[maggiecam]

Summary\n\n- record Code Ocean Standard Capsule release 1.0 and release-producing run 1130403\n- tie the platform evidence to validated adapter commit 1508651 and canonical OMIX GSVA 0.3.0 source\n- record the pinned pathway runtime and inspected output artifacts\n- explicitly leave platform validation of the alternative ssgsea method open in NIDAP-Community/OMIX#62\n\n## Scope\n\nMetadata only: OMIX_MODULE_SOURCE.md and CHANGELOG.md. No scientific code, adapter behavior, App Panel, runtime, or tests changed.\n\n## Validation\n\n- python3 tests/test-source-parity.py --canonical-root /Users/maggiec/GitHub/Maggie/NIDAP/OMIX\n- python3 tests/test-app-panel.py --canonical-schema /Users/maggiec/GitHub/Maggie/NIDAP/OMIX/modules/OMIX-GSVA/schemas/interface.yml\n- Rscript tests/test-adapter-inputs.R\n- Rscript tests/test-representative-run.R\n- git diff --check\n\nAll passed locally.\n\nTracks NIDAP-Community/OMIX#62.

[maggiecam]

Beacon post-release evidence review: READY FOR MERGE

I independently reviewed this metadata-only PR at 17c4ac762632335ee33a3988f5da3c264eb801a4 against the release-producing adapter commit 1508651439504680991eb6ef1ffe38d2cc7d5853 and the live Code Ocean records.

Live platform evidence verified

• The recorded release link https://poc-nci.codeocean.io/capsule/f60059de-0260-4e49-83a0-b367d99fbd0b/tree/v1 resolves to the live OMIX GSVA Release v1.0 capsule (Code Ocean also exposes the resolved numeric URL https://poc-nci.codeocean.io/capsule/9594263/tree/v1).
• Source capsule 3631910 shows Release Version 1.0 created 2026-10-04 and identifies Run With Parameters 1130403 as the release-producing run. Its visible run duration is 1:06 and its retained result bundle is 357.35 KB.
• Run 1130403 exposes all three claimed stable artifacts: gsva_heatmap.png (345.96 KB), gsva_results.csv (9.77 KB), and gsva_run_summary.txt (711 B). I opened the release result table and heatmap; the table is populated with Hallmark rows and sample columns and the heatmap renders.
• The live run summary records mixed input delimiters (comma for expression and metadata, tab for pathways), samples A1 through C3, MH: orthology-mapped hallmark gene sets, Mouse expression/database species, method gsva, size limits 15/1200, gene updating enabled, and 50 gene sets scored. It also records canonical OMIX GSVA 0.3.0 / interface 2, canonical source 5396be0203b94fc1e22cb2eaf74d8265a32466a7, and runtime profile r-pathway r4.4.3-bioconductor3.20-v2.
• The source capsule's live Dockerfile uses codeocean/omix-r-pathway:r4.4.3-bioconductor3.20-v2. The corresponding canonical release manifest records public immutable image ghcr.io/nidap-community/omix-r-pathway@sha256:25ad9f50df5a4d7f70a7e3debed13f8d5c9b07cbc46d57fdf5c3cf4f2e767ddc and lockfile SHA-256 66b0b93e7b1f05dd9429e542c8fdca89b38770667827b53ffca80400b286795c; the committed lock hashes to that value.
• Git history confirms master and the PR base are the claimed release-producing commit 1508651439504680991eb6ef1ffe38d2cc7d5853. Its canonical source manifest records OMIX GSVA 0.3.0, interface 2, canonical commit 5396be0203b94fc1e22cb2eaf74d8265a32466a7, and scientific-file SHA-256 2ef7ab5d3726a89676ffb6e5e6b1bc42b41c4ef59093d3754252c8035b0fa7ad; those hashes agree with canonical OMIX.

PR scope and checks

• The diff changes only OMIX_MODULE_SOURCE.md and CHANGELOG.md (46 additions, 4 deletions). No scientific source, adapter behavior, App Panel, runtime definition, or tests changed.
• The hosted contract check is green.
• I independently reran source parity, App Panel/CLI contract, adapter input discovery, representative default gsva plus local ssgsea, and git diff --check; all passed.
• The proposed remote tag v0.1.0 does not currently exist. The documented sequence is correct: merge this reviewed evidence PR first, then—only with explicit finalization approval—create the adapter tag at the exact Code Ocean-validated source commit 1508651439504680991eb6ef1ffe38d2cc7d5853, not at this metadata commit or its merge commit. Do not move or recreate the tag later.

Remaining open evidence

No Code Ocean ssgsea computation was found or claimed. OMIX issue #62 is currently open and must remain open until the alternative-method Code Ocean run and inspection evidence are recorded. Merging this PR records the actual default-gsva release; it does not establish ssgsea platform validation or complete issue #62.

Decision: READY FOR MERGE as an accurate metadata-only post-release record. This review does not authorize or perform a merge, tag, new Code Ocean run, publication, or issue closure.