Mercurial > repos > galaxyp > openms_spectrafilterthresholdmower
comparison generate-foo.sh @ 14:53fec73970ad draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:40:57 +0000 |
parents | 1db101600feb |
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13:1db101600feb | 14:53fec73970ad |
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1 #!/usr/bin/env bash | |
2 | |
3 # parse test definitions from OpenMS sources for a tool with a given id | |
4 function get_tests2 { | |
5 id=$1 | |
6 >&2 echo "generate tests for $id" | |
7 echo '<xml name="autotest_'"$id"'">' | |
8 | |
9 # get the tests from the CMakeLists.txt | |
10 # 1st remove some tests | |
11 # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399 | |
12 # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt | |
13 # - several tools with duplicated input (leads to conflict when linking) | |
14 # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) | |
15 # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) | |
16 # - some input files are originally in a subdir (degenerated cases/), but not in test-data | |
17 # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet) | |
18 # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 | |
19 # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869 | |
20 CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | | |
21 sed 's@${DATA_DIR_SHARE}/@@g' | | |
22 grep -v 'OpenSwathMzMLFileCacher .*-convert_back' | | |
23 sed 's/${TMP_RIP_PATH}/""/' | | |
24 grep -v "MaRaClusterAdapter.*-consensus_out"| | |
25 grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " | | |
26 sed 's@degenerate_cases/@@g' | | |
27 egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' | | |
28 sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | | |
29 grep -v '"TOPP_SiriusAdapter_10"') | |
30 | |
31 # 1st part is a dirty hack to join lines containing a single function call, e.g. | |
32 # addtest(.... | |
33 # ....) | |
34 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' | | |
35 grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE" | while read -r line | |
36 do | |
37 line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g') | |
38 # >&2 echo $line | |
39 test_id=$(echo "$line" | cut -d" " -f 1) | |
40 tool_id=$(echo "$line" | cut -d" " -f 2) | |
41 # >&2 echo "test_id $test_id" | |
42 if [[ $test_id =~ _out_?[0-9]? ]]; then | |
43 >&2 echo " skip $test_id $line" | |
44 continue | |
45 fi | |
46 if [[ ${id,,} != ${tool_id,,} ]]; then | |
47 >&2 echo " skip $test_id ($id != $tool_id) $line" | |
48 continue | |
49 fi | |
50 | |
51 #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1) | |
52 if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then | |
53 >&2 echo " skip failing "$test_id | |
54 continue | |
55 fi | |
56 tes=" <test>\n" | |
57 line=$(fix_tmp_files "$line") | |
58 line=$(unique_files "$line") | |
59 # >&2 echo LINE $line | |
60 #if there is an ini file then we use this to generate the test | |
61 #otherwise the ctd file is used | |
62 #other command line parameters are inserted later into this xml | |
63 if grep -lq "\-ini" <<<"$line"; then | |
64 ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/') | |
65 ini="test-data/$ini" | |
66 else | |
67 ini="ctd/$tool_id.ctd" | |
68 fi | |
69 # >&2 echo "========================================================" | |
70 # >&2 echo "USING ini $ini" | |
71 cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//') | |
72 | |
73 ctdtmp=$(mktemp) | |
74 # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) | |
75 # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" | |
76 eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp" | |
77 # >&2 echo $ctdtmp | |
78 # >&2 cat $ctdtmp | |
79 testtmp=$(mktemp) | |
80 # >&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" | |
81 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 | |
82 echo "<!-- $test_id -->" | |
83 cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' | |
84 | |
85 rm "$ctdtmp" "$testtmp" | |
86 | |
87 #> /dev/null | |
88 | |
89 #rm $testtmp | |
90 done | |
91 echo '</xml>' | |
92 } | |
93 | |
94 #some tests use the same file twice which does not work in planemo tests | |
95 #hence we create symlinks for each file used twice | |
96 function unique_files { | |
97 line=$@ | |
98 for arg in $@ | |
99 do | |
100 if [[ ! -f "test-data/$arg" ]]; then | |
101 continue | |
102 fi | |
