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comparison test-data.sh @ 18:f4be248c3d47 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:03:29 +0000
parents abffdfee3021
children 91da6dd00bbc
comparison
equal deleted inserted replaced
17:abffdfee3021 18:f4be248c3d47
1 #!/usr/bin/env bash 1 #!/usr/bin/env bash
2 2
3 VERSION=2.6 3 VERSION=2.8
4 FILETYPES="filetypes.txt" 4 FILETYPES="aux/filetypes.txt"
5 CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2" 5 CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2"
6 6
7 # import the magic 7 # import the magic
8 . ./generate-foo.sh 8 . ./generate-foo.sh
9 9
10 # install conda 10 # install conda
11 if [ -z "$tmp" ]; then 11 if [ -z "$tmp" ]; then
12 tmp=$(mktemp -d) 12 tmp=$(mktemp -d)
13 created="yes" 13 created="yes"
14 fi 14 fi
15 15
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="OpenMS$VERSION-env" 18 export OPENMSENV="OpenMS$VERSION-env"
19 19
20 if [ -z "$CTDCONVERTER" ]; then 20 if [ -z "$CTDCONVERTER" ]; then
21 export CTDCONVERTER="$tmp/CTDConverter" 21 export CTDCONVERTER="$tmp/CTDConverter"
22 fi 22 fi
23 23
24 if [[ -z "$1" ]]; then 24 if [[ -z "$1" ]]; then
25 autotests="/dev/null" 25 autotests="/dev/null"
26 else 26 else
27 autotests="$1" 27 autotests="$1"
28 fi 28 fi
29 29
30 if type conda > /dev/null; then 30 if type conda > /dev/null; then
31 true 31 true
32 else 32 else
33 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 33 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
34 bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" 34 bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
35 source "$tmp/miniconda/bin/activate" 35 source "$tmp/miniconda/bin/activate"
36 fi 36 fi
37 eval "$(conda shell.bash hook)" 37 eval "$(conda shell.bash hook)"
38 38
39 39
40 ############################################################################### 40 ###############################################################################
43 ## - the git clone of OpenMS (for generating the tests) 43 ## - the git clone of OpenMS (for generating the tests)
44 ############################################################################### 44 ###############################################################################
45 45
46 echo "Clone OpenMS $VERSION sources" 46 echo "Clone OpenMS $VERSION sources"
47 if [[ ! -d $OPENMSGIT ]]; then 47 if [[ ! -d $OPENMSGIT ]]; then
48 git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT 48 # TODO >2.8 reenable original release branch .. also in else branch
49 cd $OPENMSGIT 49 # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917
50 git submodule init 50 # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
51 git submodule update 51 git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT
52 cd - 52 cd $OPENMSGIT
53 else 53 git submodule init
54 cd $OPENMSGIT 54 git submodule update
55 git pull origin release/$VERSION.0 55 cd -
56 cd - 56 else
57 cd $OPENMSGIT
58 git pull origin release/$VERSION.0-plus
59 cd -
57 fi 60 fi
58 61
59 echo "Create OpenMS $VERSION conda env" 62 echo "Create OpenMS $VERSION conda env"
60 # TODO currently add lxml (needed by CTDConverter) 63 # TODO currently add lxml (needed by CTDConverter)
61 # TODO for some reason a to recent openjdk is used 64 # TODO for some reason a to recent openjdk is used
62 if conda env list | grep "$OPENMSENV"; then 65 if conda env list | grep "$OPENMSENV"; then
63 true 66 true
64 else 67 else
65 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml 68 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml
66 # chmod -R u-w $OPENMSENV 69 # chmod -R u-w $OPENMSENV
67 fi 70 fi
68 ############################################################################### 71 ###############################################################################
69 ## get the 72 ## get the
70 ## - conda package (for easy access and listing of the OpenMS binaries), 73 ## - conda package (for easy access and listing of the OpenMS binaries),
71 ############################################################################### 74 ###############################################################################
72 echo "Download OpenMS $VERSION package $CONDAPKG" 75 echo "Download OpenMS $VERSION package $CONDAPKG"
73 76
74 if [[ ! -d $OPENMSPKG ]]; then 77 if [[ ! -d $OPENMSPKG ]]; then
75 mkdir $OPENMSPKG 78 mkdir $OPENMSPKG
76 wget -q -P $OPENMSPKG/ "$CONDAPKG" 79 wget -q -P $OPENMSPKG/ "$CONDAPKG"
77 tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/ 80 tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/
78 rm $OPENMSPKG/"$(basename $CONDAPKG)" 81 rm $OPENMSPKG/"$(basename $CONDAPKG)"
79 fi 82 fi
80 83
81 ############################################################################### 84 ###############################################################################
82 ## Get python libaries for CTD -> Galaxy conversion 85 ## Get python libaries for CTD -> Galaxy conversion
83 ## TODO fix to main repo OR conda packkage if PRs are merged 86 ## TODO fix to main repo OR conda packkage if PRs are merged
