Mercurial > repos > galaxyp > openms_idfileconverter
diff generate-foo.sh @ 13:250d6a43f66b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 19:44:49 +0000 |
| parents | 43a1db77b7a6 |
| children | 7d0eb300f360 |
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--- a/generate-foo.sh Thu Sep 24 12:14:19 2020 +0000 +++ b/generate-foo.sh Tue Oct 13 19:44:49 2020 +0000 @@ -2,125 +2,126 @@ # 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"'">' + id=$1 + >&2 echo "generate tests for $id" + echo '<xml name="autotest_'"$id"'">' - # get the tests from the CMakeLists.txt - # 1st remove some tests - # - Filefilter with empty select_palarity value (empty is not in the list of allowed options) - # - MassTraceExtractor with outdated ini file leading to wrong parameters https://github.com/OpenMS/OpenMS/issues/4386 - # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399 + # 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) - 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/${TMP_RIP_PATH}/""/' | - sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @' | - grep -v "MaRaClusterAdapter.*-consensus_out"| - grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " | - sed 's@degenerate_cases/@@g' | - grep -v 'TOPP_SeedListGenerator_3"' | - egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"') + # - several tools with duplicated input (leads to conflict when linking) + # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525 + # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) + # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) + # - some input files are originally in a subdir (degenerated cases/), but not in test-data + # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404 + # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet) + # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002 + # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + CMAKE=$(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" | +# 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) $line" - continue - fi + # 1st part is a dirty hack to join lines containing a single function call, e.g. + # addtest(.... + # ....) + echo "$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 $testtmp + #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1) + if grep -lq "$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 $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//') - #> /dev/null + ctdtmp=$(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 - #rm $testtmp - done - echo '</xml>' + #> /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 [[ $cnt -gt 1 ]]; do + line=$@ + 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 + 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 + 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}' + grep "^$1" "$2" | awk '{print $2}' } #OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file. @@ -129,34 +130,34 @@ #(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" +# >&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 { @@ -190,28 +191,32 @@ # parse data preparation calls from OpenMS sources for a tool with a given id function prepare_test_data { -# id=$1 +# id=$1 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" - 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@${TMP_RIP_PATH}@dummy2.tmp@g'| - sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| - while read line - do - test_id=$(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 +# 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/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1) - line=$(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 $line)" - echo "$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 $test_id.stdout)\";fi" + if grep -lq "$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 }