data/legacy_deploy_k8.sh

#!/usr/bin/env bash

################################################################################
#
#   ASKCOS Deployment Utilities for Kubernetes (deprecated)
#
#    ~ To streamline deployment commands ~
#
################################################################################

echo
echo -e "\033[91m************************* DEPRECATION WARNING *************************\033[00m"
echo "This deployment script and the associated kubernetes configuration are"
echo "no longer supported, and should only be used to deploy ASKCOS 2020.07."
echo
echo "Instead, please use the Helm chart located in the ./helm directory."
echo
echo "See ./helm/README.md for basic installation instructions."
echo -e "\033[91m***********************************************************************\033[00m"

set -e  # exit with nonzero exit code if anything fails

usage() {
  echo
  echo "Deployment Utilities for ASKCOS (deprecated)"
  echo
  echo "Specify a task to perform, along with any desired options."
  echo
  echo "Valid commands:"
  echo "    deploy:                   performs initial deployment steps using http"
  echo "    apply:                    apply all k8 configurations"
  echo "    seed-db:                  seed mongo database with data"
  echo "    clean:                    stop and remove a currently running deployment"
  echo
  echo "Optional arguments:"
  echo "    -b,--buyables             buyables data for reseeding mongo database"
  echo "    -c,--chemicals            chemicals data for reseeding mongo database"
  echo "    -x,--reactions            reactions data for reseeding mongo database"
  echo "    -r,--retro-templates      retrosynthetic template data for reseeding mongo database"
  echo "    -t,--forward-templates    forward template data for reseeding mongo database"
  echo "    -i|--drop-indexes         drop any existing indexes when indexing database with index-db command"
  echo "    -u|--username             deploy token username for docker registry"
  echo "    -p|--password             deploy token password for docker registry"
  echo "    -n|--ignore-diff          ignore differences in config files (.env and customization)"
  echo
  echo "Examples:"
  echo "    bash deploy_k8.sh deploy"
  echo "    bash deploy_k8.sh update -v x.y.z"
  echo "    bash deploy_k8.sh seed-db -r retro-templates.json.gz -b buyables.json.gz"
  echo "    bash deploy_k8.sh clean"
  echo
}

# Create environment variable files from examples if they don't exist
if [ ! -f ".env" ]; then
  cp .env.example .env
fi
if [ ! -f "customization" ]; then
  cp customization.example customization
fi

# Default argument values
VERSION=""
BUYABLES=""
CHEMICALS=""
REACTIONS=""
RETRO_TEMPLATES=""
FORWARD_TEMPLATES=""
DROP_INDEXES=false
IGNORE_DIFF=false

COMMANDS=""
while (( "$#" )); do
  case "$1" in
    -h|--help|help)
      usage
      exit
      ;;
    -v|--version)
      VERSION=$2
      shift 2
      ;;
    -b|--buyables)
      BUYABLES=$2
      shift 2
      ;;
    -c|--chemicals)
      CHEMICALS=$2
      shift 2
      ;;
    -x|--reactions)
      REACTIONS=$2
      shift 2
      ;;
    -r|--retro-templates)
      RETRO_TEMPLATES=$2
      shift 2
      ;;
    -t|--forward-templates)
      FORWARD_TEMPLATES=$2
      shift 2
      ;;
    -i|--drop-indexes)
      DROP_INDEXES=true
      shift 1
      ;;
    -u|--username)
      DEPLOY_TOKEN_USERNAME=$2
      shift 2
      ;;
    -p|--password)
      DEPLOY_TOKEN_PASSWORD=$2
      shift 2
      ;;
    -n|--ignore-diff)
      IGNORE_DIFF=true
      shift 1
      ;;
    --) # end argument parsing
      shift
      break
      ;;
    -*) # any other flag
      echo "Error: Unsupported flag $1" >&2  # print to stderr
      exit 1
      ;;
    *) # preserve positional arguments
      COMMANDS="$COMMANDS $1"
      shift
      ;;
  esac
done

