diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..121947b --- /dev/null +++ b/Makefile @@ -0,0 +1,14 @@ + + +## **@AUTHOR**: Lain Pavot - lain.pavot@inrae.fr +## **@DATE**: 22/06/2022 + + +test: + python3 ./history_metadata_extractor.py \ + -d ./test-data/datasets_attrs.txt \ + -j ./test-data/jobs_attrs.txt \ + -o ./test-data/result.html \ + ; + firefox ./test-data/result.html + diff --git a/manual_test.sh b/manual_test.sh new file mode 100755 index 0000000..409af4a --- /dev/null +++ b/manual_test.sh @@ -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." diff --git a/planemo_test.sh b/planemo_test.sh new file mode 100755 index 0000000..a264e50 --- /dev/null +++ b/planemo_test.sh @@ -0,0 +1,37 @@ +#!/bin/sh + + +## **@AUTHOR**: Lain Pavot - lain.pavot@inrae.fr +## **@DATE**: 22/06/2022 + +VENV=.venv +TEST_DIR=/tmp/history_metadata_extractor + +if [ ! -d ".venv" ];then + python3 -m virtualenv ${VENV} ; +fi + + +. ${VENV}/bin/activate + +if [ "$(which planemo)" = "" ];then + pip install planemo ; +fi + + +if [ ! -d "${TEST_DIR}" ];then + planemo conda_install --conda_prefix ${TEST_DIR} . ; +fi + +planemo lint --fail_level error ./*.xml || exit 255 ; + +planemo test \ + --install_galaxy \ + --conda_dependency_resolution \ + --conda_prefix ${TEST_DIR} \ + --no_cleanup \ + --no_wait \ + --simultaneous_uploads \ + ${TEST_FLAGS} \ + history_metadata_extractor.xml \ +; diff --git a/static/app.template.html b/static/app.template.html index a30967a..cd3d15c 100644 --- a/static/app.template.html +++ b/static/app.template.html @@ -40,17 +40,17 @@ style="overflow-y: auto ; height: 100%" > {table_list} - + + + \ No newline at end of file