Mercurial > repos > galaxyp > openms_msfraggeradapter
diff generate-foo.sh @ 5:9866e1170611 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:05:24 +0000 |
| parents | 6bcc338b9dc6 |
| children |
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--- a/generate-foo.sh Mon Dec 14 16:55:52 2020 +0000 +++ b/generate-foo.sh Thu Dec 01 19:05:24 2022 +0000 @@ -8,17 +8,15 @@ # get the tests from the CMakeLists.txt # 1st remove some tests - # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399 + # - OpenSwathMzMLFileCacher with -convert_back argument 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 + # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 + # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869 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' | @@ -26,19 +24,9 @@ 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" | + sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | + grep -v '"TOPP_SiriusAdapter_10"') # 1st part is a dirty hack to join lines containing a single function call, e.g. # addtest(.... @@ -50,6 +38,7 @@ # >&2 echo $line test_id=$(echo "$line" | cut -d" " -f 1) tool_id=$(echo "$line" | cut -d" " -f 2) + # >&2 echo "test_id $test_id" if [[ $test_id =~ _out_?[0-9]? ]]; then >&2 echo " skip $test_id $line" continue @@ -67,7 +56,7 @@ tes=" <test>\n" line=$(fix_tmp_files "$line") line=$(unique_files "$line") - # >&2 echo $line + # >&2 echo LINE $line #if there is an ini file then we use this to generate the test #otherwise the ctd file is used #other command line parameters are inserted later into this xml @@ -77,19 +66,23 @@ else ini="ctd/$tool_id.ctd" fi + # >&2 echo "========================================================" + # >&2 echo "USING ini $ini" cli=$(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 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" + eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp" + # >&2 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 + # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" + CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null + echo "<!-- $test_id -->" cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' - rm $ctdtmp $testtmp + + rm "$ctdtmp" "$testtmp" #> /dev/null @@ -130,23 +123,23 @@ #(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" + # >&2 echo "FIX $line" ret="" for a in $@; do - if [[ ! $a =~ .tmp$ ]]; then + # >&2 echo " a "$a + if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then ret="$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/' <<<$g) + diff_line=$(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 " diff_line "$diff_line + in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line) # >&2 echo " in1 "$in1 if [[ "$a" != "$in1" ]]; then ret="$ret $a" continue fi - in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g) + in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line) in2=$(basename $in2 | sed 's/)$//') # >&2 echo " in2 "$in2 if [[ -f "test-data/$in2" ]]; then @@ -176,11 +169,11 @@ fi ln -f -s $in1 test-data/$in2 done - for i in test-data/*.tmp - do + + find test-data/ -name "*.tmp" -print0 | + while IFS= read -r -d '' i; 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 @@ -194,14 +187,14 @@ # id=$1 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" -# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + # 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 $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| 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@${TMP_RIP_PATH}@dummy2.tmp@g'| + sed 's@${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