serratus-bio/serratus-summary-api-debug

serving Serratus summary data via a public API

serratus-summary-api

Example routes

• /index/run=ERR2756788
• /summary/nucleotide/run=ERR2756788
• /matches/nucleotide/paged?family=Coronaviridae
• /matches/nucleotide/paged?family=Coronaviridae&page=5&perPage=10
• /matches/nucleotide/paged?family=Coronaviridae&scoreMin=90&scoreMax=100&page=5
• /matches/nucleotide/paged?family=Coronaviridae&scoreMin=90&scoreMax=100&identityMin=80&identityMax=90
  • /matches/nucleotide?family=Coronaviridae&scoreMin=90&scoreMax=100&identityMin=80&identityMax=90
• /matches/nucleotide/paged?sequence=EU769558.1
• /matches/nucleotide/paged?sequence=EU769558.1&page=5
• /matches/nucleotide/paged?sequence=EU769558.1&scoreMin=90&scoreMax=100&page=5
• /matches/nucleotide/paged?sequence=EU769558.1&scoreMin=90&scoreMax=100&identityMin=80&identityMax=90
• /counts/nucleotide?family=Coronaviridae
• /counts/nucleotide?sequence=EU769558.1
• /list/nucleotide/family
• /list/nucleotide/sequence
• /palmprint/run=ERR2756788

Local usage

Setup

Add file env.sh:

export SQL_USERNAME=web_api
export SQL_PASSWORD=serratus

# [optional] create/load virtualenv
pip install -r requirements.txt

Start server

bash run.sh

Test

bash test.sh

AWS Setup

Elastic Beanstalk

• Application name: serratus-summary-api-flask
• Environment
  • Web server environment
  • Name: serratus-summary-api
  • Platform: Python (3.7 running on 64bit Amazon Linux 2)
  • Sample app (will be overidden by CodePipeline deployment)

After creation:

• Add load balancer listener
  • Port: 443
  • Protocol: HTTPS
  • SSL certificate: *.serratus.io
• Processes
  • Health check path: /summary/nucleotide/run=ERR2756788
• Environment variables
  • Add SQL_USERNAME, SQL_PASSWORD from to env.sh

CodePipeline

1. Settings
   • Pipeline name: serratus-summary-api-flask
   • New service role
2. Source stage
   • Source provider: GitHub (Version 1)
   • Select this repo/branch
   • Change detection: GitHub webhooks
3. Build stage: skip
4. Deploy stage
   • Provider: AWS Elastic Beanstalk
   • Region: us-east-1
   • Application/environment names from above

Route 53

• A record for api.serratus.io -> Elastic Beanstalk endpoint

RDS

See https://github.com/ababaian/serratus/wiki/Serratus-SQL-Database-Management

Debugging

• Disable caches: in config.py set CACHE_DEFAULT_TIMEOUT = 1 (timeout after 1 second)

TODO

• /protein/*
• /rdrp/*
• handle timeouts e.g.

  DatabaseError: current transaction is aborted, commands ignored until end of transaction block

• investigate CACHE_TYPE = 'filesystem' and CACHE_THRESHOLD
• .