Peaklims/PeakLimsApi

What it measures: How tangled the control flow is — methods with many branches are hard to test and change.

Method: Cyclomatic complexity per method (1 + decision points), computed exhaustively across production source; test projects separated by convention. Deterministic.

Maturity: Documented → Verified → Prevented · effective 9.0 / 10 · rule-coverage 100% · ceiling Prevented

1 method(s) exceeded the cyclomatic complexity threshold of 15; the worst was PeakLimsDbContext.OnModelCreating at 35.

✓ On the Gold path — maintain.

Detailed fixes: d1_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: How hard the code is for a person to follow, beyond raw branching.

Method: Cognitive complexity per method (Sonar-style nesting-penalized score), computed exhaustively over production code, excluding test projects. Deterministic.

Maturity: Documented → Verified → Prevented · effective 9.1 / 10 · rule-coverage 100% · ceiling Prevented

1 method(s) exceeded the cognitive complexity threshold of 15; the worst was PeakLimsDbContext.OnModelCreating at 34.

✓ On the Gold path — maintain.

Detailed fixes: d2_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Over-large classes that try to do too much ("god classes").

Method: God-class detection by line and method-count thresholds per logical type (partial classes unified), filtered for generated code and registration/contract false positives. Deterministic.

Maturity: Documented → Verified → Prevented · effective 9.5 / 10 · rule-coverage 100% · ceiling Prevented

2 god class(es) detected.

✓ On the Gold path — maintain.

Detailed fixes: d3_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Copy-pasted code that should be shared instead.

Method: Code duplication via token-stream sliding windows with type-aware normalization (locals masked, type names preserved), density-scored per KLoC of production code. Deterministic.

Maturity: Documented → Verified → Prevented · effective 9.8 / 10 · rule-coverage 100% · ceiling Verified

7 duplicated block group(s) detected.

+ 1 more group(s) — more in Appendix A; the complete list is findings.md.

✓ On the Gold path — maintain.

Detailed fixes: d4_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether volatile projects sit underneath others that depend on them (so their churn ripples upward), and whether project dependencies form cycles. A widely-depended-on but stable shared/kernel project is healthy, not penalised.

Method: Dependency cycles via elementary-DFS over real .csproj references, plus Martin instability (afferent/efferent) per project. Exhaustive over the reference graph, deterministic.

Coverage: Exhaustive · type-level: afferent/efferent coupling + cycles computed over every production type — the population is all types, not a name convention.

Maturity: Documented → Verified → Prevented · effective 7.0 / 10 · rule-coverage 100% · ceiling Prevented

8 projects, 0 dependency cycle(s), 0 unstable depended-on project(s).

What to do

1. Resolve the 3 Off the main sequence finding(s) in Coupling. — One of this dimension's main actionable groups (3 warning-level).
2. Enforce Coupling in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d5_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether a class's methods are focused on a single responsibility.

Method: LCOM4 cohesion per production class with at least two methods: connected components of methods sharing state or calls, computed syntactically. Deterministic, not a proxy.

Coverage: Exhaustive · type-level: LCOM4 cohesion computed over every production class — the population is all types, not a name convention.

Maturity: Documented → Verified → Prevented · effective 6.1 / 10 · rule-coverage 100% · ceiling Verified

23 of 71 classes have LCOM4 above 3.

What to do

1. Resolve the 23 Low cohesion finding(s) in Cohesion (LCOM4) — start with AccessionAttachmentType.cs, AccessionStatus.cs, AuditLogAction.cs. — One of this dimension's main actionable groups (23 warning-level).
2. Enforce Cohesion (LCOM4) in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Verified — provenance only; does not change the score.

Detailed fixes: d6_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether the test suite has a healthy mix of unit / integration / end-to-end tests.

Method: Test projects classified (Unit/Integration/BDD/E2E) from compiled metadata; test methods counted exhaustively across projects with placement-agnostic disk fallback. Deterministic.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

370 test methods: 140 unit, 230 integration, 0 BDD, 0 e2e.

✓ On the Gold path — maintain.

Detailed fixes: d9_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether the tests truly assert behaviour rather than just running the code.

Method: Per-test assertions, skips, and mock references analyzed via Roslyn; structured skip-reason tags (BUG:/ENV:) separate documented deferrals from debt. Deterministic.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Prevented

67 skipped (67 with a documented reason), 0 zero-assertion, 4 mock references across 370 tests.

✓ On the Gold path — maintain.

Detailed fixes: d10_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether the tests pass reliably, with no flakiness.

