Mercurial > repos > galaxyp > openms_mztabexporter

annotate test-data.sh @ 14:748dfbdf2201 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:34:36 +0000
parents 2735db4dd8d9
children
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9
e270a5689e12 "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
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2
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748dfbdf2201 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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3 # set -x
748dfbdf2201 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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4
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5 VERSION=3.1
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6 FILETYPES="aux/filetypes.txt"
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7 CONDAPKG="https://anaconda.org/bioconda/openms/3.1.0/download/linux-64/openms-3.1.0-h8964181_1.tar.bz2"
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e270a5689e12 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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9 # install conda
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10 if [ -z "$tmp" ]; then
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11 tmp=$(mktemp -d)
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12 created="yes"
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13 fi
e270a5689e12 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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e270a5689e12 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 export OPENMSGIT="$tmp/OpenMS$VERSION.0-git"
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16 export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/"
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17 export OPENMSENV="OpenMS$VERSION-env"
2735db4dd8d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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19 if [ -z "$CTDCONVERTER" ]; then
2735db4dd8d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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20 export CTDCONVERTER="$tmp/CTDConverter"
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21 fi
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23 if [[ -z "$1" ]]; then
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24 autotests="/dev/null"
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25 else
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26 autotests="$1"
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27 fi
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e270a5689e12 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 if type conda > /dev/null; then
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30 true
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31 else
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2735db4dd8d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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32 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
2735db4dd8d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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33 bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
2735db4dd8d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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34 source "$tmp/miniconda/bin/activate"
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35 fi
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36 eval "$(conda shell.bash hook)"
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e270a5689e12 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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e270a5689e12 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 ###############################################################################
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40 ## get
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41 ## - conda environment (for executing the binaries) and
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42 ## - the git clone of OpenMS (for generating the tests)
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43 ###############################################################################
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44
e270a5689e12 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 echo "Clone OpenMS $VERSION sources"
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46 if [[ ! -d $OPENMSGIT ]]; then
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47 if [[ "$created" == "yes" ]]; then
748dfbdf2201 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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48 GIT_DIR=$(mktemp -d --dry-run)
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49 GIT_EXTRA_OPTS="--separate-git-dir=$GIT_DIR"
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50 fi
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51 git clone -b release/$VERSION.0 --depth 1 --recurse-submodules=THIRDPARTY --shallow-submodules $GIT_EXTRA_OPTS https://github.com/OpenMS/OpenMS.git $OPENMSGIT
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52 ## save some space by just keeping the needed binaries
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53 find $OPENMSGIT/THIRDPARTY/ -type f -not \( -name maracluster -o -name spectrast \) -delete
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54 find $OPENMSGIT/THIRDPARTY/ -empty -type d -delete
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55 if [[ "$created" == "yes" ]]; then
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56 rm -rf $GIT_DIR
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57 fi
9
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58 else
13
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59 cd $OPENMSGIT
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60 git pull origin release/$VERSION.0
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61 cd -
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62 fi
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63
e270a5689e12 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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64 echo "Create OpenMS $VERSION conda env"
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65 # TODO currently add lxml (needed by CTDConverter)
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66 # TODO for some reason a to recent openjdk is used
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67 if conda env list | grep "$OPENMSENV"; then
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68 true
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69 else
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70 conda create -y --quiet --solver libmamba --override-channels --strict-channel-priority --channel conda-forge --channel bioconda -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.5 lxml
9
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71 # chmod -R u-w $OPENMSENV
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72 fi
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73 ###############################################################################
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74 ## get the
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75 ## - conda package (for easy access and listing of the OpenMS binaries),
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76 ###############################################################################
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77 echo "Download OpenMS $VERSION package $CONDAPKG"
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78
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79 if [[ ! -d $OPENMSPKG ]]; then
13
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80 mkdir $OPENMSPKG
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81 wget -q -P $OPENMSPKG/ "$CONDAPKG"
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82 tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/
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83 rm $OPENMSPKG/"$(basename $CONDAPKG)"
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84 fi
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85
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86 ###############################################################################
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87 ## Get python libaries for CTD -> Galaxy conversion
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88 ## TODO fix to main repo OR conda packkage if PRs are merged
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89 ###############################################################################
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90 echo "Clone CTDConverter"
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91 if [[ ! -d $CTDCONVERTER ]]; then
13
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92 #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
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93 git clone -b topic/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
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94 else
13
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95 cd $CTDCONVERTER
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96 git pull origin topic/fix-selects2
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97 cd -
