cancel

#!/bin/bash
set -euo pipefail

# Copyright 2019 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
#    this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
#    notice, this list of conditions and the following disclaimer in the
#    documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its
#    contributors may be used to endorse or promote products derived from this
#    software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
# This script is used for cancelling DeepVariant pipelines API operations.
# It  gets the operation ID of the DeepVariant runner, finds all child
# operations, and cancel all together.
#
# Usage:
#   cancel <deepvariant_runner_operation_id>
#


# Label key used by DeepVariant for grouping operations in the same run.
readonly DEEPVARIANT_LABEL_KEY="deepvariant-operation-label"

# If a command fails, we retries it this number of times.
readonly CMD_RETRIES=2

err() {
  RED="\e[0;31m"
  NC='\e[0m'  # No Color
  echo -e "${RED}ERROR:${NC} $*" >&2
}

info() {
  echo "INFO: $*" >&2
}

########################################
# Finds label set by DeepVariant for the given operation.
# Arguments:
#   Pipelines API operation ID.
# Returns:
#   DeepVariant label value.
########################################
function get_deepvariant_label() {
  local operation_id="$1"
  echo "$(gcloud alpha genomics operations describe \
          --format="value(metadata.labels.${DEEPVARIANT_LABEL_KEY})" \
          "${operation_id}")"
}

########################################
# Returns running pipelines API operations with the given label.
# Arguments:
#   label value.
########################################
function get_running_operations_with_label() {
  local label_value="$1"
  echo "$(gcloud alpha genomics operations list \
          --filter="metadata.labels.$DEEPVARIANT_LABEL_KEY=$label_value AND done=false" \
          --format="value(name)" | awk -F "/" '{print $4}' | sort -u)"
}

########################################
# Cancels given pipelines API operations.
# Arguments:
#    Pipeline API operation ID.
########################################
function cancel_operations() {
  local operation_ids="$1"

  for op in ${operation_ids}; do
    is_operation_canceled "${op}" && \
      info "Operation ${op} is already canceled" && \
      continue

    cancel_operation "${op}" "${CMD_RETRIES}" && \
      info "Canceled operation ${op}" || \
      err "Failed to cancel operation ${op}\n"
  done
}

########################################
# Cancels given pipelines API operation.
# Arguments:
#   Pipeline API operation ID.
#   Number of retries in case of failure.
# Returns:
#  0 if the operation has been cancelled, and 1 otherwise.
########################################
function cancel_operation() {
  local operation_id="$1"
  local num_tries="$2"

  for i in $(seq 1 "$((num_tries+1))");do
    err_msg="$(gcloud alpha genomics operations cancel "${operation_id}" \
               --quiet 2>&1)"
    if [[ $? == 0 ]]; then
      return 0
    fi
  done
  err "$err_msg"
  return 1
}

########################################
# Returns true (0) iff pipelines API operation is in canceled.
# Arguments:
#   Pipeline API operation ID.
########################################
function is_operation_canceled() {
  local operation_id="$1"
  local error_code="$(gcloud alpha genomics operations describe \
                      --format="value(error.code)" ${operation_id})"
  # Canceled operations have error code equal to 1.
  if [[ "${error_code}" == 1 ]]; then
    return 0
  fi
  return 1
}

function main() {
  if [[ $# -ne 1 ]]; then
    err "Usage: $0 <deepvariant_runner_operation_id>"
  fi
  local deepvariant_runner_operation_id="$1"

  local label_value="$(get_deepvariant_label "${deepvariant_runner_operation_id}")"
  if [[ -z "${label_value}" ]]; then
    err "Missing required label for operation ${deepvariant_runner_operation_id}"
    exit
  fi
  local running_operations="$(get_running_operations_with_label ${label_value})"
  cancel_operations "${running_operations}"
}

main "$@"