Mercurial > repos > galaxyp > openms_featurefindermetaboident
comparison test-data.sh @ 1:59c8b1a9cf86 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author | galaxyp |
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date | Thu, 24 Sep 2020 12:21:43 +0000 |
parents | 539b683e9752 |
children | 7e29bf457263 |
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0:539b683e9752 | 1:59c8b1a9cf86 |
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16 export OPENMSGIT="$tmp/OpenMS$VERSION.0-git" | 16 export OPENMSGIT="$tmp/OpenMS$VERSION.0-git" |
17 export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/" | 17 export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/" |
18 export OPENMSENV="$tmp/OpenMS$VERSION-env" | 18 export OPENMSENV="$tmp/OpenMS$VERSION-env" |
19 export CTDCONVERTER="$tmp/CTDConverter" | 19 export CTDCONVERTER="$tmp/CTDConverter" |
20 | 20 |
21 if [[ -z "$1" ]]; then | |
22 autotests="/dev/null" | |
23 else | |
24 autotests="$1" | |
25 fi | |
21 | 26 |
22 if type conda > /dev/null; then | 27 if type conda > /dev/null; then |
23 true | 28 true |
24 else | 29 else |
25 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | 30 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
26 bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" | 31 bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" |
27 source "$tmp/miniconda/bin/activate" | 32 source "$tmp/miniconda/bin/activate" |
28 fi | 33 fi |
29 eval "$(conda shell.bash hook)" | 34 eval "$(conda shell.bash hook)" |
30 | 35 |
31 if [[ -z "$1" ]]; then | |
32 autotests="/dev/null" | |
33 else | |
34 autotests="$1" | |
35 fi | |
36 | 36 |
37 ############################################################################### | 37 ############################################################################### |
38 ## get | 38 ## get |
39 ## - conda environment (for executing the binaries) and | 39 ## - conda environment (for executing the binaries) and |
40 ## - the git clone of OpenMS (for generating the tests) | 40 ## - the git clone of OpenMS (for generating the tests) |
86 else | 86 else |
87 cd $CTDCONVERTER | 87 cd $CTDCONVERTER |
88 git pull origin topic/cdata | 88 git pull origin topic/cdata |
89 cd - | 89 cd - |
90 fi | 90 fi |
91 export PYTHONPATH=$(pwd)/CTDopts | 91 # export PYTHONPATH=$(pwd)/CTDopts |
92 | 92 |
93 ############################################################################### | 93 ############################################################################### |
94 ## copy all the test data files to test-data | 94 ## copy all the test data files to test-data |
95 ## most of it (outputs) will be overwritten later, but its needed for | 95 ## most of it (outputs) will be overwritten later, but its needed for |
96 ## prepare_test_data | 96 ## prepare_test_data |
97 ############################################################################### | 97 ############################################################################### |
98 echo "Get test data" | 98 echo "Get test data" |
99 find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete | |
100 | |
99 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ | 101 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ |
100 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ | 102 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ |
101 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ | 103 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ |
102 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ | 104 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ |
103 if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then | 105 if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then |
209 cd ./test-data || exit | 211 cd ./test-data || exit |
210 ../prepare_test_data_manual.sh | 212 ../prepare_test_data_manual.sh |
211 cd - || exit | 213 cd - || exit |
212 | 214 |
213 | 215 |
214 # # # exit | |
215 | |
216 ############################################################################### | 216 ############################################################################### |
217 ## auto generate tests | 217 ## auto generate tests |
218 ############################################################################### | 218 ############################################################################### |
219 | 219 echo "Write test macros to $autotests" |
220 echo "Write test macros to "$autotests | 220 echo "<macros>" > "$autotests" |
221 echo "<macros>" > $autotests | |
222 for i in $(ls *xml |grep -v macros) | 221 for i in $(ls *xml |grep -v macros) |
223 do | 222 do |
224 b=$(basename "$i" .xml) | 223 b=$(basename "$i" .xml) |
225 get_tests2 "$b" >> $autotests | 224 get_tests2 "$b" >> "$autotests" |
226 done | 225 done |
227 echo "</macros>" >> $autotests | 226 echo "</macros>" >> "$autotests" |
228 | 227 |
229 echo "Create test data links" | 228 echo "Create test data links" |
230 link_tmp_files | 229 link_tmp_files |
231 | 230 |
232 # tests for tools using output_prefix parameters can not be auto generated | 231 # tests for tools using output_prefix parameters can not be auto generated |
233 # hence we output the tests for manual curation in macros_test.xml | 232 # hence we output the tests for manual curation in macros_test.xml |
234 # and remove them from the autotests | 233 # and remove them from the autotests |
234 # -> OpenSwathFileSplitter IDRipper MzMLSplitter | |
235 # | |
236 # Furthermore we remove tests for tools without binaries in conda | |
237 # -> MSFragger MaRaClusterAdapter NovorAdapter | |
238 # | |
239 # not able to specify composite test data | |
240 # -> SpectraSTSearchAdapter | |
235 if [[ ! -z "$1" ]]; then | 241 if [[ ! -z "$1" ]]; then |
236 echo "" > macros_discarded_auto.xml | 242 echo "" > macros_discarded_auto.xml |
237 for i in OpenSwathFileSplitter IDRipper MzMLSplitter | 243 for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter |
238 do | 244 do |
239 echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml | 245 echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml |
240 xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml | 246 xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml |
241 echo "</xml>" >> macros_discarded_auto.xml | 247 echo "</xml>" >> macros_discarded_auto.xml |
242 xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp | 248 xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp |
243 mv tmp macros_autotest.xml | 249 mv tmp macros_autotest.xml |
244 done | 250 done |
245 >&2 "discarded autogenerated macros for curation in macros_discarded_auto.xml" | 251 >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" |
246 fi | 252 fi |
247 conda deactivate | 253 conda deactivate |
248 | 254 |
249 ## remove broken symlinks in test-data | 255 ## remove broken symlinks in test-data |
250 find test-data/ -xtype l -delete | 256 find test-data/ -xtype l -delete |