103 cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) | |
104 while [[ $cnt -gt 1 ]]; do | |
105 new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./") | |
106 ln -fs $arg test-data/$new_arg | |
107 line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/") | |
108 cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) | |
109 done | |
110 done | |
111 | |
112 echo $line | |
113 } | |
114 | |
115 # options of out_type selects need to be fixed to Galaxy data types | |
116 function fix_out_type { | |
117 grep "^$1" "$2" | awk '{print $2}' | |
118 } | |
119 | |
120 #OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file. | |
121 #problem: the extension of the tmp files is unusable for test generation. | |
122 #unfortunately the extensions used in the DIFF lines are not always usable for the CLI | |
123 #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) | |
124 #this function replaces the tmp file by the expected file. | |
125 function fix_tmp_files { | |
126 # >&2 echo "FIX $line" | |
127 ret="" | |
128 for a in $@; do | |
129 # >&2 echo " a "$a | |
130 if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then | |
131 ret="$ret $a" | |
132 continue | |
133 fi | |
134 diff_line=$(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") | |
135 # >&2 echo " diff_line "$diff_line | |
136 in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line) | |
137 # >&2 echo " in1 "$in1 | |
138 if [[ "$a" != "$in1" ]]; then | |
139 ret="$ret $a" | |
140 continue | |
141 fi | |
142 in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line) | |
143 in2=$(basename $in2 | sed 's/)$//') | |
144 # >&2 echo " in2 "$in2 | |
145 if [[ -f "test-data/$in2" ]]; then | |
146 ln -fs "$in1" "test-data/$in2" | |
147 ret="$ret $in2" | |
148 else | |
149 ret="$ret $a" | |
150 fi | |
151 done | |
152 # >&2 echo "--> $ret" | |
153 echo "$ret" | |
154 } | |
155 | |
156 function link_tmp_files { | |
157 # note this also considers commented lines (starting with a #) | |
158 # because of tests where the diff command is commented and we | |
159 # still want to use the extension of these files | |
160 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@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep "\${DIFF}" | while read -r line | |
161 do | |
162 in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$line) | |
163 in1=$(basename $in1 | sed 's/)$//') | |
164 in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$line) | |
165 in2=$(basename $in2 | sed 's/)$//') | |
166 if [[ "$in1" == "$in2" ]]; then | |
167 >&2 echo "not linking equal $in1 $in2" | |
168 continue | |
169 fi | |
170 ln -f -s $in1 test-data/$in2 | |
171 done | |
172 | |
173 find test-data/ -name "*.tmp" -print0 | | |
174 while IFS= read -r -d '' i; do | |
175 if [ ! -e test-data/$(basename $i .tmp) ]; then | |
176 ln -s $(basename $i) test-data/$(basename $i .tmp) | |
177 else | |
178 ln -fs $(basename $i) test-data/$(basename $i .tmp) | |
179 fi | |
180 done | |
181 } | |
182 | |
183 | |
184 | |
185 # parse data preparation calls from OpenMS sources for a tool with a given id | |
186 function prepare_test_data { | |
187 # id=$1 | |
188 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" | |
189 | |
190 # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 | |
191 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@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | | |
192 sed 's/degenerate_cases\///' | | |
193 egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | | |
194 grep add_test | | |
195 egrep "TOPP|UTILS" | | |
196 sed 's@${DATA_DIR_SHARE}/@@g;'| | |
197 sed 's@${TMP_RIP_PATH}@./@g'| | |
198 sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| | |
199 sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | | |
200 while read line | |
201 do | |
202 test_id=$(echo "$line" | sed 's/add_test(//; s/"//g; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1) | |
203 | |
204 if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then | |
205 >&2 echo " skip failing "$test_id | |
206 continue | |
207 fi | |
208 | |
209 line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-) | |
210 # line="$(fix_tmp_files $line)" | |
211 echo 'echo executing "'$test_id'"' | |
212 echo "$line > $test_id.stdout 2> $test_id.stderr" | |
213 echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/ /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi" | |
214 done | |
215 } |