# Set positional arguments in their proper place
eval set -- "$COMMANDS"

# Define various functions
diff-env() {
  if [ "$IGNORE_DIFF" = "true" ]; then
    return 0
  fi

  output1="$(diff -u .env .env.example)" || true
  if [ -n "$output1" ]; then
    echo -e "\033[91m*** WARNING ***\033[00m"
    echo "Local .env file is different from .env.example"
    echo "This could be due to changes to the example or local changes."
    echo "Please review the diff to determine if any changes are necessary:"
    echo
    echo "$output1"
    echo
  fi

  output2="$(diff -u customization customization.example)" || true
  if [ -n "$output2" ]; then
    echo -e "\033[91m*** WARNING ***\033[00m"
    echo "Local customization file is different from customization.example"
    echo "This could be due to changes to the example or local changes."
    echo "Please review the diff to determine if any changes are necessary:"
    echo
    echo "$output2"
    echo
  fi

  if [ -n "$output1" ] || [ -n "$output2" ]; then
    echo "Local configuration files differ from examples (see above)! What would you like to do?"
    echo "  (c)ontinue without changes  (use -n flag to skip prompt and continue in the future)"
    echo "  (o)verwrite your local files with the examples  (the above diff(s) will be applied)"
    echo "  (s)top and make changes manually"
    read -rp '>>> ' response
    case "$response" in
      [Cc])
        echo "Continuing without changes."
        ;;
      [Oo])
        echo "Overwriting local files."
        cp .env.example .env
        cp customization.example customization
        ;;
      [Ss])
        echo "Stopping."
        exit 1
        ;;
      *)
        echo "Unrecognized option. Stopping."
        exit 1
        ;;
    esac
  fi
}

create-secret() {
  set +e
  if ! kubectl get secret/regcred &> /dev/null; then
    echo "Creating new secret..."
    if [ -z "$DEPLOY_TOKEN_USERNAME" ]; then
      read -rp 'Deploy token username: ' DEPLOY_TOKEN_USERNAME
    fi
    if [ -z "$DEPLOY_TOKEN_PASSWORD" ]; then
      read -rp 'Deploy token password: ' DEPLOY_TOKEN_PASSWORD
    fi
    kubectl create secret docker-registry regcred --docker-server=registry.gitlab.com --docker-username=$DEPLOY_TOKEN_USERNAME --docker-password=$DEPLOY_TOKEN_PASSWORD
  fi
  set -e
}

start-db-services() {
  echo "Starting database services..."
  kubectl apply -f legacy_k8/mysql
  kubectl apply -f legacy_k8/mongo
  kubectl apply -f legacy_k8/redis
  kubectl apply -f legacy_k8/rabbitmq
  echo "Start up complete."
  echo
}

wait-for-mongo() {
  while [[ $(kubectl get pods -l pod=mongo -o 'jsonpath={..status.conditions[?(@.type=="Ready")].status}') != "True" ]]; do
    echo "Waiting for mongo db to start..." && sleep 1
  done
}

wait-for-django() {
  while [[ $(kubectl get pods -l pod=django -o 'jsonpath={..status.conditions[?(@.type=="Ready")].status}') != "True" ]]; do
    echo "Waiting for django app to start..." && sleep 1
  done

  kubectl get svc/django
  echo
}

set-db-defaults() {
  # Set default values for seeding database if values are not already defined
  BUYABLES=${BUYABLES:-default}
  RETRO_TEMPLATES=${RETRO_TEMPLATES:-default}
  FORWARD_TEMPLATES=${FORWARD_TEMPLATES:-default}
  CHEMICALS=${CHEMICALS:-default}
}

run-mongo-js() {
  # arg 1 is js command
  kubectl exec $mongo -- bash -c 'mongo --username ${MONGO_USER} --password ${MONGO_PW} --authenticationDatabase admin ${MONGO_HOST}/askcos --quiet --eval '"'$1'"
}

