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1 #!/bin/bash
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5 ## **@AUTHOR**: Lain Pavot - lain.pavot@inrae.fr
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6 ## **@DATE**: 22/06/2022
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7
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8
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9 envs_directory=$(pwd)
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10 envs_directory=/tmp/history_metadata_extractor-envs
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11 mkdir -p ${envs_directory}
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12
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13 VENV=${envs_directory}/.manual-venv
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14 CENV=${envs_directory}/.manual-conda
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15
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16 MAMBA_SOLVER=
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17 ## comment to deactivate mamba solver
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18 MAMBA_SOLVER="--experimental-solver libmamba"
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19
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20 ENV_NAME=history_metadata_extractor
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21 XML_PATH=./history_metadata_extractor.xml
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22 SCRIPT_NAME=history_metadata_extractor.py
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23 output_name=out.html
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24 options=" \
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25 -d ./test-data/datasets_attrs.txt \
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26 -j ./test-data/jobs_attrs.txt \
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27 -o ./${output_name} \
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28 "
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29 expected_result=test-data/out.html
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30 runner=python3.10
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31 dependencies=python=3.10.5
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32 miniconda_version=py37_4.12.0-Linux-x86_64
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33
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34
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35
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36 if [ ! -e "${VENV}" ];then
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37 echo "virtualenv not created yet, creating..."
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38 python3 -m virtualenv "${VENV}"
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39 echo "venv created"
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40 else
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41 echo "virtualenv already exist: ok"
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42 fi
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43 . ${VENV}/bin/activate
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44
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45 if [ ! -e "${CENV}" ];then
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46 echo "conda env not created yet, creating..."
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47 if [ ! -e ./install_conda.sh ];then
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48 wget \
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49 -O install_conda.sh \
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50 https://repo.anaconda.com/miniconda/Miniconda3-${miniconda_version}.sh \
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51 ;
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52 fi
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53 bash ./install_conda.sh -b -p "${CENV}"
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54
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55 ${CENV}/bin/conda install -y -n base conda-libmamba-solver
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56 ${CENV}/bin/conda create \
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57 -y \
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58 --quiet \
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59 --override-channels \
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60 --channel conda-forge \
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61 --channel bioconda \
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62 --channel defaults \
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63 --name "${ENV_NAME}" \
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64 ${MAMBA_SOLVER} \
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65 ${dependencies}
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66 echo "conda env created"
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67 fi
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68
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69 echo ""
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70 echo "===== preparing ====="
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71
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72 oldwd=$(pwd)
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73 tmp=$(mktemp -d)
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74 echo "Working in ${tmp}"
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75 files=$(find . -maxdepth 1 -regex "./.+")
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76 cd "${tmp}"
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77 echo "creating links..."
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78 echo "${files}" | xargs -I file ln -s "${oldwd}"/file file
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79 echo "ready to work"
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80
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81 echo ""
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82 echo "===== processing ====="
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83
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84 . "${CENV}/bin/activate" "${CENV}/envs/${ENV_NAME}" ;
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85
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86 ${runner} ./${SCRIPT_NAME} ${options};
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87
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88 echo ""
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89 echo "Error code: ${?}" ;
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90
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91 lines=$(diff "${output_name}" "${expected_result}" 2>&1)
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92
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93 echo ""
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94 echo "===== results ====="
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95
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96 if [ "${lines}" = "" ];then
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97 echo "Result equal to expected."
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98 else
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99 echo "Some lines are different:"
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100 echo "${lines}"
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101 fi
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102
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103 echo ""
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104 echo "===== cleaning ====="
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105
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106 echo "Removing ${tmp}..."
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107 rm -rf "${tmp}"
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108
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109 echo ""
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110 echo "Done."
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