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98 fi
13
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99 conda activate $OPENMSENV
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100 cd $CTDCONVERTER
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101 python -m pip install . --no-deps
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102 cd -
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103 conda deactivate
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104
13
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105
14
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106 # # ###############################################################################
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107 # # ## copy all the test data files to test-data
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108 # # ## most of it (outputs) will be overwritten later, but its needed for
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109 # # ## prepare_test_data
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110 # # ###############################################################################
9
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111 echo "Get test data"
14
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112 find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" ! -name MetaboliteSpectralDB.mzML -delete
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113
9
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114 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
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115 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
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116 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
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117 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
13
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118 if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then
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119 wget -nc https://raw.githubusercontent.com/sneumann/OpenMS/master/share/OpenMS/CHEMISTRY/MetaboliteSpectralDB.mzML
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120 # wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
13
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121 mv MetaboliteSpectralDB.mzML test-data/
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122 fi
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123 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
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124 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv
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125
14
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126 # if [ ! -d test-data/pepnovo_models/ ]; then
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127 # mkdir -p /tmp/pepnovo
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128 # wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
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129 # unzip PepNovo.20120423.zip -d /tmp/pepnovo/
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130 # mv /tmp/pepnovo/Models test-data/pepnovo_models/
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131 # rm PepNovo.20120423.zip
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132 # rm -rf /tmp/pepnovo
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133 # fi
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134 ###############################################################################
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135 ## generate ctd files using the binaries in the conda package
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136 ###############################################################################
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137 echo "Create CTD files"
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138 conda activate $OPENMSENV
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139 rm -rf ctd
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140 mkdir -p ctd
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141
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142 for i in $OPENMSPKG/bin/*
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143 do
13
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144 b=$(basename $i)
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145 echo $b
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146 $b -write_ctd ctd/
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147 sed -i -e 's/²/^2/' ctd/$b.ctd
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148 done
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149 ###############################################################################
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150 ## fix ini files: OpenMS test data contains ini files with outdated ini files.
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151 ## e.g. variables might be in different nodes, outdated variables present, new
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152 ## variables missing, ...
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153 ## OpenMS tools fix this on the fly (so its no problem for the OpenMS tests)
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154 ## but it is for the generation of the tests
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155 ## see https://github.com/OpenMS/OpenMS/issues/4462
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156 ###############################################################################
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157 echo "Update test INI files"
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158 for ini in test-data/*ini
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159 do
13
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160 tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
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161 bin=$(which $tool)
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162 if [[ -z $bin ]]; then
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163 >&2 echo "missing binary to convert $ini"
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164 continue
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165 fi
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166 cp $ini $ini.backup
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167 $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
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168 if [[ "$?" -ne "0" ]]; then
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169 >&2 echo "could not convert $ini"
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170 fi
9
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171 done
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172
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173 ###############################################################################
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174 ## create script to create results for the tests and run it
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175 ###############################################################################
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176 # parse data preparation calls from OpenMS sources for a tool with a given id
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177 function prepare_test_data {
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178 # id=$1
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179 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
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180
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181 OLD_OSW_PARAM=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt |sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' |awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep OLD_OSW_PARAM | head -n 1 | sed 's/^[^"]\+//; s/)$//; s/"//g')
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182 # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
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183 cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |
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184 sed "s/\${OLD_OSW_PARAM}/$OLD_OSW_PARAM/" |
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185 grep -v "\.ini\.json" |
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186 sed 's/.ini.json /ini /' |
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187 sed 's/#.*$//'|
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188 sed 's/^\s*//; s/\s*$//' |
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189 grep -v "^$" |
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190 awk '{printf("%s@NEWLINE@", $0)}' |
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191 sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' |
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192 sed 's/degenerate_cases\///' |
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193 egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" |
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194 grep add_test |
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195 egrep "TOPP|UTILS" |
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196 sed 's@${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/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
