setup.sh

#!/bin/bash

export APP_DIR=`pwd`

if [ -z "$PIPELINES_DIR" ]; then
    export PIPELINES_DIR=$APP_DIR
fi

if [ -z "$DATASETS_DIR" ]; then
    export DATASETS_DIR=$APP_DIR/data-example
fi

echo "The directory containing the pipelines is: " "$PIPELINES_DIR"
read -p "Enter 'yes' to confirm the installation or 'no' to exit and reconfigure the variable PIPELINES_DIR " pinput

if [ "$pinput" != "yes" ]; then
	echo Exiting...
	exit 1
fi

echo "The directory containing the datasets is: " $DATASETS_DIR
read -p "Enter 'yes' to confirm the installation or 'no' to exit and reconfigure the variable DATASETS_DIR " dinput

if [ "$dinput" != "yes" ]; then
	echo Exiting...
	exit 1
fi

sed "s|<PIPELINES_DIR>|$PIPELINES_DIR|g" $PIPELINES_DIR/pipelines.template.yaml > $PIPELINES_DIR/pipelines.yaml
# sed "s|<DATASETS_DIR>|$DATASETS_DIR|g" $DATASETS_DIR/datasets.template.yml > $DATASETS_DIR/datasets.yml

for pipe in $( ls ${PIPELINES_DIR}/*/config.template.yaml)
do
    echo $pipe
    # sed -i'' -e "s|<DATASETS_DIR>|$DATASETS_DIR|g" $pipe
    DIRCONF=`dirname $pipe`
    echo $DIRCONF
    sed "s|<DATASETS_DIR>|$DATASETS_DIR|g" $pipe > $DIRCONF/config.yaml
done

sed "s|<APP_DIR>|$APP_DIR|g" $APP_DIR/env.template.sh > $APP_DIR/env.sh
sed -i'' -e "s|<DATASETS_DIR>|$DATASETS_DIR|g" $APP_DIR/env.sh
sed -i'' -e "s|<PIPELINES_DIR>|$PIPELINES_DIR|g" $APP_DIR/env.sh

# source `dirname $CONDA_EXE`/activate || { echo "Failed to activate Conda environment"; exit 1; }

# HASENV=`conda env list | grep pz_pipelines`

# if [ -z "$HASENV" ]; then
#     echo "Create virtual environment..."
#     conda env create -f environment.yml
#     echo "Virtual environment created and packages installed."
# else
#     if [ "$CONDA_FORCE_UPDATE" == "yes" ]; then
#         echo "Virtual environment already exists. Updating..."
#         conda env update --file environment.yml --prune
#     fi
# fi

# for pipe in $( ls ${PIPELINES_DIR}/*/install.sh)
# do
#     echo "Installing: ${pipe}"
#     . "$pipe"
# done

# conda activate pz_pipelines
# echo "Conda Environment: $CONDA_DEFAULT_ENV"