Galaxy data types function fix_out_type { grep "^$1" "$2" | awk '{print $2}' } #OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file. #problem: the extension of the tmp files is unusable for test generation. #unfortunately the extensions used in the DIFF lines are not always usable for the CLI #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) #this function replaces the tmp file by the expected file. function fix_tmp_files { # >&2 echo "FIX $line" ret="" for a in $@; do if [[ ! $a =~ .tmp$ ]]; then ret="$ret $a" continue fi # >&2 echo " a "$a g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") # >&2 echo " g "$g in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g) # >&2 echo " in1 "$in1 if [[ "$a" != "$in1" ]]; then ret="$ret $a" continue fi in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g) in2=$(basename $in2 | sed 's/)$//') # >&2 echo " in2 "$in2 if [[ -f "test-data/$in2" ]]; then ln -fs "$in1" "test-data/$in2" ret="$ret $in2" else ret="$ret $a" fi done # >&2 echo "--> $ret" echo "$ret" } function link_tmp_files { # note this also considers commented lines (starting with a #) # because of tests where the diff command is commented and we # still want to use the extension of these files cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep "\${DIFF}" | while read -r line do in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$line) in1=$(basename $in1 | sed 's/)$//') in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$line) in2=$(basename $in2 | sed 's/)$//') if [[ "$in1" == "$in2" ]]; then >&2 echo "not linking equal $in1 $in2" continue fi ln -f -s $in1 test-data/$in2 done for i in test-data/*.tmp do if [ ! -e test-data/$(basename $i .tmp) ]; then ln -s $(basename $i) test-data/$(basename $i .tmp) #ln -s $(basename $i) test-data/$(basename $i .tmp) else ln -fs $(basename $i) test-data/$(basename $i .tmp) fi done } # 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)?" # TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| 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}@dummy2.tmp@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 }