--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manual_test.sh	Tue Jul 19 07:36:57 2022 +0000
@@ -0,0 +1,110 @@
+#!/bin/bash
+
+
+
+## **@AUTHOR**: Lain Pavot - lain.pavot@inrae.fr
+## **@DATE**: 22/06/2022
+
+
+envs_directory=$(pwd)
+envs_directory=/tmp/history_metadata_extractor-envs
+mkdir -p ${envs_directory}
+
+VENV=${envs_directory}/.manual-venv
+CENV=${envs_directory}/.manual-conda
+
+MAMBA_SOLVER=
+## comment to deactivate mamba solver
+MAMBA_SOLVER="--experimental-solver libmamba"
+
+ENV_NAME=history_metadata_extractor
+XML_PATH=./history_metadata_extractor.xml
+SCRIPT_NAME=history_metadata_extractor.py
+output_name=out.html
+options=" \
+  -d ./test-data/datasets_attrs.txt \
+  -j ./test-data/jobs_attrs.txt \
+  -o ./${output_name} \
+"
+expected_result=test-data/out.html
+runner=python3.10
+dependencies=python=3.10.5
+miniconda_version=py37_4.12.0-Linux-x86_64
+
+
+
+if [ ! -e "${VENV}" ];then
+  echo "virtualenv not created yet, creating..."
+  python3 -m virtualenv "${VENV}"
+  echo "venv created"
+else
+  echo "virtualenv already exist: ok"
+fi
+. ${VENV}/bin/activate
+
+if [ ! -e "${CENV}" ];then
+  echo "conda env not created yet, creating..."
+  if [ ! -e ./install_conda.sh ];then
+    wget \
+      -O install_conda.sh \
+      https://repo.anaconda.com/miniconda/Miniconda3-${miniconda_version}.sh \
+    ;
+  fi
+  bash ./install_conda.sh -b -p "${CENV}"
+
+  ${CENV}/bin/conda install -y -n base conda-libmamba-solver
+  ${CENV}/bin/conda create \
+    -y \
+    --quiet \
+    --override-channels \
+    --channel conda-forge \
+    --channel bioconda \
+    --channel defaults \
+    --name "${ENV_NAME}" \
+    ${MAMBA_SOLVER} \
+    ${dependencies}
+  echo "conda env created"
+fi
+
+echo ""
+echo "===== preparing ====="
+
+oldwd=$(pwd)
+tmp=$(mktemp -d)
+echo "Working in ${tmp}"
+files=$(find . -maxdepth 1 -regex "./.+")
+cd "${tmp}"
+echo "creating links..."
+echo "${files}" | xargs -I file ln -s "${oldwd}"/file file
+echo "ready to work"
+
+echo ""
+echo "===== processing ====="
+
+. "${CENV}/bin/activate" "${CENV}/envs/${ENV_NAME}" ;
+
+${runner} ./${SCRIPT_NAME} ${options};
+
+echo ""
+echo "Error code: ${?}" ;
+
+lines=$(diff "${output_name}" "${expected_result}" 2>&1)
+
+echo ""
+echo "===== results ====="
+
+if [ "${lines}" = "" ];then
+  echo "Result equal to expected."
+else
+  echo "Some lines are different:"
+  echo "${lines}"
+fi
+
+echo ""
+echo "===== cleaning ====="
+
+echo "Removing ${tmp}..."
+rm -rf "${tmp}"
+
+echo ""
+echo "Done."