Mercurial > repos > galaxyp > openms_idrtcalibration

annotate generate-foo.sh @ 12:28805cf9b024 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:15:58 +0000
parents 8bd1fe67a9b1
children 7ff821b34ebc
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8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 #!/usr/bin/env bash
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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2
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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3 # parse test definitions from OpenMS sources for a tool with a given id
8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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4 function get_tests2 {
12
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5 id=$1
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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6 >&2 echo "generate tests for $id"
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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7 echo '<xml name="autotest_'"$id"'">'
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8
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9 # get the tests from the CMakeLists.txt
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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10 # 1st remove some tests
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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11 # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399
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8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
12
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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13 # - several tools with duplicated input (leads to conflict when linking)
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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14 # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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15 # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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16 # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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17 # - some input files are originally in a subdir (degenerated cases/), but not in test-data
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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18 # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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19 # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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20 # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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21 # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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22 CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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23 sed 's@${DATA_DIR_SHARE}/@@g' |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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24 grep -v 'OpenSwathMzMLFileCacher .*-convert_back' |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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25 sed 's/${TMP_RIP_PATH}/""/' |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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26 grep -v "MaRaClusterAdapter.*-consensus_out"|
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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27 grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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28 sed 's@degenerate_cases/@@g' |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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29 grep -v 'TOPP_SeedListGenerator_3"' |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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30 egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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31 egrep -v '"TOPP_FeatureFinderIdentification_4"' |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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32 sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/')
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8bd1fe67a9b1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34
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35 # grep -v 'FileFilter.*-spectra:select_polarity ""' |
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36 # grep -v 'MassTraceExtractor_2.ini ' |
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37 # grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |
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38 # grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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39 # grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |
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40 # grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |
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41 # grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |
10
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12
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43 # 1st part is a dirty hack to join lines containing a single function call, e.g.
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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44 # addtest(....
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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45 # ....)
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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46 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' |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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47 grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE" | while read -r line
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48 do
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49 line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g')
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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50 # >&2 echo $line
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51 test_id=$(echo "$line" | cut -d" " -f 1)
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52 tool_id=$(echo "$line" | cut -d" " -f 2)
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53 if [[ $test_id =~ _out_?[0-9]? ]]; then
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54 >&2 echo " skip $test_id $line"
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55 continue
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56 fi
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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57 if [[ ${id,,} != ${tool_id,,} ]]; then
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58 >&2 echo " skip $test_id ($id != $tool_id) $line"
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59 continue
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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60 fi
10
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61
12
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62 #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1)
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63 if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
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64 >&2 echo " skip failing "$test_id
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65 continue
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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66 fi
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67 tes=" <test>\n"
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68 line=$(fix_tmp_files "$line")
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69 line=$(unique_files "$line")
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70 # >&2 echo $line
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71 #if there is an ini file then we use this to generate the test
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72 #otherwise the ctd file is used
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73 #other command line parameters are inserted later into this xml
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74 if grep -lq "\-ini" <<<"$line"; then
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75 ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/')
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76 ini="test-data/$ini"
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77 else
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78 ini="ctd/$tool_id.ctd"
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79 fi
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80 cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
10
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81
12
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82 ctdtmp=$(mktemp)
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83 #echo python3 fill_ctd_clargs.py --ctd $ini $cli
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84 # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
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85 # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli"
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86 eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp"
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87 # echo $ctdtmp
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88 # >&2 cat $ctdtmp
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89 testtmp=$(mktemp)
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90 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
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91 cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
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92 rm $ctdtmp $testtmp
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93
12
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94 #> /dev/null
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95
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96 #rm $testtmp
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97 done
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98 echo '</xml>'
10
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99 }
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100
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101 #some tests use the same file twice which does not work in planemo tests
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102 #hence we create symlinks for each file used twice
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103 function unique_files {
12
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104 line=$@
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105 for arg in $@
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106 do
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107 if [[ ! -f "test-data/$arg" ]]; then
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108 continue
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109 fi
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110 cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
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111 while [[ $cnt -gt 1 ]]; do
10
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112 new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./")
12
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113 ln -fs $arg test-data/$new_arg
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114 line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/")
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115 cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
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116 done
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117 done
10
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118
12
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119 echo $line
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120 }
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121
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122 # options of out_type selects need to be fixed to Galaxy data types
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123 function fix_out_type {
12
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124 grep "^$1" "$2" | awk '{print $2}'
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125 }
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126
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127 #OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file.
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128 #problem: the extension of the tmp files is unusable for test generation.
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129 #unfortunately the extensions used in the DIFF lines are not always usable for the CLI
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130 #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
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131 #this function replaces the tmp file by the expected file.
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132 function fix_tmp_files {
12
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133 # >&2 echo "FIX $line"
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134 ret=""
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135 for a in $@; do
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136 if [[ ! $a =~ .tmp$ ]]; then
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137 ret="$ret $a"
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138 continue
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139 fi
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140 # >&2 echo " a "$a
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141 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")
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142 # >&2 echo " g "$g
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143 in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g)
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144 # >&2 echo " in1 "$in1
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145 if [[ "$a" != "$in1" ]]; then
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146 ret="$ret $a"
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147 continue
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148 fi
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149 in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g)
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150 in2=$(basename $in2 | sed 's/)$//')
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151 # >&2 echo " in2 "$in2
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152 if [[ -f "test-data/$in2" ]]; then
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153 ln -fs "$in1" "test-data/$in2"
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154 ret="$ret $in2"
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155 else
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156 ret="$ret $a"
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157 fi
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158 done
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159 # >&2 echo "--> $ret"
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160 echo "$ret"
10
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161 }
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162
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163 function link_tmp_files {
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164 # note this also considers commented lines (starting with a #)
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165 # because of tests where the diff command is commented and we
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166 # still want to use the extension of these files
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167 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@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep "\${DIFF}" | while read -r line
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168 do
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169 in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$line)
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170 in1=$(basename $in1 | sed 's/)$//')
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171 in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$line)
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172 in2=$(basename $in2 | sed 's/)$//')
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173 if [[ "$in1" == "$in2" ]]; then
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174 >&2 echo "not linking equal $in1 $in2"
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175 continue
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176 fi
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177 ln -f -s $in1 test-data/$in2
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178 done
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179 for i in test-data/*.tmp
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180 do
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181 if [ ! -e test-data/$(basename $i .tmp) ]; then
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182 ln -s $(basename $i) test-data/$(basename $i .tmp)
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183 #ln -s $(basename $i) test-data/$(basename $i .tmp)
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184 else
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185 ln -fs $(basename $i) test-data/$(basename $i .tmp)
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186 fi
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187 done
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188 }
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189
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190
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191
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192 # parse data preparation calls from OpenMS sources for a tool with a given id
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193 function prepare_test_data {
12
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194 # id=$1
10
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195 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
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196
12
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197 # TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
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198 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@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' |
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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199 sed 's/degenerate_cases\///' |
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200 egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" |
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201 grep add_test |
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202 egrep "TOPP|UTILS" |
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203 sed 's@${DATA_DIR_SHARE}/@@g;'|
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204 sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'|
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205 sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'|
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206 sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
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207 while read line
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208 do
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209 test_id=$(echo "$line" | sed 's/add_test(//; s/"//g; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
10
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210
12
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211 if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
28805cf9b024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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212 >&2 echo " skip failing "$test_id
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213 continue
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214 fi
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215
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216 line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
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217 # line="$(fix_tmp_files $line)"
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218 echo 'echo executing "'$test_id'"'
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219 echo "$line > $test_id.stdout 2> $test_id.stderr"
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220 echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/ /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"
10
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221 done
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222 }