seed-db-collection() {
  # arg 1 is collection name
  # arg 2 is file path
  kubectl exec $mongo -- bash -c 'gunzip -c '$2' | mongoimport --host ${MONGO_HOST} --username ${MONGO_USER} --password ${MONGO_PW} --authenticationDatabase admin --db askcos --collection '$1' --type json --jsonArray --drop'
}

copy-file() {
  # Convenience function for copying files using kubectl exec
  # Not using kubectl cp because it does not support symlinks
  src_pod=$1
  src_path=$2
  src_cont=$3
  dst_pod=$4
  dst_path=$5
  dst_cont=$6

  if [ -n "$src_pod" ] && [ -z "$dst_pod" ]; then
    # copying from pod to local
    if [ -n "$src_cont" ]; then
      kubectl exec "$src_pod" -c "$src_cont" -- tar cf - -C "$(dirname "$src_path")" "$(basename "$src_path")" | tar xf - -C "$(dirname "$dst_path")"
    else
      kubectl exec "$src_pod" -- tar cf - -C "$(dirname "$src_path")" "$(basename "$src_path")" | tar xf - -C "$(dirname "$dst_path")"
    fi
  elif [ -n "$src_pod" ] && [ -n "$dst_pod" ]; then
    # copying from pod to pod, copy to /tmp first
    tmp="$(mktemp -d /tmp/askcos.XXXXXXXX)/$(basename "$src_path")"
    if [ -n "$src_cont" ]; then
      kubectl exec "$src_pod" -c "$src_cont" -- tar cf - -C "$(dirname "$src_path")" "$(basename "$src_path")" | tar xf - -C "$(dirname "$tmp")"
    else
      kubectl exec "$src_pod" -- tar cf - -C "$(dirname "$src_path")" "$(basename "$src_path")" | tar xf - -C "$(dirname "$tmp")"
    fi
    src_path="$tmp"
  fi

  if [ -n "$dst_pod" ]; then
    # copying to a pod
    if [ -n "$dst_cont" ]; then
      tar cf - -C "$(dirname "$src_path")" "$(basename "$src_path")" | kubectl exec -i "$dst_pod" -c "$dst_cont" -- tar xf - -C "$(dirname "$dst_path")"
    else
      tar cf - -C "$(dirname "$src_path")" "$(basename "$src_path")" | kubectl exec -i "$dst_pod" -- tar xf - -C "$(dirname "$dst_path")"
    fi
  fi

  if [ -d "$tmp" ]; then
    rm -rf "$tmp"
  fi
}

seed-db() {
  if [ -z "$BUYABLES" ] && [ -z "$CHEMICALS" ] && [ -z "$REACTIONS" ] && [ -z "$RETRO_TEMPLATES" ] && [ -z "$FORWARD_TEMPLATES" ]; then
    echo "Nothing to seed!"
    echo "Example usages:"
    echo "    bash deploy_k8.sh seed-db -r default                  seed only the default retro templates"
    echo "    bash deploy_k8.sh seed-db -r <templates.json.gz>      seed retro templates from local file <templates.json.gz>"
    echo "    bash deploy_k8.sh set-db-defaults seed-db             seed all default collections"
    return
  fi

  echo "Seeding mongo database..."

  django=$(kubectl get pod -l pod=django -o jsonpath="{.items[0].metadata.name}")
  mongo=$(kubectl get pod -l pod=mongo -o jsonpath="{.items[0].metadata.name}")

  if [ -n "$BUYABLES" ]; then
    if [ "$BUYABLES" = "default" ]; then
      echo "Loading default buyables data in background..."
      buyables_src="/usr/local/askcos-core/askcos/data/buyables/buyables.json.gz"
      buyables_dest="/data/buyables.json.gz"
      copy-file "$django" "$buyables_src" django "$mongo" "$buyables_dest" ""
    elif [ -n "$BUYABLES" ]; then
      echo "Loading buyables data from $BUYABLES in background..."
      buyables_src=$BUYABLES
      buyables_dest="/data/$(basename "$BUYABLES")"
      copy-file "" "$buyables_src" "" "$mongo" "$buyables_dest" ""
    fi
    seed-db-collection buyables "$buyables_dest" &> seed-buyables.log &
  fi

