One-year Accomplishment Report on i5k@NAL

1. One-year Accomplishment
Report on i5k@NAL
Jun-Wei Lin
May 13, 2015

2. Programming and Engineering
Challenges
• Task queue
• Automatic build and regression testing
• Load testing
• Single sign-on
• Job automation and integration

3. Task Queue for BLAST Requests

4. Build and Deploy the Code
• People develop different parts of a project on
their local machines
• Deal with conflicts with a version control
system (GitHub)
• Keep the system running on dev server
updated – semi-automated by a script

5. Regression Testing
• Rerun previously completed tests
• Check
– Program behavior has changed
– Previously fixed faults have re-emerged

6. Regression Testing with Scripts

7. Regression Testing with Scripts
demo

8. Integration with Jenkins

9. Automatic Deployment (blast_build)

10. Automatic Regression Testing
(blast_test)

11. Load Testing
• Conducted to understand the behavior of the
system under a specific expected load

12. Load Testing on Web Apollo 1.0.4-RC3
• 30 instances, each with 5 users annotating on 3
different scaffolds
• 3 million requests in 13.5 hours (60 requests per
second)
• 12 of the 3 million requests failed. e.g. responded
with status code 400 (Bad request headers)
• “WA-RC3 looks robust. 99.9996% of the requests
responded normally under average arrival rate of
60 requests/sec”

13. Load Testing with Jmeter

14. Load Testing with Jmeter
demo

15. Load Testing with Jmeter and
Command Line Interface Integration
• Randomly pick 4 organisms
• Test each organism with 3 users running pre-
defined actions 2 times

16. Load Testing with Jmeter and Jenkins
Integration

17. Single Sign-on
• Current registration process for annotating
organisms

18. Annotating multiple organisms
https://apollo.nal.usda.gov/agrpla
https://apollo.nal.usda.gov/cercap
https://apollo.nal.usda.gov/drofic
https://apollo.nal.usda.gov/lepdec
…

19. Single Sign-on for All Our Resources
• An unified interface with customized
information
– Submitted BLAST queries
– Organisms they can access
– List of created annotations
– Request access to another organisms
– Approve/reject potential annotators
– Tightly connected to our developing dataset
submission workflow

20. One Time Registration

21. User Dashboard (Prototype)

22. Apply for Annotation

23. Panel for Project Owner

24. Sum Up
• Deal with programming and engineering
challenges
• In an automated and integrated way
• Facilitate the i5k project
• Save our time and make us more productive