Our use of Athena has been abandoned in favor of Aurora. New API: https://github.com/serratus-bio/serratus-summary-api

serratus-summary-api-athena

Endpoints with examples

• /family/<family_id>
  • /family/Coronaviridae
  • /family/Coronaviridae?identityMin=80&identityMax=90
• /sequence/<sequence_id>
  • /sequence/AY874537_3000883
  • /sequence/AY874537_3000883?scoreMin=50&scoreMax=100&identityMin=50&identityMax=100

Setup

Elastic Beanstalk instance

• CodePipeline: serratus-summary-api

  • CodeBuild: serratus-summary-api
  • Elastic Beanstalk: serratus-summary-api

• IAM arn:aws:iam::797308887321:role/aws-elasticbeanstalk-ec2-role

  • Attach policy AmazonAthenaFullAccess

Athena

https://console.aws.amazon.com/athena/home?region=us-east-1

CREATE DATABASE `summarytest`

CREATE EXTERNAL TABLE `family`(
    famcvg string,
    fam string,
    score int,
    pctid int,
    depth double,
    aln int,
    glb int,
    len int,
    top string,
    topscore int,
    toplen int,
    topname string,
    run string
)
ROW FORMAT SERDE 'org.openx.data.jsonserde.JsonSerDe'
LOCATION 's3://serratus-athena/family/'

CREATE EXTERNAL TABLE `sequence`(
    seqcvg string,
    seq string,
    score int,
    pctid int,
    depth double,
    aln int,
    glb int,
    len int,
    family string,
    name string,
    run string
)
ROW FORMAT SERDE 'org.openx.data.jsonserde.JsonSerDe'
LOCATION 's3://serratus-athena/sequence/'

S3

• s3://serratus-athena
  • family/ : public
  • sequence/ : public

Bucket policy

{
    "Version": "2012-10-17",
    "Id": "SerratusAthena-ElasticBeanstalk",
    "Statement": [
        {
            "Sid": "ListObjectsInBucket",
            "Effect": "Allow",
            "Principal": {
                "AWS": "arn:aws:iam::797308887321:role/aws-elasticbeanstalk-ec2-role"
            },
            "Action": "s3:ListBucket",
            "Resource": "arn:aws:s3:::serratus-athena"
        },
        {
            "Sid": "AllObjectActions",
            "Effect": "Allow",
            "Principal": {
                "AWS": "arn:aws:iam::797308887321:role/aws-elasticbeanstalk-ec2-role"
            },
            "Action": "s3:*Object",
            "Resource": "arn:aws:s3:::serratus-athena/*"
        }
    ]
}

TODO

• API
  • add query result caching
  • support nested summary
• AWS
  • DNS: serratus-summary-api.serratus.io