Method: Suite re-run N times within tiered wall-clock budgets (unit to e2e); tests failing non-deterministically across runs flagged; guarded tests retried when #if guards detected.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Verified

0 flaky across 3 measured tier(s). unit: measured (0 flaky); integration: measured (0 flaky); other: measured (0 flaky).

✓ On the Gold path — maintain.

Detailed fixes: d11_recommendation.md.

What it measures: Whether dependencies are current, secure, and not bloated.

Method: Manifest scan via dotnet list package across all projects; worst-signal-per-package deduction (saturating for vulnerabilities, capped-linear for deprecation/outdated) per KLoC. Exhaustive, deterministic.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Verified

0 outdated, 0 vulnerable, 0 deprecated packages.

✓ On the Gold path — maintain.

Detailed fixes: d12_recommendation.md.

What it measures: Whether any secrets (keys, tokens, passwords) have leaked into the code.

Method: In-process native secret scanner (entropy plus signature patterns) across all tracked files; no external tool. A clean result is a measured 10, not no-data zero. Deterministic.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Prevented

Secret scan ran and found no leaked secrets.

✓ On the Gold path — maintain.

Detailed fixes: d13_recommendation.md.

What it measures: Whether the licenses of third-party packages are compatible with your policy.

Method: Third-party package licenses resolved from declared package metadata and checked against the configured policy (allow/deny/copyleft). Deterministic; clean = no incompatible license found at metadata depth.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Verified

0 of 62 packages use a banned license.

✓ On the Gold path — maintain.

Detailed fixes: d14_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Files that change often and are also complex — the riskiest hotspots.

Method: Per production file churn times cyclomatic complexity over a rolling window, computed from git and Roslyn/JS/Razor analysis. Exhaustive, deterministic per commit date.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

No churn × complexity hotspots in the window.

✓ On the Gold path — maintain.

Detailed fixes: d15_recommendation.md.

What it measures: Whether knowledge is concentrated in too few people (the "bus factor").

Method: Living knowledge per author via time-decayed commit attribution (6-month half-life, focus weighting) across largest source files. Deterministic, avoids blame's mechanical-refactor false positives.

Maturity: Documented → Verified → Prevented · effective 7.8 / 10 · rule-coverage 100% · ceiling Documented

70 source file(s) have their living knowledge concentrated in one author (≥90% of recent, decayed contribution). The largest is PeakLims/src/PeakLims/Domain/Gaia/Features/Generators/PanelTestGenerator.cs, held by pdevito3@gmail.com.

What to do

1. Resolve the 1 Small-team knowledge concentration finding(s) in Bus Factor. — One of this dimension's main actionable groups (1 recommendation-level).
2. Resolve the 1 Off-boarding risk finding(s) in Bus Factor. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d16_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Acknowledged debt left in the code — TODOs, dead code, suppressed warnings.

Method: Roslyn syntactic debt markers (suppressions/TODO/FIXME/HACK/empty-catch/commented-code/Obsolete) plus SymbolFinder dead-code analysis; weighted-debt-per-KLoC density deducted 2.0x per unit. Deterministic, exhaustive.

Maturity: Documented → Verified → Prevented · effective 8.4 / 10 · rule-coverage 100% · ceiling Prevented

50 deducted debt markers + 5 dead symbols across 17218 LoC (0.8/KLoC) → score 8.4.

What to do

1. Resolve the 8 NoWarnInCsproj finding(s) in Explicit Debt — start with PeakLims.csproj (8). — One of this dimension's main actionable groups (8 issue-level).
2. Resolve the 22 TodoComment finding(s) in Explicit Debt — start with Accession.cs (6), Lifespan.cs (2), Address.cs. — One of this dimension's main actionable groups (22 warning-level).
3. Resolve the 16 CommentedOutCode finding(s) in Explicit Debt — start with UserPolicyHandlerTests.cs (11), FakeAccessionContactBuilder.cs (2), PeakLimsOptions.cs. — One of this dimension's main actionable groups (16 warning-level).
4. Enforce Explicit Debt in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d17_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether the solution is laid out in a sensible, conventional structure.

Method: Solution structure: project count, decomposition, shell-project detection, build success (confirmed failures cap the score); traced to actual .sln files and binaries. Deterministic.

Maturity: Documented → Verified → Prevented · effective 9.0 / 10 · rule-coverage 100% · ceiling Documented

8 projects, 762 .cs files, 28405 hand-written lines of code (17218 production / 11187 test), plus 15972 generated (EF migrations / designer / snapshots, excluded from quality), 12 inter-project edges.

+ 4 more group(s) — more in Appendix A; the complete list is findings.md.

✓ On the Gold path — maintain.

Detailed fixes: d18_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether the project's documentation is clear, complete, and useful.

