--- a/generate-foo.sh	Thu Dec 01 19:20:30 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,215 +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 $id"
-    echo '<xml name="autotest_'"$id"'">'
-
-    # 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 $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake  |
-        sed 's@${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 $line
-        test_id=$(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="  <test>\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 "<!-- $test_id -->"
-        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 $@; do
-        # >&2 echo "    a "$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)?"
-
-    # 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}@./@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
-}