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203
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204 if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
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205 >&2 echo " skip failing "$test_id
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206 continue
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207 fi
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208
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209 line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
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210 # line="$(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 $test_id.stdout)\";fi"
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214 done
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215 }
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216
9
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217 echo "Create test shell script"
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218
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219 echo -n "" > prepare_test_data.sh
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220 echo 'export COMET_BINARY="comet"' >> prepare_test_data.sh
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221 echo 'export CRUX_BINARY="crux"' >> prepare_test_data.sh
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222 echo 'export FIDOCHOOSEPARAMS_BINARY="FidoChooseParameters"' >> prepare_test_data.sh
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223 echo 'export FIDO_BINARY="Fido"' >> prepare_test_data.sh
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224 echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh
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225
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226 echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh
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227 echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-3.5/MSFragger-3.5.jar"'>> prepare_test_data.sh
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228 echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh
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229 echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh
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230 echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh
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231 echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh
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232 echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh
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233 echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh
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234 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
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235 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh
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236 echo 'export SAGE_BINARY=sage' >> prepare_test_data.sh
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237
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238 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh
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239
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240 echo "Execute test shell script"
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241 chmod u+x prepare_test_data.sh
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242 cd ./test-data || exit
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243 ../prepare_test_data.sh
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244 cd - || exit
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245
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246
13
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247 # ###############################################################################
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248 # ## create/update test data for the manually generated tests
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249 # ## - run convert once with the manual tests only and
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250 # ## - update test-data (needs to run 2x)
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251 # ###############################################################################
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252 echo "Execute test shell script for manually curated tests"
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253 chmod u+x prepare_test_data_manual.sh
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254 cd ./test-data || exit
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255 ../prepare_test_data_manual.sh
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256 cd - || exit
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257
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258
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259 ###############################################################################
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260 ## auto generate tests
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261 ###############################################################################
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262
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263 echo "Write test macros to $autotests"
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264 echo "<macros>" > "$autotests"
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265
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266 for i in $(ls ctd/*ctd)
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267 do
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268 b=$(basename "$i" .ctd)
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269 ./get_tests.py --id "$b" --cmake "$OPENMSGIT"/src/tests/topp/CMakeLists.txt "$OPENMSGIT"/src/tests/topp/THIRDPARTY/third_party_tests.cmake >> "$autotests"
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270 wc -l "$autotests"
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271 done
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272 echo "</macros>" >> "$autotests"
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273
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274 # tests for tools using output_prefix parameters can not be auto generated
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275 # hence we output the tests for manual curation in macros_test.xml
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276 # and remove them from the autotests
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277 # -> OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator
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278 # TODO reevaluate in >2.8
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279 # - https://github.com/OpenMS/OpenMS/pull/5873
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280 # - https://github.com/OpenMS/OpenMS/pull/5912
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281 #
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282 # Furthermore we remove tests for tools without binaries in conda
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283 # -> MSFragger MaRaClusterAdapter NovorAdapter
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284 #
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285 # not able to specify composite test data
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286 # -> SpectraSTSearchAdapter
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287 echo "Discard some tests"
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288 if [[ ! -z "$1" ]]; then
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289 echo "" > macros_discarded_auto.xml
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290 for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
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291 do
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292 echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml
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293 xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml
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294 echo "</xml>" >> macros_discarded_auto.xml
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295 xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
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296 mv tmp macros_autotest.xml
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297 done
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298 >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"
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299 fi
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300 conda deactivate
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301
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302 ## remove broken symlinks in test-data
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303 find test-data/ -xtype l -delete
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304
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305 if [[ "$created" == "yes" ]]; then
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306 echo "Removing temporary directory"
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307 rm -rf "$tmp"
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308 fi