handler.py

import json
import urllib.parse
import boto3
import os

import dynamodb_operations
import s3_restore
import sqs_operations

s3 = boto3.client('s3')

snakemake_table = os.environ['SNAKEMAKE_TABLE']
status_table = os.environ['STATUS_TABLE']
sqs_queue_url = os.environ['SQS_QUEUE_URL']

def handler(event, context):
  # Get the object from the event and show its content type
  bucket = event['Records'][0]['s3']['bucket']['name']
  key = urllib.parse.unquote_plus(event['Records'][0]['s3']['object']['key'], encoding='utf-8')
  try:
      content_object = s3.get_object(Bucket=bucket, Key=key)
      file_content = content_object['Body'].read().decode('utf-8')
      json_content = json.loads(file_content)
      execution_id = json_content['execution_id']
      bcl_paths = json_content['bcl_paths']
      print("CONTENT TYPE: " + content_object['ContentType'] + " Execution ID: " + json_content['execution_id'])
      s3_restore.s3_restore(bcl_paths, execution_id, status_table)
      dynamodb_operations.populate_job_details(execution_id, snakemake_table)
      sqs_operations.send_message(execution_id, sqs_queue_url)
      return {
        'statusCode': 200,
        'body':       json.dumps(json_content)
      }
  except Exception as e:
      print(e)
      print(str(json_content))
      print('Error getting object {} from bucket {}. Make sure they exist and your bucket is in the same region as this function.'.format(key, bucket))
      raise e