Standard Scripts - Project 2Proposal for Qualification

July 2014Project 2 Update

Main Sections

• Summary of prior proposal, 2013• Updated proposal, July 2014

Main Sections

Summary of prior proposalo Concepts, definitions & meta datao Test data considerationso Heavy vs. Light qualification

• Updated proposal

Proposal from 2013http://

www.phusewiki.org/wiki/index.php?title=File:FDA_Scrips.ppt

• Anyone should be able to submit a script, according to a check list

• Categorize scripts according to complexity– Complexity:

low, medium, high, software– Output:

tabulated data, analysis data, table, figure, listing

• Metadata for script should indicate– Type of output:

tabulated data, analysis data, table, figure, listing– Study design:

parallel, crossover, etc– State of qualification:

?

Proposal through CSS 2104

• Test data– Overall project should have minimum test data (SDTM & ADaM)– Scripts can propose new test data, must pass (Data fit? Open CDISC?)– Share program to produce test data, never binary test data

• 2 levels of qualification to match script complexity/output– Light vs. Heavy qualification– Common elements include

• header• good programming practices• clearly declared scope of script (e.g., study design(s))• test data matches scope & passes "FDA Data Fit" assessment (?)• documentation inputs/outputs/dependencies/usage

Proposal through CSS 2104

• Heavy qualification– Beta package includes

minimal elements for contribution• Specification & Documentation (could be in pgm header)• Test data (Data Fit? or Open CDISC or other, as appropriate)• Tests & Expected results defined• Peer Review: GPP, Specs & Docn reviewed, Tests reproduced

– Draft• Write qualification plan, Review tests for completeness/suitability

(e.g., Branch testing – are all conditional blocks/combos tested?)

– Test• Peer Review: Write qualification report, incl. log/output from tests

– Final

Proposal through CSS 2104

• Light qualification– Beta package includes

skip if >1 yr production use without ERROR– Draft

minimal elements for contribution• Specification & Documentation (could be in pgm header)• Test data (Data Fit? or Open CDISC or other, as appropriate)• Tests & Expected results defined• Peer Review: GPP, Specs & Docn reviewed, Tests reproduced• Write qualification plan, Review tests for completeness/suitability (e.g.,

Branch testing – are all conditional blocks/combos tested?)– Test

• Peer Review: Write qualification report, incl. log/output from tests– Final

Proposal through CSS 2104

Peer Review Checklist Heavy Light

Requirement specification X ?

Documented or perhaps only documented in header X

User Guide X X

SDTM/ADaM used in input/output X X

Open CDISC validator or Data Fit used to check input/output X X

GPP in source X X

Run according to Requirement specification X ?

Tested by qualification plan, tests & results all Peer reviewed X ?

Tested by End users X ?

Robust without red errors in contributor's production environment X X

Robust and used in FDA (other) scripts repository, ranked ****** X

Main Sections

• Summary of prior proposalUpdated proposal

oMotivation & objectives, as justification for elements of proposal

Proposal 2014Motivation

• End-user Objectives– Clear overview of resources available, and the purpose & state of each– Inspire confidence from first user experience– Ease of script use, clear messaging from first run of scripts– Reproducible results in user's own environment– Consistency of scripts, learning first one makes remaining familiar– Ease of converting users to contributors

• Contributor & Team Objectives– Clear, standardized workflows and checklists– Modularize routine components (e.g., FUTS for dependency

checking?)– Automate testing, issue identification (e.g., concept similar to Spotfire/R compatibility)– Centralize & consolidate information & results

Qualification Proposalmeaningful terms in blue

http://www.phusewiki.org/wiki/index.php?title=File:WG5_P02_Proposal_-_2014.pptx

• Qualification Instructions (see embedded template ð) – Certification phase of Qualification applies to new scripts and tests– Confirmation phase applies to updates of existing scripts

• States:

Contributed, Development, Testing, Qualified• Roles

– Contributor: Anyone with appropriate skills & interests– Developer: CSS Working Group 5 volunteer familiar with objectives**– Tester: CSS WG 05 volunteer familiar with objectives**– Environment Tester: Anyone in industry community able to set up

automatic test replication in their work environment– Reviewer: Author of white papers, designers of script targets**

** suggests a quick-start onboarding page in CSS Phusewiki

WG05-P02 Qualification plan (template).do

ProposalQualification

• Metadata for script should indicate– Whitepaper ID & output ID– Programming language & version (e.g., R v3.1.1, SAS v9.4)– Type of output:

tabulated data, analysis data, table, figure, listing– Study design:

parallel, crossover, etc– State of qualification:

Contributed, Development, Testing, Qualified– OS is not included, since should be indicated in OS compatibility report

• Test Data requirements– available as a program or script (text, not binary)– based on expected standards (SDTM, ADaM)– data requirements clearly & accurately specified for each script– include expected results from these data for defined tests/checks

ProposalQualification

• Transitions

"Contributed" is the original State of all scripts– to Development, checklist includes

by Developer & Reviewer• R & D confer on suitability of contribution. Suitable starting point?

[ may require analysis details, specs, from contributor ]• D reviews components (checklist to be completed)• D works with Contributor to complete minimum components

[ including Test Data and Coverage of defined tests ]• D adds standard parameter, dependency checking• D writes Qualification instructions .docx (see template, above)

– to Testing, checklist includes

by Tester• Review Qualification instructions, consider coverage of tests• Execute Qualification instructions• Work with Developer to complete execution successfully

ProposalQualification

• Transitions continued– to Qualified

by Tester & Environment Tester & Reviewer• T updates reference test outputs from certification/confirmation• E updates & executes local tests (posting PASS/FAIL results)• R confirms script output matches intention• R confirms qualification process covers important elements and

considerations. • R also provides user (rather than technical) feedback?• Achieve "Qualified" state when all tests in all test environments PASS

(i.e., match outputs that T has certified and/or confirmed) and that R agrees that target is achieved

ProposalQualification

• Efforts Required– Top priority

• Finalize Qualification states, roles, workflow, checklists, and templates – Next priorities

• Design test structure in google code• Develop scripts that will allow Environment Testing• Develop general components (e.g. parameter, dependency checking)• Identify Environment Testers based on

– Host environment– SAS or R version

• Identify opportunities to automate qualification. E.g.,– Environment Testers to post results back as machine readable– Script green-light/red-light qualification matrix on Phusewiki