#!/bin/bash -e

export AWS_DEFAULT_OUTPUT=text

create_stack() {

  local stack_name=${1}

  local template_name=${2}

  local ResourcePrefix=${3}

  local ResourcePrefix_lowercase=$(echo ${ResourcePrefix} | tr '[:upper:]' '[:lower:]')

  aws cloudformation create-stack --stack-name ${stack_name} --template-body file://${template_name} --parameters ParameterKey=ResourcePrefix,ParameterValue=${ResourcePrefix} ParameterKey=ResourcePrefixLowercase,ParameterValue=${ResourcePrefix_lowercase} --capabilities CAPABILITY_NAMED_IAM --no-enable-termination-protection; aws cloudformation wait stack-create-complete --stack-name ${stack_name}

}

clone_and_commit() {

  local stack_name=${1}

  local repo_http_url=$(aws cloudformation describe-stacks --stack-name ${stack_name} --query 'Stacks[].Outputs[?OutputKey==`RepoHttpUrl`].OutputValue')

  git init .; git remote add origin ${repo_http_url}

  git add *; git commit -m "first commit"; git push --set-upstream origin master

}

wait_for_pipeline() {

  local pipeline_name=${1}

  local commit_id=${2}

  local message="Max attempts reached. Pipeline execution failed for commit: ${commit_id}"

  for i in {1..60}; do

    stage_status=$(aws codepipeline list-pipeline-executions --pipeline-name ${pipeline_name} --query 'pipelineExecutionSummaries[?sourceRevisions[0].revisionId==`'${commit_id}'`].status')

    if [ "${stage_status}" == "InProgress" ] || [ -z "${stage_status}" ]; then

      printf '.'

      sleep 30

    elif [ "${stage_status}" == "Succeeded" ]; then

      message="CodePipeline execution succeeded for commit: ${commit_id}"

      break

    elif [ "${stage_status}" == "Failed" ]; then

      message="CodePipeline execution Failed for commit: ${commit_id}"

      break

    fi

  done

  printf "\n${message}\n"

  if [ "${stage_status}" == "Failed" ]; then exit 1; fi

}

copy_unpack_zip() {

  local source_artifact=${1}

  local dest_prefix=${2}

  echo "Unpacking ${source_artifact} to ${dest_prefix}"

  aws s3 cp ${source_artifact} ./temporary.zip

  mkdir stage

  pushd stage; unzip ../temporary.zip; popd

  aws s3 sync stage/ ${dest_prefix}

  rm -rf stage temporary.zip

}

copy_and_upload() {

  local source_artifact=${1}

  local dest_artifact=${2}

  local filename=${3}

  aws s3 cp ${source_artifact} ${filename}

  aws s3 cp ${filename} ${dest_artifact}

  rm ${filename}

}

copy_test_data() {

  local artifact_bucket=${1}

  local artifact_key_prefix=${2}

  local pipe_stackname=${3}

  local data_lake_bucket=$(aws cloudformation describe-stacks --stack-name ${pipe_stackname} --query 'Stacks[].Outputs[?OutputKey==`DataLakeBucket`].OutputValue' --output text)

  copy_unpack_zip s3://${artifact_bucket}/${artifact_key_prefix}/tcga/tcga-clinical.zip s3://${data_lake_bucket}/

  copy_unpack_zip s3://${artifact_bucket}/${artifact_key_prefix}/tcga/tcga-cnv.zip s3://${data_lake_bucket}/

  copy_unpack_zip s3://${artifact_bucket}/${artifact_key_prefix}/tcga/tcga-expression.zip s3://${data_lake_bucket}/

  copy_unpack_zip s3://${artifact_bucket}/${artifact_key_prefix}/tcga/tcga-mutation.zip s3://${data_lake_bucket}/

  copy_unpack_zip s3://${artifact_bucket}/${artifact_key_prefix}/tcga/tcia-metadata.zip s3://${data_lake_bucket}/

  copy_unpack_zip s3://${artifact_bucket}/${artifact_key_prefix}/tcga/tcga-summary.zip s3://${data_lake_bucket}/

  copy_and_upload s3://${artifact_bucket}/${artifact_key_prefix}/annotation/clinvar/clinvar.vcf.gz s3://${data_lake_bucket}/annotation/vcf/clinvar/clinvar.vcf.gz clinvar.vcf.gz 

  copy_and_upload s3://${artifact_bucket}/${artifact_key_prefix}/variants/vcf/variants.vcf.gz s3://${data_lake_bucket}/variants/vcf/variants.vcf.gz variants.vcf.gz

  copy_and_upload s3://${artifact_bucket}/${artifact_key_prefix}/variants/1kg/ALL.chr22.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.filtNA.vcf.gz s3://${data_lake_bucket}/variants/1kg/ALL.chr22.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.filtNA.vcf.gz ALL.chr22.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.filtNA.vcf.gz  

  copy_and_upload s3://${artifact_bucket}/${artifact_key_prefix}/references/hg38/Homo_sapiens_assembly38.fasta s3://${data_lake_bucket}/references/hg38/Homo_sapiens_assembly38.fasta Homo_sapiens_assembly38.fasta 

}

setup() {

  local resource_prefix=$1

  local artifact_bucket=$2

  local artifact_key_prefix=$3

  local dir_prefix="GenomicsAnalysis"

  local zone_dir="${dir_prefix}Zone"

  local pipe_dir="${dir_prefix}Pipe"

  local code_dir="${dir_prefix}Code"

  local zone_stackname=${resource_prefix}-LandingZone

  local pipe_stackname=${resource_prefix}-Pipeline

  # Create stacks

  create_stack "${zone_stackname}" "${zone_dir}/zone_cfn.yml" "${resource_prefix}"

  create_stack "${pipe_stackname}" "${pipe_dir}/pipe_cfn.yml" "${resource_prefix}"

  # Clone and commit resources

  cd "${pipe_dir}"; clone_and_commit "${zone_stackname}"; cd ..

  cd "${code_dir}"; clone_and_commit "${pipe_stackname}";

  # Get the last commit id

  commit_id=$(git log -1 --pretty=format:%H)

  cd ..

  # Get pipeline name

  pipeline_name=$(aws cloudformation describe-stack-resource --stack-name ${pipe_stackname} --logical-resource-id CodePipeline --query 'StackResourceDetail.PhysicalResourceId')

  # Copy Test Data

  copy_test_data "${artifact_bucket}" "${artifact_key_prefix}" "${pipe_stackname}"

  # Wait for pipeline execution using commit id

  wait_for_pipeline "${pipeline_name}" "${commit_id}"

  # Run Crawlers for TCGA data

  "${code_dir}/run_crawlers.sh" "${resource_prefix}"

}

project_name=${PROJECT_NAME:-GenomicsAnalysis}

setup "$project_name" "${ARTIFACT_BUCKET}" "${ARTIFACT_KEY_PREFIX}"