84 ############################################################################### 87 ###############################################################################
85 echo "Clone CTDConverter" 88 echo "Clone CTDConverter"
86 if [[ ! -d $CTDCONVERTER ]]; then 89 if [[ ! -d $CTDCONVERTER ]]; then
87 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter 90 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
88 git clone -b topic/fix-selects https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER 91 git clone -b topic/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
89 else 92 else
90 cd $CTDCONVERTER 93 cd $CTDCONVERTER
91 git pull origin topic/fix-selects 94 git pull origin topic/fix-selects2
92 cd - 95 cd -
93 fi 96 fi
94 97 conda activate $OPENMSENV
95 ############################################################################### 98 cd $CTDCONVERTER
96 ## copy all the test data files to test-data 99 python -m pip install . --no-deps
97 ## most of it (outputs) will be overwritten later, but its needed for 100 cd -
98 ## prepare_test_data 101 conda deactivate
99 ############################################################################### 102
103
104 # ###############################################################################
105 # ## copy all the test data files to test-data
106 # ## most of it (outputs) will be overwritten later, but its needed for
107 # ## prepare_test_data
108 # ###############################################################################
100 echo "Get test data" 109 echo "Get test data"
101 find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete 110 find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete
102 111
103 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ 112 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
104 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ 113 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
105 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ 114 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
106 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ 115 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
107 if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then 116 if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then
108 wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML 117 wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
109 mv MetaboliteSpectralDB.mzML test-data/ 118 mv MetaboliteSpectralDB.mzML test-data/
110 fi 119 fi
111 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt 120 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
112 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv 121 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv
113 122
114 if [ ! -d test-data/pepnovo_models/ ]; then 123 if [ ! -d test-data/pepnovo_models/ ]; then
115 mkdir -p /tmp/pepnovo 124 mkdir -p /tmp/pepnovo
116 wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip 125 wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
117 unzip PepNovo.20120423.zip -d /tmp/pepnovo/ 126 unzip PepNovo.20120423.zip -d /tmp/pepnovo/
118 mv /tmp/pepnovo/Models test-data/pepnovo_models/ 127 mv /tmp/pepnovo/Models test-data/pepnovo_models/
119 rm PepNovo.20120423.zip 128 rm PepNovo.20120423.zip
120 rm -rf /tmp/pepnovo 129 rm -rf /tmp/pepnovo
121 fi 130 fi
122 ############################################################################### 131 ###############################################################################
123 ## generate ctd files using the binaries in the conda package 132 ## generate ctd files using the binaries in the conda package
124 ############################################################################### 133 ###############################################################################
125 echo "Create CTD files" 134 echo "Create CTD files"
126 conda activate $OPENMSENV 135 conda activate $OPENMSENV
127 rm -rf ctd 136 rm -rf ctd
128 mkdir -p ctd 137 mkdir -p ctd
129 138
130 # TODO because of https://github.com/OpenMS/OpenMS/issues/4641
131 # this needs to be done from within test-data
132 cd test-data
133 for i in $OPENMSPKG/bin/* 139 for i in $OPENMSPKG/bin/*
134 do 140 do
135 b=$(basename $i) 141 b=$(basename $i)
136 echo $b 142 echo $b
137 $b -write_ctd ../ctd/ 143 $b -write_ctd ctd/
138 sed -i -e 's/²/^2/' ../ctd/$b.ctd 144 sed -i -e 's/²/^2/' ctd/$b.ctd
139 done 145 done
140 cd -
141 ############################################################################### 146 ###############################################################################
142 ## fix ini files: OpenMS test data contains ini files with outdated ini files. 147 ## fix ini files: OpenMS test data contains ini files with outdated ini files.
143 ## e.g. variables might be in different nodes, outdated variables present, new 148 ## e.g. variables might be in different nodes, outdated variables present, new
144 ## variables missing, ... 149 ## variables missing, ...
