chore: bolster omics tests to prep for seqera deprecation

[Kevin Loftus (kevin-loftus-dept)]

Title*

Bolster HealthOmics test coverage ahead of Seqera deprecation (EGV-268)

Type of Change*

• New feature
• Bug fix
• Documentation update
• Refactoring
• Hotfix
• Security patch
• UI/UX improvement

(Also: test coverage / chore — no production behavior change.)

Description

Prepares for Seqera removal by locking in HealthOmics-only behavior in mixed HealthOmics/Seqera files before any hard removal or branch extraction.

No Seqera removal or production logic changes are included. This PR adds unit tests and a coverage inventory doc:

• Back-end: gaps closed for process-update-laboratory-run, process-classify-laboratory-run-failure, unified-workflow-catalog-service, and run-cost-capture-service (progress failure handling, terminal-status task listing skip, Anthropic/SSM failure paths, Omics catalog pagination/sorting/disabled labs, cost-capture edge cases).
• Front-end: new coverage for useMultiplatform HealthOmics routing and run-store Omics WIP mutate/unset/omicsRunsForLab paths.
• Docs: docs/development/healthomics-mixed-file-coverage.md maps existing coverage, what was added, and accepted residual gaps (Vue SFCs without VTU; Collections modal, Dashboard favourites, Workflow Lab Access UI).

Related: EGV-268

Testing*

• Added/extended unit tests in:
  • packages/back-end/test/.../process-update-laboratory-run.lambda.test.ts
  • packages/back-end/test/.../process-classify-laboratory-run-failure.lambda.test.ts
  • packages/back-end/test/.../run-cost-capture-service.test.ts
  • packages/back-end/test/.../unified-workflow-catalog-service.test.ts
  • packages/front-end/test/app/composables/useMultiplatform.test.ts (new)
  • packages/front-end/test/app/stores/run.test.ts (new)
• Verified with pnpm test in packages/back-end and packages/front-end.

Impact

• Improves regression safety for HealthOmics paths that currently share files with Seqera logic.
• No runtime, API, or UI behavior changes; test-only + documentation.
• Residual risk documented: some FE Vue SFCs remain without unit mounts; hard Seqera removal should not assume full unit safety there without e2e or post-extraction coverage.

Additional Information

• Omics run-store loads left as residual (need Nuxt $api harness).
• FE components such as EGRunFromCollectionsModal, EGDashboard, and EGWorkflowLabAccessPage are gap-documented rather than newly unit-tested in this ticket.

Checklist*

• No new errors or warnings have been introduced.
• All tests pass successfully and new tests added as necessary.
• Documentation has been updated accordingly.
• Code adheres to the coding and style guidelines of the project.
• Code has been commented in particularly hard-to-understand areas.

[diegomayorga-dept]

PR Review: chore: bolster omics tests to prep for seqera deprecation (#907)

Summary

• 0 blockers, 1 major, 3 minor
• Confirmed clean: no production code touched, no security issues, no breaking changes, test coverage is genuinely solid
• Top concern: the new coverage-inventory doc contains a factually inaccurate claim about a "compile fix" that never happened in this diff

Conventions (2)

major — docs/development/healthomics-mixed-file-coverage.md:34

The doc's "Note on process-update compile fix" section claims process-update-laboratory-run.lambda.ts "failed to typecheck" and that a broken buildProgressUpdate/updateWithAttributeRemoval call "was restored to the prior correct pattern." The diff contains zero changes to that lambda file — only its test file was touched. Two independent reviewers (correctness + conventions) verified the current code at that call site is already type-correct and behaviorally sound, and traced the actual fix to an earlier, already-merged commit (7e3c17c2, "fix: broken unit test"). The note misrepresents what this PR changed.

Suggestion: Remove the "compile fix" note, or rewrite it to say the lambda required no code changes in this PR — only new test coverage was added.

minor — docs/development/README.md:12

healthomics-mixed-file-coverage.md isn't registered in docs/development/README.md's index table, unlike its sibling docs.

Suggestion: Add a row for the new doc to the docs/development/README.md table for consistency.

Simplification (2)

minor — packages/back-end/test/app/controllers/easy-genomics/laboratory/run/process-classify-laboratory-run-failure.lambda.test.ts:253

"skips HealthOmics OpenAI when SSM key is missing" and "skips HealthOmics LLM when getParameter throws" are near-identical — same mocks, same assertions, differing only in how mockGetParameter resolves/rejects.

Suggestion: Collapse into a single it.each over the two SSM failure modes.

minor — packages/back-end/test/app/services/easy-genomics/run-cost-capture-service.test.ts:92

"uses cost-capture as Omics userId" and "omits ActualStorageCostUsd" duplicate the same large listAllRunTasks/getRun mock literal, varying only storageCapacity and UserId.

Suggestion: Factor the repeated createOmicsServiceForLab mock into a small local helper reused across these tests.

[Kevin Loftus (kevin-loftus-dept)]

PR Review: chore: bolster omics tests to prep for seqera deprecation (#907)

Summary

• 0 blockers, 1 major, 3 minor
• Confirmed clean: no production code touched, no security issues, no breaking changes, test coverage is genuinely solid
• Top concern: the new coverage-inventory doc contains a factually inaccurate claim about a "compile fix" that never happened in this diff

Conventions (2)

major — docs/development/healthomics-mixed-file-coverage.md:34

The doc's "Note on process-update compile fix" section claims process-update-laboratory-run.lambda.ts "failed to typecheck" and that a broken buildProgressUpdate/updateWithAttributeRemoval call "was restored to the prior correct pattern." The diff contains zero changes to that lambda file — only its test file was touched. Two independent reviewers (correctness + conventions) verified the current code at that call site is already type-correct and behaviorally sound, and traced the actual fix to an earlier, already-merged commit (7e3c17c2, "fix: broken unit test"). The note misrepresents what this PR changed.

Suggestion: Remove the "compile fix" note, or rewrite it to say the lambda required no code changes in this PR — only new test coverage was added.

minor — docs/development/README.md:12

healthomics-mixed-file-coverage.md isn't registered in docs/development/README.md's index table, unlike its sibling docs.

Suggestion: Add a row for the new doc to the docs/development/README.md table for consistency.

Simplification (2)

minor — packages/back-end/test/app/controllers/easy-genomics/laboratory/run/process-classify-laboratory-run-failure.lambda.test.ts:253

"skips HealthOmics OpenAI when SSM key is missing" and "skips HealthOmics LLM when getParameter throws" are near-identical — same mocks, same assertions, differing only in how mockGetParameter resolves/rejects.

Suggestion: Collapse into a single it.each over the two SSM failure modes.

minor — packages/back-end/test/app/services/easy-genomics/run-cost-capture-service.test.ts:92

"uses cost-capture as Omics userId" and "omits ActualStorageCostUsd" duplicate the same large listAllRunTasks/getRun mock literal, varying only storageCapacity and UserId.

Suggestion: Factor the repeated createOmicsServiceForLab mock into a small local helper reused across these tests.

Fixed all issues, please re-review.

[diegomayorga-dept]

LGTM