--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate-foo.sh	Wed Sep 09 20:09:56 2020 +0000
@@ -0,0 +1,217 @@
+#!/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
+	# - 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+	# - MassTraceExtractor with outdated ini file leading to wrong parameters https://github.com/OpenMS/OpenMS/issues/4386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
+    # - 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/${TMP_RIP_PATH}/""/' |
+		sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @' |
+		grep -v "MaRaClusterAdapter.*-consensus_out"|
+ 		grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
+		sed 's@degenerate_cases/@@g' |
+		grep -v 'TOPP_SeedListGenerator_3"' | 
+		egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"')
+
+
+# 		grep -v 'FileFilter.*-spectra:select_polarity ""' |
+# 		grep -v 'MassTraceExtractor_2.ini ' |
+# 		grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |
+# 		grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |
+# 		grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |
+# 		grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |
+# 		grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |
+
+	# 1st part is a dirty hack to join lines containing a single function call, e.g.
+	# addtest(....
+	#         ....)
+	echo "$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)?"
+	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
+
+		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"	
+    done
+}