Standard Scripts Project 2 2014 - Proposal for Qualification of Standard Scripts

Main Sections Summary of prior proposal, 2013 Updated proposal, July 2014

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

Proposal from 2013 Anyone can submit a script, according to a check list Categorize scripts by 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 from 2013 Test data 2 levels of qualification 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 Light vs. Heavy: according to complexity of script & output Common elements include header adhere to good programming practices clear scope of script (e.g., study design(s)) test data matche scope & pass "FDA Data Fit" assessment (Open CDISC?) documentation available for: usage, inputs, outputs, dependencies

Proposal from 2013 Heavy qualification Beta package includes: minimal elements for contribution Specification & Documentation (could be in pgm header) Test data (Data Fit? or Open CDISC?) 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 from 2013 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 DDT comment on "light" qualification plan: I think the suggestion was to replace this with a statement of ERROR-free production use >1 yr prior to contribution to PhUSE Standard Scripts

Proposal through CSS 2104 Peer Review Checklist Heavy Light Requirement specification X ? Documented or perhaps only documented in header User Guide SDTM/ADaM used in input/output Open CDISC validator or Data Fit used to check input/output GPP in source Run according to Requirement specification Tested by qualification plan, tests & results all Peer reviewed Tested by End users Robust without red errors in contributor's production environment Robust and used in FDA (other) scripts repository, ranked ****** DDT comment on "light" qualification plan: I think the suggestion was to replace this with a statement of ERROR-free production use >1 yr prior to contribution to PhUSE Standard Scripts

Main Sections Summary of prior proposal Updated proposal Objectives Definitions: Qualification, States, Roles Metadata and Test data State Transitions

Proposal 2014 - Objectives For End-users Clear overview of resources available, incl. purpose & state of each Inspire confidence from first user experience Ease-of-use: clear messaging from scripts Reproducible results in user's own environment Consistency of scripts, learning first one makes remaining familiar Ease of converting users to contributors For Contributors & Standard Scripts Team Standardize 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 DDT comment on "Ease of converting users ..." Contribution should be easy! And should accommodate the willing contributor, however much or little time they have available.

Qualification Proposal meaningful terms in blue http://www. phusewiki 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 Qualification phase vs. State: First time a script is developed/tested, we perform Certification phase Upon later updates, developer/tester perform Confirmation phase

Qualification Proposal 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 "OS is not included ..." See related concepts of automated testing and Environment Testers, above

Qualification Proposal 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 R & D confer: This is essentially an investment decision. Does the contribution warrant development by the Standard Scripts volunteers? Is it a sufficient starting point? D reviews components ... partial list: Clear scope & requirements for target output (from White Paper?) Good Programming Practices Program header Documentation (just in header?) Test Data D adds standard parameter, ... See for e.g., http://thotwave.com/resources/futs-framework-unit-testing-sas/ ThotWave may be interested to contribute with FUTS, their Framework for Unit Testing SAS. We could probably use much of this framework & components D writes Qualification instructions ... See Word docx template, embedded above

Qualification Proposal 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

Qualification Proposal 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