One-year Accomplishment Report on i5k@NAL
-
Upload
jun-wei-lin -
Category
Engineering
-
view
166 -
download
4
Transcript of One-year Accomplishment Report on i5k@NAL
![Page 1: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/1.jpg)
One-year Accomplishment Report on i5k@NAL
Jun-Wei Lin
May 13, 2015
![Page 2: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/2.jpg)
Programming and Engineering Challenges
• Task queue
• Automatic build and regression testing
• Load testing
• Single sign-on
• Job automation and integration
![Page 3: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/3.jpg)
Task Queue for BLAST Requests
![Page 4: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/4.jpg)
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
![Page 5: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/5.jpg)
Regression Testing
• Rerun previously completed tests
• Check
– Program behavior has changed
– Previously fixed faults have re-emerged
![Page 6: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/6.jpg)
Regression Testing with Scripts
![Page 7: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/7.jpg)
Regression Testing with Scripts
demo
![Page 8: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/8.jpg)
Integration with Jenkins
![Page 9: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/9.jpg)
Automatic Deployment (blast_build)
![Page 10: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/10.jpg)
Automatic Regression Testing (blast_test)
![Page 11: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/11.jpg)
Load Testing
• Conducted to understand the behavior of the system under a specific expected load
![Page 12: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/12.jpg)
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”
![Page 13: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/13.jpg)
Load Testing with Jmeter
![Page 14: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/14.jpg)
Load Testing with Jmeter
demo
![Page 15: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/15.jpg)
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
![Page 16: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/16.jpg)
Load Testing with Jmeter and Jenkins Integration
![Page 17: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/17.jpg)
Single Sign-on
• Current registration process for annotating organisms
![Page 18: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/18.jpg)
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
…
![Page 19: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/19.jpg)
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
![Page 20: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/20.jpg)
One Time Registration
![Page 21: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/21.jpg)
User Dashboard (Prototype)
![Page 22: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/22.jpg)
Apply for Annotation
![Page 23: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/23.jpg)
Panel for Project Owner
![Page 24: One-year Accomplishment Report on i5k@NAL](https://reader034.fdocuments.us/reader034/viewer/2022052706/587542a91a28abb8208b5505/html5/thumbnails/24.jpg)
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