145 ## OpenMS tools fix this on the fly (so its no problem for the OpenMS tests) 150 ## OpenMS tools fix this on the fly (so its no problem for the OpenMS tests)
147 ## see https://github.com/OpenMS/OpenMS/issues/4462 152 ## see https://github.com/OpenMS/OpenMS/issues/4462
148 ############################################################################### 153 ###############################################################################
149 echo "Update test INI files" 154 echo "Update test INI files"
150 for ini in test-data/*ini 155 for ini in test-data/*ini
151 do 156 do
152 tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/') 157 tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
153 bin=$(which $tool) 158 bin=$(which $tool)
154 if [[ -z $bin ]]; then 159 if [[ -z $bin ]]; then
155 >&2 echo "missing binary to convert $ini" 160 >&2 echo "missing binary to convert $ini"
156 continue 161 continue
157 fi 162 fi
158 cp $ini $ini.backup 163 cp $ini $ini.backup
159 $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr 164 $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
160 if [[ "$?" -ne "0" ]]; then 165 if [[ "$?" -ne "0" ]]; then
161 >&2 echo "could not convert $ini" 166 >&2 echo "could not convert $ini"
162 fi 167 fi
163 done 168 done
164 169
165 ############################################################################### 170 ###############################################################################
166 ## create script to create results for the tests and run it 171 ## create script to create results for the tests and run it
167 ############################################################################### 172 ###############################################################################
190 195
191 ## prepare_test_data > tmp_test_data.sh 196 ## prepare_test_data > tmp_test_data.sh
192 ## # remove calls not needed for the tools listed in any .list file 197 ## # remove calls not needed for the tools listed in any .list file
193 ## echo LIST $LIST 198 ## echo LIST $LIST
194 ## if [ ! -z "$LIST" ]; then 199 ## if [ ! -z "$LIST" ]; then
195 ## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') 200 ## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
196 ## else 201 ## else
197 ## REX=".*" 202 ## REX=".*"
198 ## fi 203 ## fi
199 ## echo REX $REX 204 ## echo REX $REX
200 ## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh 205 ## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
201 ## rm tmp_test_data.sh 206 ## rm tmp_test_data.sh
202 207
205 cd ./test-data || exit 210 cd ./test-data || exit
206 ../prepare_test_data.sh 211 ../prepare_test_data.sh
207 cd - || exit 212 cd - || exit
208 213
209 214
210 ############################################################################### 215 # ###############################################################################
211 ## create/update test data for the manually generated tests 216 # ## create/update test data for the manually generated tests
212 ## - run convert once with the manual tests only and 217 # ## - run convert once with the manual tests only and
213 ## - update test-data (needs to run 2x) 218 # ## - update test-data (needs to run 2x)
214 ############################################################################### 219 # ###############################################################################
215 echo "Execute test shell script for manually curated tests" 220 echo "Execute test shell script for manually curated tests"
216 chmod u+x prepare_test_data_manual.sh 221 chmod u+x prepare_test_data_manual.sh
217
218 cd ./test-data || exit 222 cd ./test-data || exit
219 ../prepare_test_data_manual.sh 223 ../prepare_test_data_manual.sh
220 cd - || exit 224 cd - || exit
221 225
222 226
223 ############################################################################### 227 ###############################################################################
224 ## auto generate tests 228 ## auto generate tests
225 ############################################################################### 229 ###############################################################################
230
226 echo "Write test macros to $autotests" 231 echo "Write test macros to $autotests"
227 echo "<macros>" > "$autotests" 232 echo "<macros>" > "$autotests"
228 for i in $(ls *xml |grep -v macros) 233
234 for i in $(ls ctd/*ctd)
229 do 235 do
230 b=$(basename "$i" .xml) 236 b=$(basename "$i" .ctd)
231 get_tests2 "$b" >> "$autotests" 237 get_tests2 "$b" >> "$autotests"
232 done 238 done
233 echo "</macros>" >> "$autotests" 239 echo "</macros>" >> "$autotests"
234 240
235 echo "Create test data links" 241 # echo "Create test data links"
236 link_tmp_files 242 # Breaks DecoyDatabase
243 # link_tmp_files
237 244
238 # tests for tools using output_prefix parameters can not be auto generated 245 # tests for tools using output_prefix parameters can not be auto generated
239 # hence we output the tests for manual curation in macros_test.xml 246 # hence we output the tests for manual curation in macros_test.xml
240 # and remove them from the autotests 247 # and remove them from the autotests
241 # -> OpenSwathFileSplitter IDRipper MzMLSplitter 248 # -> OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator
249 # TODO reevaluate in >2.8
250 # - https://github.com/OpenMS/OpenMS/pull/5873
251 # - https://github.com/OpenMS/OpenMS/pull/5912
242 # 252 #
243 # Furthermore we remove tests for tools without binaries in conda 253 # Furthermore we remove tests for tools without binaries in conda
244 # -> MSFragger MaRaClusterAdapter NovorAdapter 254 # -> MSFragger MaRaClusterAdapter NovorAdapter
245 # 255 #
246 # not able to specify composite test data 256 # not able to specify composite test data
247 # -> SpectraSTSearchAdapter 257 # -> SpectraSTSearchAdapter
248 if [[ ! -z "$1" ]]; then 258 if [[ ! -z "$1" ]]; then
249 echo "" > macros_discarded_auto.xml 259 echo "" > macros_discarded_auto.xml
250 for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter 260 for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
251 do 261 do
252 echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml 262 echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml
253 xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml 263 xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml
254 echo "</xml>" >> macros_discarded_auto.xml 264 echo "</xml>" >> macros_discarded_auto.xml
255 xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp 265 xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
256 mv tmp macros_autotest.xml 266 mv tmp macros_autotest.xml
257 done 267 done
258 >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" 268 >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"
259 fi 269 fi
260 conda deactivate 270 conda deactivate
261 271
262 ## remove broken symlinks in test-data 272 ## remove broken symlinks in test-data
263 find test-data/ -xtype l -delete 273 find test-data/ -xtype l -delete
264 274
265 # if [ ! -z "$created" ]; then 275 if [ ! -z "$created" ]; then
266 # echo "Removing temporary directory" 276 echo "Removing temporary directory"
267 # rm -rf "$tmp" 277 rm -rf "$tmp"
268 # fi 278 fi