Ingenuity Systems aims to enhance decision-making for life science researchers through advanced information and analytics solutions, primarily utilizing the ingenuity knowledge base for biological data analysis. The presentation discusses the challenges of traditional models in managing complex biological information and outlines a strategy for transitioning to a service-oriented architecture with automated testing and continuous integration using tools like FitNesse and Hudson. Key goals include reducing release cycle times, improving testing practices, and fostering a DevOps culture to streamline product development and deployment.

1. Proprietary and ConfidentialContinuous Integration using Hudson and FitnesseNorman Boccone | Lead Engineer | twitter: @dropslowlyJennifer Wong | Lead QE Engineer | twitter: @jenlwongVasu Durgavarjhula | Director of Development | twitter: @d_vasu

2. Proprietary and Confidential2Overview► Who we are ?► The Challenge► Tools and Processes► Test Strategy► Conclusion

3. Ingenuity Systems We are a leading provider of information and analytics solutions for life science researchers Our goal is to help life science researchers get biological insights from their data quickly and reliablyOur products are used by thousands of researchers worldwidePartial Customer ListProprietary and Confidential3

4. ?Scientists Need a Tool to Make Good Decisions From Complex Biological DataToxicologyBiomarkersPharmacogenomicsDiscoveryUse understanding of disease mechanisms to identify and validate targetsElucidate biological mechanisms of drug action and toxicityIdentify and prioritize novel biomarkers by understanding role in disease pathwaysUnderstand mechanisms behind differential response to R(x)Hard to synthesize the picture of what that data means in a broader biological context, and how the pieces work together… Traditional publishing models are good for learning but not applying knowledge …Enormous volume and complexity of biological and chemical data…CancerPublishing and CollaborationExperimental DataSearchProprietary and Confidential4

5. The Ingenuity® Knowledge Base Is the core technology behind all of Ingenuity’s products and servicesTHE INGENUITY KNOWLEDGE BASEANALYSISHYPOTHESIS GENERATIONVISUALIZATIONECOMMERCE ENABLEMENTPATHWAY, REAGENT & GENE SEARCHENABLES SCIENTIFIC UNDERSTANDINGDiscover existing relationships and function, as well as inference of relationships that may not have been studied in a particular context yetGeneratetestable hypotheses, build pathways, ability to inferenceGet answers by asking detailed and in-depth scientific questions

6. The Ingenuity® Knowledge Base How is it different?THE INGENUITY KNOWLEDGE BASE► Structured-to capture relevant details Scientific statements are modeled into Findings using the Ingenuity Ontology► Expert Review Process- for accuracy Findings go through QC process► Comprehensive- leverage knowledge in one place Largest scientific knowledge base of its kind with modeled relationships between proteins, genes, complexes, cells, tissues, drugs, pathways and diseases► Timely- for access to up-to-date knowledge Findings are added weekly

7. Proprietary and ConfidentialThe Challenge7

8. Proprietary and Confidential8Single product

9. Proprietary and Confidential9multiple productsIngenuity Variant AnalysisNext Generation Sequencing Analysis ReportsIngenuity Product SearchReagent Portals for BD, Sigma, Thermo Fischer

10. Proprietary and Confidential10Large monolithic code base

11. Proprietary and Confidential11Modular ServicesSingle Sign OnUserManagementViews & ReportsUser DataContentServiceiReportMaster Graph

12. Proprietary and Confidential12Long release cycles

13. Proprietary and Confidential13Faster release cycles

14. Proprietary and Confidential14Speeding up the feedback loopDeveloperStakeholders

15. Proprietary and Confidential15Do all of this while supporting the existing product

16. Proprietary and Confidential16ApproachMove to a Service Oriented ArchitectureDon’t miss Jeff’s talk on Sunday 10:45 am “Learning to Love Services: Experiences from the Transition to a Service-oriented Architecture”Develop a test strategy focused on automated testingBuild a continuous integration systemAdopt agile product managementImprove infrastructure to create and deploy servicesFoster a Dev/Ops culture