  if [ -n "$CHEMICALS" ]; then
    if [ "$CHEMICALS" = "default" ]; then
      echo "Loading default chemicals data in background..."
      chemicals_src="/usr/local/askcos-core/askcos/data/historian/chemicals.json.gz"
      chemicals_dest="/data/chemicals.json.gz"
      copy-file "$django" "$chemicals_src" django "$mongo" "$chemicals_dest" ""
    elif [ -n "$CHEMICALS" ]; then
      echo "Loading chemicals data from $CHEMICALS in background..."
      chemicals_src=$CHEMICALS
      chemicals_dest="/data/$(basename "$CHEMICALS")"
      copy-file "" "$chemicals_src" "" "$mongo" "$chemicals_dest" ""
    fi
    seed-db-collection chemicals "$chemicals_dest" &> seed-chemicals.log &
  fi

  if [ -n "$REACTIONS" ]; then
    if [ "$REACTIONS" = "default" ]; then
      echo "Loading default reactions data in background..."
      reactions_src="/usr/local/askcos-core/askcos/data/historian/reactions.json.gz"
      reactions_dest="/data/reactions.json.gz"
      copy-file "$django" "$reactions_src" django "$mongo" "$reactions_dest" ""
    elif [ -n "$REACTIONS" ]; then
      echo "Loading reactions data from $REACTIONS in background..."
      reactions_src=$REACTIONS
      reactions_dest="/data/$(basename "$REACTIONS")"
      copy-file "" "$reactions_src" "" "$mongo" "$reactions_dest" ""
    fi
    seed-db-collection reactions "$reactions_dest" &> seed-reactions.log &
  fi

  if [ -n "$RETRO_TEMPLATES" ]; then
    if [ "$RETRO_TEMPLATES" = "default" ]; then
      echo "Loading default retrosynthetic templates..."
      retro_src="/usr/local/askcos-core/askcos/data/templates/retro.templates.json.gz"
      retro_dest="/data/retro.templates.json.gz"
      copy-file "$django" "$retro_src" django "$mongo" "$retro_dest" ""
    elif [ -n "$RETRO_TEMPLATES" ]; then
      echo "Loading retrosynthetic templates from $RETRO_TEMPLATES ..."
      retro_src=$RETRO_TEMPLATES
      retro_dest="/data/$(basename "$RETRO_TEMPLATES")"
      copy-file "" "$retro_src" "" "$mongo" "$retro_dest" ""
    fi
    seed-db-collection retro_templates "$retro_dest"
  fi

  if [ -n "$FORWARD_TEMPLATES" ]; then
    if [ "$FORWARD_TEMPLATES" = "default" ]; then
      echo "Loading default retrosynthetic templates..."
      forward_src="/usr/local/askcos-core/askcos/data/templates/forward.templates.json.gz"
      forward_dest="/data/forward.templates.json.gz"
      copy-file "$django" "$forward_src" django "$mongo" "$forward_dest" ""
    elif [ -n "$FORWARD_TEMPLATES" ]; then
      echo "Loading retrosynthetic templates from $FORWARD_TEMPLATES ..."
      forward_src=$FORWARD_TEMPLATES
      forward_dest="/data/$(basename "$FORWARD_TEMPLATES")"
      copy-file "" "$forward_src" "" "$mongo" "$forward_dest" ""
    fi
    seed-db-collection forward_templates "$forward_dest"
  fi