Method: Judged by language model at low temperature (0.0-0.1) on a deterministic doc sample (READMEs plus first 25 architecture docs), with two-pass stability filtering. Advisory, sampled.

Maturity: Documented → Verified → Prevented · effective Fair / 10 · rule-coverage 100% · ceiling Documented

The project contains a functional README and a detailed architecture guide, but suffers from incomplete content and low code documentation. The README provides basic setup steps but is truncated and lacks critical context. The architecture document is well-structured but cuts off before completing key sections. Additionally, the majority of the codebase (PeakLims, PeakLimsIdp, PeakLimsSpa.Bff) lacks XML documentation, indicating a significant gap in inline code documentation.

What to do

1. Resolve the 3 Low XML-doc coverage finding(s) in Documentation Quality — start with PeakLims.csproj, PeakLimsIdp.csproj, PeakLimsSpa.Bff.csproj. — One of this dimension's main actionable groups (3 warning-level).

Detailed fixes: d19_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether architecture decisions are recorded well (context, decision, consequences).

Method: Per-ADR judgment by language model at low temperature with two-pass stability; confidence is share of ADRs evaluated; enforcement-field presence detected deterministically. Advisory.

Maturity: Documented → Verified → Prevented · effective Critical / 10 · rule-coverage 100% · ceiling Documented

No architecture decision records were found.

What to do

1. Resolve the 1 No ADRs found finding(s) in ADR Quality. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d20_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether names — types, methods, variables — are clear and consistent.

Method: Judged by language model at low temperature (0.0-0.1) on a deterministic random symbol sample (fixed size, not exhaustive), with disclosed confidence band. Advisory, sampled.

Maturity: Documented → Verified → Prevented · effective Exemplary / 10 · rule-coverage 100% · ceiling Verified

0 naming inconsistencies across 200 sampled symbols.

✓ On the Gold path — maintain.

Detailed fixes: d21_recommendation.md.

What it measures: Whether the internal API surface is consistent and coherent.

Method: Judged by language model at low temperature over a sample of the public API surface (IsPackable or .Contracts types). Sampled, advisory; confidence discounted by model uncertainty.

Maturity: Documented → Verified → Prevented · effective Exemplary / 10 · rule-coverage 100% · ceiling Verified

No public API surface exposed; nothing to be inconsistent.

✓ On the Gold path — maintain.

Detailed fixes: d22_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether comments are worth it — explaining WHY (valuable) rather than WHAT (redundant).

Method: Judged by language model at low temperature (0.0-0.1) on deterministically sampled inline comments with surrounding code; findings verified back to sampled comments by substring match. Advisory, sampled.

Maturity: Documented → Verified → Prevented · effective Poor / 10 · rule-coverage 100% · ceiling Documented

12 valuable / 45 redundant across 200 sampled comments; 5 shown with locations.

What to do

1. Resolve the 4 redundant comment finding(s) in Comment Value — start with AccessionCommentConfiguration.cs, ContainersController.cs, DeleteAccessionAttachmentCommandTests.cs. — One of this dimension's main actionable groups (4 recommendation-level).

Detailed fixes: d24_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether each project is a focused, coherent unit rather than an oversized grab-bag.

Method: Project size overshoot penalties (LoC / public-type count / namespace count, 2-of-3 flag) weighted by log magnitude. Exhaustive across projects, deterministic, LLM-independent.

Maturity: Documented → Verified → Prevented · effective 7.5 / 10 · rule-coverage 100% · ceiling Documented

1 of 8 projects flagged as possibly oversized/incoherent.

What to do

1. Resolve the 1 Split PeakLims finding(s) in Project Cohesion. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d26_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: How far you must trace to follow a call — low indirection and co-located slices read easier.

Method: Call indirection (interface hops, cross-namespace calls, slice-locality scaled) over a sampled set of method invocations, size-aware baseline. Sampled; confidence discounted by symbol-resolution gaps.

Coverage: Slice locality from the first namespace segments, SAMPLED (≤400 methods) — not exhaustive.

Maturity: Documented → Verified → Prevented · effective 7.4 / 10 · rule-coverage 100% · ceiling Documented

95 % of calls cross a namespace and 17 % go through an interface, but 90 % of collaborators are co-located — so a call's collaborators sit together and tracing stays easy. Baseline: medium — clean/modular boundaries expected.

What to do

1. Improve Navigability — currently 7.4/10. — 95 % of calls cross a namespace and 17 % go through an interface, but 90 % of collaborators are co-located — so a call's collaborators sit together and tracing stays easy. Baseline: medium — clean/modular boundaries expected.

