Mercurial > repos > galaxyp > openms_metaboliteadductdecharger

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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 19:11:25 +0000
parents ebc51eae71cd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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68e3317532cb "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
68e3317532cb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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68e3317532cb "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
68e3317532cb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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4 function get_tests2 {
6
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5 id=$1
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6 >&2 echo "generate tests for $id"
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7 echo '<xml name="autotest_'"$id"'">'
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8
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9 # get the tests from the CMakeLists.txt
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10 # 1st remove some tests
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11 # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
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12 # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
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13 # - several tools with duplicated input (leads to conflict when linking)
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14 # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
ebc51eae71cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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15 # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
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16 # - some input files are originally in a subdir (degenerated cases/), but not in test-data
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17 # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
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18 # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
7e7e6a5b9c01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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19 # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869
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20 CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |
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21 sed 's@${DATA_DIR_SHARE}/@@g' |
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22 grep -v 'OpenSwathMzMLFileCacher .*-convert_back' |
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23 sed 's/${TMP_RIP_PATH}/""/' |
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24 grep -v "MaRaClusterAdapter.*-consensus_out"|
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25 grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
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26 sed 's@degenerate_cases/@@g' |
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27 egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' |
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28 sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
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29 grep -v '"TOPP_SiriusAdapter_10"')
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30
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31 # 1st part is a dirty hack to join lines containing a single function call, e.g.
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32 # addtest(....
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33 # ....)
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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' |
ebc51eae71cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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35 grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE" | while read -r line
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36 do
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37 line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g')
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38 # >&2 echo $line
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39 test_id=$(echo "$line" | cut -d" " -f 1)
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40 tool_id=$(echo "$line" | cut -d" " -f 2)
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41 # >&2 echo "test_id $test_id"
6
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42 if [[ $test_id =~ _out_?[0-9]? ]]; then
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43 >&2 echo " skip $test_id $line"
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44 continue
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45 fi
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46 if [[ ${id,,} != ${tool_id,,} ]]; then
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47 >&2 echo " skip $test_id ($id != $tool_id) $line"
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48 continue
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49 fi
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50
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51 #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1)
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52 if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
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53 >&2 echo " skip failing "$test_id
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54 continue
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55 fi
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56 tes=" <test>\n"
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57 line=$(fix_tmp_files "$line")
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58 line=$(unique_files "$line")
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59 # >&2 echo LINE $line
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60 #if there is an ini file then we use this to generate the test
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61 #otherwise the ctd file is used
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62 #other command line parameters are inserted later into this xml
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63 if grep -lq "\-ini" <<<"$line"; then
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64 ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/')
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65 ini="test-data/$ini"
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66 else
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67 ini="ctd/$tool_id.ctd"
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68 fi
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69 # >&2 echo "========================================================"
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70 # >&2 echo "USING ini $ini"
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71 cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
4
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72
6
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73 ctdtmp=$(mktemp)
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74 # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
8
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75 # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli"
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76 eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp"
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77 # >&2 echo $ctdtmp
6
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78 # >&2 cat $ctdtmp
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79 testtmp=$(mktemp)
8
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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"
7e7e6a5b9c01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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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
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82 echo "<!-- $test_id -->"
6
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83 cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
8
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84
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85 rm "$ctdtmp" "$testtmp"
4
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86
6
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87 #> /dev/null
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88
ebc51eae71cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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89 #rm $testtmp
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90 done
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91 echo '</xml>'
4
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92 }
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93
68e3317532cb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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94 #some tests use the same file twice which does not work in planemo tests
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95 #hence we create symlinks for each file used twice
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96 function unique_files {
6
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97 line=$@
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98 for arg in $@
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99 do
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100 if [[ ! -f "test-data/$arg" ]]; then
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101 continue
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102 fi
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103 cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
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104 while [[ $cnt -gt 1 ]]; do
4
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105 new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./")
6
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106 ln -fs $arg test-data/$new_arg
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107 line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/")
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108 cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
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109 done
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diff changeset
110 done
4
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111
6
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112 echo $line
4
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113 }
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114
68e3317532cb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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115 # options of out_type selects need to be fixed to Galaxy data types
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116 function fix_out_type {
6
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117 grep "^$1" "$2" | awk '{print $2}'
4
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118 }
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119
68e3317532cb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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120 #OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file.
