diff --git a/tools/openms/PSMFeatureExtractor.xml b/tools/openms/PSMFeatureExtractor.xml
index 196b60dae..f512faaa3 100644
--- a/tools/openms/PSMFeatureExtractor.xml
+++ b/tools/openms/PSMFeatureExtractor.xml
@@ -172,33 +172,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
-
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diff --git a/tools/openms/generate.sh b/tools/openms/aux/generate.sh
similarity index 100%
rename from tools/openms/generate.sh
rename to tools/openms/aux/generate.sh
diff --git a/tools/openms/aux/hardcoded_params.json b/tools/openms/aux/hardcoded_params.json
index df3482253..0c4b36f90 100644
--- a/tools/openms/aux/hardcoded_params.json
+++ b/tools/openms/aux/hardcoded_params.json
@@ -191,7 +191,6 @@
"#": "IDFileConverter remove xml",
"#": "OpenSwathWorkflow make in single file input and all outputs non-optional",
"#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release",
- "#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. ",
"in": [{
"CTD:restrictions": "oms,idXML,mzid,fasta,pepXML,protXML,mascotXML,omssaXML,psms,tsv,xquest.xml",
"tools": ["IDFileConverter"]
@@ -201,9 +200,6 @@
}, {
"CTD:restrictions": "idXML,mzid,xquest.xml",
"tools": ["XFDR"]
- }, {
- "CTD:restrictions": "mzML,idXML,featureXML",
- "tools": ["SeedListGenerator"]
}],
"#": "IDMapper has in and spectra:in params, in is used in out as format_source",
diff --git a/tools/openms/fill_ctd_clargs.py b/tools/openms/fill_ctd_clargs.py
deleted file mode 100644
index f36e0ee86..000000000
--- a/tools/openms/fill_ctd_clargs.py
+++ /dev/null
@@ -1,70 +0,0 @@
-#!/usr/bin/env python3
-
-import operator
-from argparse import ArgumentParser
-from functools import reduce # forward compatibility for Python 3
-from io import StringIO
-
-from CTDopts.CTDopts import (
- _Null,
- CTDModel,
- ModelTypeError,
- Parameters
-)
-
-
-def getFromDict(dataDict, mapList):
- return reduce(operator.getitem, mapList, dataDict)
-
-
-def setInDict(dataDict, mapList, value):
- getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
-
-
-if __name__ == "__main__":
- # note add_help=False since otherwise arguments starting with -h will
- # trigger an error (despite allow_abbreviate)
- parser = ArgumentParser(prog="fill_ctd_clargs",
- description="fill command line arguments"
- "into a CTD file and write the CTD file to stdout",
- add_help=False, allow_abbrev=False)
- parser.add_argument("--ini_file", dest="ini_file", help="input ini file",
- metavar='INI', default=None, required=True)
- parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file"
- "if given then optional parameters from the ini file"
- "will be filled with the defaults from this CTD file",
- metavar='CTD', default=None, required=False)
- args, cliargs = parser.parse_known_args()
-
- # load CTDModel
- ini_model = None
- try:
- ini_model = CTDModel(from_file=args.ini_file)
- except ModelTypeError:
- pass
- try:
- ini_model = Parameters(from_file=args.ini_file)
- except ModelTypeError:
- pass
- assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file)
-
- # get a dictionary of the ctd arguments where the values of the parameters
- # given on the command line are overwritten
- ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True)
-
- if args.ctd_file:
- ctd_model = CTDModel(from_file=args.ctd_file)
- ctd_values = ctd_model.get_defaults()
- for param in ini_model.get_parameters():
- if not param.required and (param.default is None or type(param.default) is _Null):
- lineage = param.get_lineage(name_only=True)
- try:
- default = getFromDict(ctd_values, lineage)
- except KeyError:
- continue
- setInDict(ini_values, lineage, default)
-
- # write the ctd with the values taken from the dictionary
- out = StringIO()
- ctd_tree = ini_model.write_ctd(out, ini_values)
- print(out.getvalue())
diff --git a/tools/openms/generate-foo.sh b/tools/openms/generate-foo.sh
deleted file mode 100644
index a9315c73a..000000000
--- a/tools/openms/generate-foo.sh
+++ /dev/null
@@ -1,225 +0,0 @@
-#!/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 $id"
- echo ''
-
- # get the tests from the CMakeLists.txt
- # 1st remove some tests
- # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
- # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
- # - several tools with duplicated input (leads to conflict when linking)
- # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
- # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
- # - some input files are originally in a subdir (degenerated cases/), but not in test-data
- # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
- # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
- # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869
- CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |
- grep -v "\.ini\.json" |
- sed 's@${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' |
- egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' |
- 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(....
- # ....)
- 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 $line"
- test_id=$(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
- 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=" \n"
- line=$(fix_tmp_files "$line")
- line=$(unique_files "$line")
- # >&2 echo LINE $line
- #if there is an ini file then we use this to generate the test
- #otherwise the ctd file is used
- #other command line parameters are inserted later into this xml
- if grep -lq "\-ini" <<<"$line"; then
- ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/')
- ini="test-data/$ini"
- else
- ini="ctd/$tool_id.ctd"
- fi
- # >&2 echo "========================================================"
- # >&2 echo "USING ini $ini"
- cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
-
- ctdtmp=$(mktemp)
- # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
- # >&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)
- # >&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 ""
- cat $testtmp | grep -v ' /dev/null
-
- #rm $testtmp
- done
- echo ''
-}
-
-#some tests use the same file twice which does not work in planemo tests
-#hence we create symlinks for each file used twice
-function unique_files {
- line=$@
- 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 $@; do
- # >&2 echo " a "$a
- if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then
- ret="$ret $a"
- continue
- fi
- diff_line=$(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/' <<<$diff_line)
- in2=$(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
-
- 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)
- 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)?"
-
- 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
-}
diff --git a/tools/openms/macros_discarded_auto.xml b/tools/openms/macros_discarded_auto.xml
deleted file mode 100644
index 2a01c0a5f..000000000
--- a/tools/openms/macros_discarded_auto.xml
+++ /dev/null
@@ -1,525 +0,0 @@
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