17. Proprietary and Confidential17Continuous Integration WorkflowApplicationBundleDeploy ApplicationRun Fitnesse Tests(Nightly suite)Nightly Build(Clover)Run JUnitTestspublish summaryFitnesseBundleDeploy FitnessepublishpublishHudson Dashboard(JUnit, Fitnesse summary, Code Coverage)Fitnesse Wiki(Test history, Details, Test Case Management)LinkSVNCommit(Test Cases)

18. Proprietary and Confidential18Tools and Processes

19. Proprietary and Confidential19Service Oriented Architecture

20. Proprietary and Confidential20SOA: Beforelots of modules, separate but dependenteasy to develop on but also easy to add circular dependencieshard to keep track of purpose/value of all the modulesproduct consisted of bunches of modules put togetherreference was typically to latest devcodeto ensure "latest," individual modules of a product were rebuilt for every releasejunittests were run every time as wellnew product version meant build everything, test everythingbuilds were slow

21. Proprietary and Confidential21SOA: “Current”components: module grouped together. Access through api module onlyless chance of circular dependencieseasier to comprehend modulesmore flexibility to change code: just do not change apicomponents built/tested separatelyfaster buildsless repetitive testingsome shared modules still exist (they are not part of any component)

22. Proprietary and Confidential22SOA: Conversion Notesfind a logical group of modulesConvert groupput group into hierarchical structure, hide things behind an apilayerconvert outside modules to use apissee Jeff's talk

23. Proprietary and Confidential23Build System

24. Proprietary and Confidential24Build System: Beforein-house ant scriptslots of control but it required lots of resourcesno real industry standardglobal scripts/property files, overrides allowedoffered consistency but (busy) people would override instead of follow patternscripts got complicatedanyone could add a new featureif anyone wanted a new feature, just tell them to add itinefficient additions, different code styles made scripts hard to readvery little dependency managementmultiple repositories for binary files

25. Proprietary and Confidential25Build System: “Current” mavennot much control, and very rigid (a good thing, in a way)steep learning curvedifferent from previous way of doing thingsstandard structure; difficult to not follow structurehierarchical structure easily followedversions for all dependencies well definedeasy to add new features (after a short burst of intense agony)only one repository

26. Proprietary and Confidential26Build System: Conversion Notes get a maven repository manager (nexus? Turn on search!)add antrun plugin to publish artifacts to old systemchoose a simple component to start, make lots of little submodules(1 module per artifact, plus assembly)manually add needed dependencies to repositorybuild up company parent pom, use hierarchyPut all plugin management into parentKey maven plugins: buildnumber, buildhelper, release, assembly,

27. Proprietary and Confidential27Build System: TODOcleaner release plugincontinue learning mavencontribute to pluginsImprove internal maven FAQLook into git

28. Proprietary and Confidential28Continuous Builds

29. Proprietary and Confidential29Continuous Builds: BeforeHudson (no plugins)auto build start for each module, with artifacts publishedmanual build start for productsshell scripts to copy artifacts to release dir

30. Proprietary and Confidential30Continuous Builds: “Current”Hudsondevmaster for auto build of modules/submodules, auto published to repository manager (dev area)release master for components/products, auto published to repository manager (release area)modules/submodulesbuilt on checkincomponents/products built on schedule or on demandprocess includes various tests and deployments (Jen)

31. Proprietary and Confidential31Continuous Builds: Conversion Notesuse Jenkins, not Hudson (more activity for Jenkins)startup new, clean serverscopy/create job that we wantTry to make Jenkins be the portal to everything fingerprintingPlugins we use: clover, fitnesse, findbugs, checkstyle, disk-usage, downstream build view, (custom) dashboard view, promoted builds, ssh slaves

32. Proprietary and Confidential32Continuous Builds: TODObetter job rollupjob templatesmore maven/hudson pluginssubmit hudson plugin(s) to community

33. Proprietary and Confidential33Deployment: Beforeproprietary shell/perl scriptstargeted to install app only (not machine set up)multiple proprietary property config scripts

34. Proprietary and Confidential34Deployment: “Current”PuppetConfigures machines and appsWork on our machines and EC2Use of .erb files everywhere for property configuration

35. Proprietary and Confidential35Deployment: Conversion Notesmodify tar formatmoved to one tomcatused erb filessplit properties into app