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121 #problem: the extension of the tmp files is unusable for test generation.
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122 #unfortunately the extensions used in the DIFF lines are not always usable for the CLI
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123 #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
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124 #this function replaces the tmp file by the expected file.
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125 function fix_tmp_files {
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126 # >&2 echo "FIX $line"
6
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127 ret=""
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128 for a in $@; do
8
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129 # >&2 echo " a "$a
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130 if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then
6
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131 ret="$ret $a"
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132 continue
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133 fi
8
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134 diff_line=$(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")
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135 # >&2 echo " diff_line "$diff_line
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136 in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line)
6
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137 # >&2 echo " in1 "$in1
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138 if [[ "$a" != "$in1" ]]; then
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139 ret="$ret $a"
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140 continue
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141 fi
8
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142 in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line)
6
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143 in2=$(basename $in2 | sed 's/)$//')
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144 # >&2 echo " in2 "$in2
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145 if [[ -f "test-data/$in2" ]]; then
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146 ln -fs "$in1" "test-data/$in2"
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147 ret="$ret $in2"
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148 else
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149 ret="$ret $a"
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150 fi
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151 done
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152 # >&2 echo "--> $ret"
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153 echo "$ret"
4
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154 }
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155
68e3317532cb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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156 function link_tmp_files {
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157 # note this also considers commented lines (starting with a #)
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158 # because of tests where the diff command is commented and we
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159 # still want to use the extension of these files
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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@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep "\${DIFF}" | while read -r line
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161 do
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162 in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$line)
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163 in1=$(basename $in1 | sed 's/)$//')
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164 in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$line)
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165 in2=$(basename $in2 | sed 's/)$//')
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166 if [[ "$in1" == "$in2" ]]; then
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167 >&2 echo "not linking equal $in1 $in2"
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168 continue
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169 fi
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170 ln -f -s $in1 test-data/$in2
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171 done
8
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172
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173 find test-data/ -name "*.tmp" -print0 |
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174 while IFS= read -r -d '' i; do
4
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175 if [ ! -e test-data/$(basename $i .tmp) ]; then
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176 ln -s $(basename $i) test-data/$(basename $i .tmp)
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177 else
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178 ln -fs $(basename $i) test-data/$(basename $i .tmp)
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179 fi
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180 done
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181 }
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182
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183
68e3317532cb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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184
68e3317532cb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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185 # parse data preparation calls from OpenMS sources for a tool with a given id
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186 function prepare_test_data {
6
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187 # id=$1
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188 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
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189
8
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190 # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
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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@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' |
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192 sed 's/degenerate_cases\///' |
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193 egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" |
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194 grep add_test |
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195 egrep "TOPP|UTILS" |
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196 sed 's@${DATA_DIR_SHARE}/@@g;'|
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197 sed 's@${TMP_RIP_PATH}@./@g'|
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198 sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'|
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199 sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
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200 while read line
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201 do
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202 test_id=$(echo "$line" | sed 's/add_test(//; s/"//g; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
4
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203
6
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204 if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
ebc51eae71cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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205 >&2 echo " skip failing "$test_id
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206 continue
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207 fi
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208
ebc51eae71cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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209 line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
ebc51eae71cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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210 # line="$(fix_tmp_files $line)"
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211 echo 'echo executing "'$test_id'"'
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212 echo "$line > $test_id.stdout 2> $test_id.stderr"
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213 echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/ /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"
4
68e3317532cb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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214 done
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215 }