deploy.sh

#!/bin/bash

usage() {
  cat <<EOF
  Usage: $0 --workdir=/path/to/workdir/for/anfisa
EOF
}

for flag in "$@"; do
  case $flag in
  --workdir=*)
    WORKDIR=${flag#*=}
    echo WORKDIR=$WORKDIR
    if [[ $WORKDIR != /* ]]; then
      echo "ERROR! $WORKDIR is a relative path. Specify absolute path to the working directory."
      usage
      exit 1
    fi
    if [ ! -d "$WORKDIR" ]; then
      mkdir -p $WORKDIR
      chmod a+rwx $WORKDIR
    fi
    ASETUP=$WORKDIR/a-setup
    echo A-Setup=$ASETUP
    if [ ! -d "$ASETUP" ]; then
      mkdir -p $ASETUP
      mkdir -p $ASETUP/data/examples
      mkdir -p $ASETUP/vault
      mkdir -p $ASETUP/ui
      mkdir -p $ASETUP/export
      mkdir -p $ASETUP/logs
      chmod -R a+rwx $ASETUP
    fi
    if [ ! -d "$ASETUP/../data" ]; then
      mkdir -p $ASETUP/../data
    fi
    DRUID=$WORKDIR/druid
    echo DRUID=$DRUID
    if [ ! -d "$DRUID" ]; then
      mkdir -p $DRUID
      mkdir -p $DRUID/coordinator
      mkdir -p $DRUID/data
      mkdir -p $DRUID/historical-var
      mkdir -p $DRUID/middlemanager
      mkdir -p $DRUID/router
      mkdir -p $DRUID/broker
      chmod -R a+rwx $DRUID
    fi
    ;;
  esac
done

if [ ! -z "$ASETUP" ] && [ ! -z "$DRUID" ]; then
  chmod -R a+rwx $ASETUP
  chmod -R a+rwx $DRUID

  cp -R doc setup export LICENSE README.md $WORKDIR/

  pushd $ASETUP/data/examples || exit
  if [ ! -d pgp3140_wgs_hlpanel/docs ]; then
    curl -fsSLO https://forome-dataset-public.s3.us-south.cloud-object-storage.appdomain.cloud/pgp3140_wgs_hlpanel.zip
    mkdir pgp3140_wgs_hlpanel
    unzip pgp3140_wgs_hlpanel.zip -d ./pgp3140_wgs_hlpanel
  fi

  pushd $ASETUP/data || exit
  if [ ! -f gene_db.js ]; then
    curl -fsSLO https://forome-dataset-public.s3.us-south.cloud-object-storage.appdomain.cloud/gene_db.zip
    unzip gene_db.zip
  fi

  cd $WORKDIR || exit
  sed "s#ASETUP_PATH#${ASETUP}#g" setup/docker-compose.yml.template | sed "s#DRUID_WORK#${DRUID}#g" >docker-compose.yml

  docker compose >/dev/null
  if [ $? -eq 0 ]; then
    echo "docker compose exists"
    FOR_DOCKER_COMPOSE="docker compose"
  else
    FOR_DOCKER_COMPOSE="docker-compose"
    echo "using docker-compose" >&2
  fi
  $FOR_DOCKER_COMPOSE pull
  $FOR_DOCKER_COMPOSE up -d
  $FOR_DOCKER_COMPOSE ps
  docker exec -it anfisa-backend sh -c 'echo "Initializing ..."; while ! test -f "/anfisa/anfisa.json"; do sleep 5; done'
  docker exec -it anfisa-backend sh -c 'PYTHONPATH=/anfisa/anfisa/ python3 -m app.adm_mongo -c /anfisa/anfisa.json -m GeneDb /anfisa/a-setup/data/gene_db.js'
  docker exec -it anfisa-backend sh -c 'PYTHONPATH=/anfisa/anfisa/ python3 -u -m app.storage -c /anfisa/anfisa.json -m create --reportlines 200 -f -k ws -i /anfisa/a-setup/data/examples/pgp3140_wgs_hlpanel/pgp3140_wgs_hlpanel.cfg PGP3140_HL_GENES'
  docker exec -it anfisa-backend sh -c 'PYTHONPATH=/anfisa/anfisa/ python3 -u -m app.storage -c /anfisa/anfisa.json -m create --reportlines 200 -f -k xl -i /anfisa/a-setup/data/examples/pgp3140_wgs_hlpanel/pgp3140_wgs_hlpanel.cfg XL_PGP3140_HL_GENES'

  popd || exit

  echo "Open URL http://localhost:9010/app/dir - The internal UI"
  echo "Open URL http://localhost:3000 - Anfisa's graphical interface"
else
  echo ERROR! All parameters are required!
  usage
fi