  index-db
  echo "Seeding complete."
  echo
}

index-db() {
  if [ "$DROP_INDEXES" = "true" ]; then
    echo "Dropping existing indexes in mongo database..."
    run-mongo-js 'db.buyables.dropIndexes()'
    run-mongo-js 'db.chemicals.dropIndexes()'
    run-mongo-js 'db.reactions.dropIndexes()'
    run-mongo-js 'db.retro_templates.dropIndexes()'
  fi
  echo "Adding indexes to mongo database..."
  run-mongo-js 'db.buyables.createIndex({smiles: 1, source: 1})'
  run-mongo-js 'db.chemicals.createIndex({smiles: 1, template_set: 1})'
  run-mongo-js 'db.reactions.createIndex({reaction_id: 1, template_set: 1})'
  run-mongo-js 'db.retro_templates.createIndex({index: 1, template_set: 1})'
  echo "Indexing complete."
  echo
}

count-mongo-docs() {
  mongo=$(kubectl get pod -l pod=mongo -o jsonpath="{.items[0].metadata.name}")
  echo "Buyables collection:          $(run-mongo-js "db.buyables.countDocuments({})" | tr -d '\r') / 280469 expected (default)"
  echo "Chemicals collection:         $(run-mongo-js "db.chemicals.countDocuments({})" | tr -d '\r') / 17562038 expected (default)"
  echo "Reactions collection:         $(run-mongo-js "db.reactions.countDocuments({})" | tr -d '\r') / 0 expected (default)"
  echo "Retro template collection:    $(run-mongo-js "db.retro_templates.countDocuments({})" | tr -d '\r') / 163723 expected (default)"
  echo "Forward template collection:  $(run-mongo-js "db.forward_templates.countDocuments({})" | tr -d '\r') / 17089 expected (default)"
}

create-config-maps() {
  echo "Creating config maps..."
  kubectl create configmap django-env --from-env-file=.env --dry-run=client -o yaml | kubectl apply -f -
  kubectl create configmap django-customization --from-env-file=customization --dry-run=client -o yaml | kubectl apply -f -
}

start-web-services() {
  echo "Starting web services..."
  kubectl apply -f legacy_k8/django
  echo "Start up complete."
  echo
}

start-tf-server() {
  echo "Starting tensorflow serving worker..."
  kubectl apply -f legacy_k8/tf-serving
  echo "Start up complete."
  echo
}

start-celery-workers() {
  echo "Starting celery workers..."
  kubectl apply -f legacy_k8/celery
  echo "Start up complete."
  echo
}

# Handle positional arguments, which should be commands
if [ $# -eq 0 ]; then
  # No arguments
  echo "Must provide a valid task, e.g. deploy|apply|update."
  echo "See 'deploy_k8.sh help' for more options."
  exit 1;
else
  for arg in "$@"
  do
    case "$arg" in
      create-secret | start-db-services | start-web-services | set-db-defaults | seed-db | count-mongo-docs | \
      start-tf-server | start-celery-workers | index-db | create-config-maps | diff-env )
        # This is a defined function, so execute it
        $arg
        ;;
      deploy)
        # Normal first deployment, do everything
        diff-env
        create-secret
        create-config-maps
        start-db-services
        start-web-services
        wait-for-mongo
        wait-for-django
        set-db-defaults
        seed-db  # Must occur after starting app
        start-tf-server
        start-celery-workers
        ;;
      update)
        # Update an existing configuration, database seeding is not performed
        echo "Not implemented."
        ;;
      config)
        # Update config maps for django app
        diff-env
        create-config-maps
        ;;
      apply)
        # (Re)apply all configurations, no database seeding
        start-db-services
        start-web-services
        start-tf-server
        start-celery-workers
        ;;
      clean)
        # Clean up current deployment
        echo "This will delete all deployments, services, and pods. Are you sure you want to continue?"
        read -rp 'Continue (y/N): ' response
        case "$response" in
          [Yy] | [Yy][Ee][Ss])
            echo "Cleaning deployment."
            kubectl delete deployments -l app.kubernetes.io/part-of=askcos
            kubectl delete services -l app.kubernetes.io/part-of=askcos
            kubectl delete pods -l app.kubernetes.io/part-of=askcos
            ;;
          *)
            echo "Doing nothing."
            ;;
        esac
        ;;
      *)
        echo "Error: Unsupported command $1" >&2  # print to stderr
        exit 1
        ;;
    esac
  done
fi