36. Proprietary and Confidential36Deployment: TODOstandard server configuration types (e.g. “build machine”, “app machine”, …)more puppet scripts

37. Proprietary and Confidential37Visibility

38. Proprietary and Confidential38Visibility: Beforecfmap (IT server diagnostic tool)Hudson status pageFitNesse server

39. Proprietary and Confidential39Visibility: “Current”cfmapHudson status pageHudson dashboardextra tests built in to HudsonFitNesse serverService status page

40. Proprietary and Confidential40Visibility: Conversion Notesuse Hudson plugins, with drill downget everything to report in a standard way (junit xml)

41. Proprietary and Confidential41Visibility: TODOmore widgets for the dashboardIntegrate outside reports into dashboardcfmapstatus pagesdm? (service discovery manager)

42. Proprietary and Confidential42Test Strategy

43. Proprietary and Confidential43Testing For CI/CDTest Automation is keyHow and what to automateMezarosCohnCrispin

44. Proprietary and Confidential44Test ChallengesTestability: some products are difficult to test at lower levelsLegacy Apps: one of our main products was a ‘Legacy App’. Tests used to look like this:

45. Proprietary and Confidential45Test Challengesvarying levels of coveragesome of our newer components have great coverageother components have lower coverage: legacy, proof of concept

46. Proprietary and Confidential46SolutionsTest and code refactoringLegacy Apps: Strangulation approachautomate new and refactored featuresincremental work on tests: reserve time in each iteration for adding to testsChange in culture: team ownership of tests and statusCycle time for ipa was 2.5 weeksNow for most of our services, it is 20-40 minutes

47. Proprietary and Confidential47Test Infrastructure and Environments

48. Proprietary and Confidential48Process: Build PromotionBuild Promotion through Quality GatesBetaDeployed to BetaProprietary and Confidential49Test EnvironmentsStable EnvironmentMultiple nodes

49. Deployment Tests

50. System and performance tests

51. Manual/exploratoryCI EnvironmentSingle nodes

52. functional testsService1Service1Service2Service2Service3Service3Service4Service4Service5Service5Service6

53. Proprietary and Confidential50Test Types

54. Proprietary and Confidential51Test Types: Deployment and HealthEach of our components has a built-in status page

55. Proprietary and Confidential52Test Types: Deployment and HealthStatus pageReflects app statusResource availability: DB Connections, Services

56. Proprietary and Confidential53Test Types: Deployment and HealthInformation is used for:DeploymentHealth MonitoringService Compatibility and Dependency checking

57. Proprietary and Confidential54Test Types: FitNesseFitNesse is a wiki-based web server test toolHelps abstract test definition from technical implementationProvides visual reporting and result history tracking

58. Proprietary and Confidential55Test Types: FitNesseThe FitNesse Server http://localhost:8080/FitNesse.UserGuide.TwoMinuteExamplehttp://localhost:8080/FitNesse.UserGuide.TwoMinuteExample?pageHistoryWiki view Editing the wiki Test Results

59. Proprietary and Confidential56Test Types: FitNesse Integration with Hudson- Views, drilldown, configuration Test results converted to junit formatView of fitnesse test job in Hudson

60. Proprietary and Confidential57Drill downs on fitnesse test results in Hudson

61. Proprietary and Confidential58FitNessePlugin ConfigurationConvert results to Junit format

62. Proprietary and Confidential59Publish FitNesse Results and Coverage

63. Proprietary and Confidential60Test Types: FitNesseWhat we use it for:

64. Functional tests

65. Integration tests

66. UI Tests (com.jbergin.HtmlFixture)

67. DB Tests (dbfit)What we’ve done with it that is differentUse as execution framework for more complex tests Extension of fitnesse server for data-driven testsjson fixture – pass in javascriptExecution of Selenium tests

68. Proprietary and Confidential61Test Types: FitNesseLessons learnedFitNesse is good for straightforward verification of dataTo do more, you have to get creativeFixture and test ownership needs to be a shared responsibility

69. Proprietary and Confidential62Test Types: SeleniumWe fire off Selenium tests in two ways: via Hudson job or through FitNesse.Test results converted to junit format for display in hudsonHudson job in dashboard: Hudson job view: