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comparison manual_test.sh @ 0:426b0f85a311 draft

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" master branch Updating"
author lain
date Tue, 19 Jul 2022 07:36:57 +0000
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-1:000000000000 0:426b0f85a311
1 #!/bin/bash
2
3
4
5 ## **@AUTHOR**: Lain Pavot - lain.pavot@inrae.fr
6 ## **@DATE**: 22/06/2022
7
8
9 envs_directory=$(pwd)
10 envs_directory=/tmp/history_metadata_extractor-envs
11 mkdir -p ${envs_directory}
12
13 VENV=${envs_directory}/.manual-venv
14 CENV=${envs_directory}/.manual-conda
15
16 MAMBA_SOLVER=
17 ## comment to deactivate mamba solver
18 MAMBA_SOLVER="--experimental-solver libmamba"
19
20 ENV_NAME=history_metadata_extractor
21 XML_PATH=./history_metadata_extractor.xml
22 SCRIPT_NAME=history_metadata_extractor.py
23 output_name=out.html
24 options=" \
25 -d ./test-data/datasets_attrs.txt \
26 -j ./test-data/jobs_attrs.txt \
27 -o ./${output_name} \
28 "
29 expected_result=test-data/out.html
30 runner=python3.10
31 dependencies=python=3.10.5
32 miniconda_version=py37_4.12.0-Linux-x86_64
33
34
35
36 if [ ! -e "${VENV}" ];then
37 echo "virtualenv not created yet, creating..."
38 python3 -m virtualenv "${VENV}"
39 echo "venv created"
40 else
41 echo "virtualenv already exist: ok"
42 fi
43 . ${VENV}/bin/activate
44
45 if [ ! -e "${CENV}" ];then
46 echo "conda env not created yet, creating..."
47 if [ ! -e ./install_conda.sh ];then
48 wget \
49 -O install_conda.sh \
50 https://repo.anaconda.com/miniconda/Miniconda3-${miniconda_version}.sh \
51 ;
52 fi
53 bash ./install_conda.sh -b -p "${CENV}"
54
55 ${CENV}/bin/conda install -y -n base conda-libmamba-solver
56 ${CENV}/bin/conda create \
57 -y \
58 --quiet \
59 --override-channels \
60 --channel conda-forge \
61 --channel bioconda \
62 --channel defaults \
63 --name "${ENV_NAME}" \
64 ${MAMBA_SOLVER} \
65 ${dependencies}
66 echo "conda env created"
67 fi
68
69 echo ""
70 echo "===== preparing ====="
71
72 oldwd=$(pwd)
73 tmp=$(mktemp -d)
74 echo "Working in ${tmp}"
75 files=$(find . -maxdepth 1 -regex "./.+")
76 cd "${tmp}"
77 echo "creating links..."
78 echo "${files}" | xargs -I file ln -s "${oldwd}"/file file
79 echo "ready to work"
80
81 echo ""
82 echo "===== processing ====="
83
84 . "${CENV}/bin/activate" "${CENV}/envs/${ENV_NAME}" ;
85
86 ${runner} ./${SCRIPT_NAME} ${options};
87
88 echo ""
89 echo "Error code: ${?}" ;
90
91 lines=$(diff "${output_name}" "${expected_result}" 2>&1)
92
93 echo ""
94 echo "===== results ====="
95
96 if [ "${lines}" = "" ];then
97 echo "Result equal to expected."
98 else
99 echo "Some lines are different:"
100 echo "${lines}"
101 fi
102
103 echo ""
104 echo "===== cleaning ====="
105
106 echo "Removing ${tmp}..."
107 rm -rf "${tmp}"
108
109 echo ""
110 echo "Done."