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Code Ocean validation plan

This plan is required after the reviewed adapter commit is merged. Local and GitHub checks do not constitute Code Ocean validation.

Candidate identity

Before each run, record:

  • the exact merged adapter commit;
  • canonical OMIX source commit 53b2ca65aa23f54477f698c4ab6ce0d6ab637a5f;
  • the Code Ocean capsule or release identifier;
  • runtime tag codeocean/omix-r-pathway:r4.4.3-bioconductor3.20-v2; and
  • the immutable runtime digest resolved by the platform.

Required runs

  1. Attached demo, named parameters
    • Leave DEG Table blank.
    • Keep Mouse and ordered comparisons B-A,C-A,B-C.
    • Confirm the adapter selects exactly one table under /data/deg_table.
  2. Explicit user table
    • Select a compatible CSV with DEG Table.
    • Use at least two comparisons in a nonalphabetical requested order.
    • Confirm the returned and serialized result rows are grouped in the requested order and ranked by ascending p-value within each comparison.
    • Confirm analysis provenance and every rendered plot axis preserve that same requested order.
  3. Workflow result
    • Connect one upstream wide DEG result with comparison-specific t-statistic, p-value, and fold-change columns.
    • Leave the three column overrides blank and confirm deterministic mapping.
  4. Ambiguity failure
    • Attach two eligible DEG tables without selecting one explicitly.
    • Confirm the run stops and prints every candidate path.
  5. Advanced controls
    • Run a table whose ordered columns use _statistic, _adjpval, and _logFC; leave the three exact column-list overrides blank and set the corresponding suffix controls.
    • Run once with exact ordered column lists and deliberately nonmatching suffix settings; confirm the exact lists retain precedence.
    • Run once with pathway_bubble_significance_statistic=pval, collection_color_scale=shared, and a nondefault pathway_bubble_top_n.
    • Run once with a small custom pathway table and verify its configured pathway-name and gene-symbol columns. Clear collections_to_include and confirm provenance/results contain only the custom database.

Required artifacts and assertions

  • l2p_multi_results.csv contains every pathway meeting the selected export criteria; the figure row limit does not truncate it. Its comparison blocks follow the requested order, with ascending p-values inside each block.
  • l2p_multi_results_provenance.csv is present.
  • Shared combined, faceted, and collection-specific L2P-Multi-Pathway-Bubble_*.png files and the manifest are present when bubble plots are enabled.
  • l2p_multi_results_provenance.csv records requested comparison order and the aligned statistic, significance, and fold-change columns; rendered plot axes use that same order.
  • The manifest records the significance statistic, selection scopes, dimensions, selected counts, and color-scale ranges. It does not currently carry comparison order.
  • No retired capsule-local legacy plot or user-selected output path is used.
  • No files are written outside /results.

Record the run links, output checks, runtime digest, and any approved exception in OMIX_MODULE_SOURCE.md before creating an adapter release tag.