setup.sh

## Script to make it a little easier to run phenotools
# 1. Check that protoc is installed
# 2. Download the latest phenopackets version
# 3. create the generated C++ code
# 4. make the phenotools exectuable

# Not portable, will not work on Windows (sorry)

#1 protoc does not seem to work with pkg-config
# therefore, the following hack
LOC=`protoc`
# if not found, we would see:
NOTFOUND='proto: command not found'
# if it is found, then we should see a help message but not the above ...
L1=${#NOTFOUND}

echo

if [ ${#LOC} \> $L1 ];
then
    echo "[INFO] protoc library found"
    echo
else
    echo "[ERROR] could not find protoc library, terminating script"
    exit 1
fi


#2 download the phenopackets repository
#  note if you want a more recent version, you must delete the current one


if [ -d 'phenopacket-schema' ]; then
    echo "[INFO] found phenopacket-schema directory. "
    echo "[INFO] delete it to download a newer version"
    echo
else
    git clone https://github.com/phenopackets/phenopacket-schema.git
fi

#3 create the C++ code

export PROTO_PATH='phenopacket-schema/src/main/proto'
## Generate the C++ files with protoc
if [ -e 'lib/base.pb.h' ]; then
    echo "[INFO] base.pb.h previously generated"
else
    protoc --proto_path=${PROTO_PATH} --cpp_out=lib ${PROTO_PATH}/base.proto
fi

if [ -e 'lib/interpretation.pb.h' ]; then
    echo "[INFO] interpretation.pb.h previously generated"
else
    protoc --proto_path=${PROTO_PATH} --cpp_out=lib ${PROTO_PATH}/interpretation.proto
fi

if [ -e 'lib/phenopackets.pb.h' ]; then
    echo "[INFO] phenopackets.pb.h previously generated"
else
    protoc --proto_path=${PROTO_PATH} --cpp_out=lib ${PROTO_PATH}/phenopackets.proto
fi

echo

## Make the executable

if [ ! -e build ]; then
    mkdir build
fi
cd build; cmake ..; make
if [ $? -eq 0 ]; then
    echo "make: success!"
else    
    echo "make: failure!"
    exit 1
fi
mv app/phenotools ..

echo

# Run the unit tests
echo "[INFO] Running the unit tests ..."
echo
./lib/tests/phenotools_tests
echo "[INFO] DONE"
echo