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Standard Scripts - Project 2 Proposal for Qualification

Standard Scripts - Project 2 Proposal for Qualification. July 2014 Project 2 Update. Main Sections. Summary of prior proposal, 2013 Updated proposal, July 2014. Main Sections. Summary of prior proposal Concepts, definitions & meta data Test data considerations

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Standard Scripts - Project 2 Proposal for Qualification

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  1. Standard Scripts - Project 2Proposal for Qualification July 2014 Project 2 Update

  2. Main Sections • Summary of prior proposal, 2013 • Updated proposal, July 2014

  3. Main Sections • Summary of prior proposal • Concepts, definitions & meta data • Test data considerations • Heavy vs. Light qualification • Updated proposal

  4. 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: ?

  5. 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

  6. 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

  7. Proposal through CSS 2104 • Light qualification • Beta package includes skip if >1 yr production usewithout ERROR • Draftminimal 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

  8. Proposal through CSS 2104

  9. Main Sections • Summary of prior proposal • Updated proposal • Motivation & objectives, as justification for elements of proposal

  10. 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

  11. Qualification Proposalmeaningful terms in bluehttp://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

  12. 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

  13. 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

  14. ProposalQualification • Transitionscontinued • 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

  15. 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

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