Detailed fixes: d27_recommendation.md.

What it measures: Whether any secrets were ever committed — scanned across the full git history, not just now.

Method: Git-history secret scan via gitleaks detect over full history in an isolated checkout; each match flagged High. Exhaustive; degrades cleanly when tool absent.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

gitleaks scanned the full history AND the current working tree and found no secrets.

✓ On the Gold path — maintain.

Detailed fixes: d28_recommendation.md.

What it measures: Real static-analysis (SAST) findings — likely security bugs in the code, any language.

Method: Polyglot static analysis via semgrep --config auto across the repo; severity rules (ERROR/WARNING/INFO) map to a 0-10 wide normalizer. Exhaustive, deterministic; degrades on parse failure.

Coverage: semgrep pattern rules over all files — exhaustive for the rule set, blind to classes of bug without a rule (clean = no rule matched).

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

semgrep found no security issues.

✓ On the Gold path — maintain.

Detailed fixes: d29_recommendation.md.

What it measures: Whether any dependencies have known published vulnerabilities (CVEs), direct or transitive.

Method: NuGet CVE scan via dotnet list package --vulnerable including transitive; severity tally (Critical/High/Medium/Low) to 0-10 tight normalizer. Exhaustive, deterministic; degrades when absent.

Maturity: Documented → Verified → Prevented · effective 5.5 / 10 · rule-coverage 100% · ceiling Documented

8 vulnerable package(s): 2 critical, 2 high, 4 medium, 0 low.

What to do

1. Resolve the 4 Medium CVE finding(s) in Dependency Vulnerabilities. — One of this dimension's main actionable groups (4 warning-level).
2. Resolve the 2 Critical CVE finding(s) in Dependency Vulnerabilities. — One of this dimension's main actionable groups (2 issue-level).
3. Resolve the 2 High CVE finding(s) in Dependency Vulnerabilities. — One of this dimension's main actionable groups (2 issue-level).

Detailed fixes: d30_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether Dockerfiles / Terraform / Kubernetes config follow security best practices.

Method: IaC/container misconfiguration scan via trivy config (Dockerfile/Terraform/K8s/Helm/CloudFormation); severity rules to 0-10 moderate normalizer. NotApplicable without manifests. Exhaustive, deterministic.

Maturity: Documented → Verified → Prevented · effective 9.6 / 10 · rule-coverage 100% · ceiling Documented

2 finding(s): 0 critical, 1 high, 0 medium, 1 low.

✓ On the Gold path — maintain.

Detailed fixes: d31_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether anyone still has living knowledge of each file, or it has been orphaned — last understood long ago by someone now gone quiet. The sibling of the bus factor: D16 asks who owns it, D34 asks whether anyone still knows it.

Method: File orphaning as total living-knowledge decay below one focused-commit's worth within a year, computed per-file from the D16 decay model. Exhaustive, deterministic over fixed history.

Maturity: Documented → Verified → Prevented · effective 1.9 / 10 · rule-coverage 100% · ceiling Documented

66 of 80 significant source file(s) are orphaned — their living knowledge has decayed to nothing, so no one currently understands them. The largest is PeakLims/src/PeakLims/Domain/RelationshipTypes/RelationshipType.cs.

What to do

1. Resolve the 1 Dormant codebase finding(s) in Knowledge Freshness. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d34_recommendation.md · top locations in Appendix A, every location in findings.md.

What it measures: Whether files that change together actually belong together — pairs that repeatedly co-change in git history despite having no explicit code dependency, surfacing the hidden/logical coupling (and boundaries in the wrong place) a static scan can't see.

Method: Pairwise co-occurrence over the per-commit file sets in git history (production source only — tests and generated dropped): Degree-of-Coupling = shared ÷ min individual revisions, reported above noise floors (each file ≥10 revisions, ≥5 shared commits, ≥50% strength); sweeping commits excluded. Deterministic over fixed history.

Coverage: Population: PRODUCTION source files only — test and generated files are dropped before pairing, so a class co-changing with its own test (trivially ~100%) can't drown the real production↔production coupling. Pairs ranked by Degree-of-Coupling; coupling through a build step, config, or non-source file isn't seen.

Maturity: Documented → Verified → Prevented · effective 9.9 / 10 · rule-coverage 100% · ceiling Documented

Strongest change-coupling: EditableAccessionDto.cs↔AccessionMapper.cs 90%; GetEditableAccessionAggregate.cs↔AccessionMapper.cs 73%; EditableAccessionDto.cs↔GetEditableAccessionAggregate.cs 60%

✓ On the Gold path — maintain.

Detailed fixes: d35_recommendation.md.

Other · Architecture — Whether any singleton service captures a scoped/transient dependency — a silent lifetime/threading bug.

Method: Roslyn scan: DI registrations parsed from AddSingleton/Scoped/Transient; each singleton checked for captured shorter-lifetime dependencies. Exhaustive, deterministic.

Other · Architecture — How the codebase splits by code ROLE — domain, application, infrastructure, test, generated. The significance map behind the knowledge/coupling weighting, and a DDD signal in its own right: a thin domain core under fat infrastructure is the anemic-domain smell, quantified.

Method: Roslyn line-count by code ROLE: every source file classified Domain/Application/Infrastructure/Test/Generated by namespace + path convention (the shared CodeRoleClassifier), then significant lines summed per role. Deterministic; the advisory score is the business-logic (domain+application) share of production code.

Coverage: Population: ALL source files, each bucketed into ONE of five roles (Domain/Application/Infrastructure/Test/Generated) by namespace + path convention — a file whose layer isn't named in the convention falls to Application (the neutral default), and the split is line-count, not semantic depth or business value.

Other · Architecture — Whether the project-reference graph is acyclic (cycles block independent build/deploy and signal eroding boundaries).

Method: Project reference cycles via elementary-DFS over real .csproj references, using the engine shared with D5/D7; cyclic versus acyclic. Exhaustive, deterministic.

Other · Architecture — Whether the codebase has a recognisable, scale-appropriate structure (a named architectural style, or modular enough for its size) rather than being an ad-hoc ball of mud.

Method: Roslyn plus csproj analysis: architecture style detection (DDD, clean, vertical-slice, CQRS) and structure fitness for repo size. Deterministic.

Other · Architecture — Whether interfaces stay focused rather than fat — the Interface-Segregation principle (SOLID 'I').

Method: Roslyn scan: public interface member counts; fat-interface threshold (over 15 members) flagged per type. Deterministic, type-level.

• `ICurrentUserService` declares 23 members. A wide interface forces every implementer and caller to depend on methods they don't use (the Interface-Segregation 'I' in SOLID). Split it into focused role-interfaces. — CurrentUserService.cs:7

What to do

• Split fat interfaces into focused role-interfaces so clients depend only on what they use.

Other · Architecture — Whether feature slices stay independent (no direct cross-slice references) — the discipline that makes vertical-slice architecture pay off.

Method: Roslyn scan (vertical-slice gated): feature slices resolved from namespaces (.Features.*, .Slices.*) or project names; cross-slice type references detected. Deterministic, traceable.

Other · Architecture — Whether production projects stay free of references to test projects — tests may depend on production, never the reverse.

Method: Csproj graph: each production project checked for references to test projects (identified by test-framework presence, not name). Zero violations is clean. Deterministic.

Other · Architecture — Whether read (query) handlers stay side-effect-free — a query that writes persistent state or raises events breaks CQS and makes reads unsafe to retry, cache, or route to a read replica.

Method: Roslyn scan: CQRS handlers classified query-vs-command by interface (IQueryHandler/ICommandHandler/IRequestHandler<TQuery,TResult>) and name convention (*Query/Get*/Find* vs *Command); each query handler's body checked for persistent-state writes (SaveChanges/repository Add-Update) or event publishes by resolved invocation. Deterministic, type-level, exhaustive over the detected handlers.

Coverage: Population: CQRS handlers identified by IQueryHandler/ICommandHandler/IRequestHandler interface + *Query/Get*/Find*/*Command NAME convention; query purity then checked exhaustively within that set — a query handler using neither convention is invisible, and mutation is a resolved persistence/publish CALL, not full dataflow.

Other · Security — Whether sensitive data is encrypted at rest and in transit and keys are vaulted.

Method: Roslyn plus filesystem scan: encryption presence (EF ColumnEncryption, key-vault references, HTTPS enforcement) and key-derivation KDF detection. Deterministic.

• No data-protection or encryption usage (ASP.NET Data Protection, AES, column encryption, PBKDF2) was found — sensitive data at rest may be unprotected. If TDE/KMS/vault is delegated to infrastructure, ignore.

What to do

• Encrypt sensitive data at rest (ASP.NET Core Data Protection / column encryption) and manage keys in a vault. Skip if delegated to infra (Postgres TDE, KMS, etc.).

Other · Security — Whether access is authorized by default — [Authorize]/policies or imperative guard methods (throw-on-violation) called from handlers.

Method: Roslyn scan: [Authorize] usage and authorization policies, plus imperative throw-on-violation guard methods detected via syntax. Deterministic.

Other · Security — Whether changes to sensitive data are recorded (who, what, when) for compliance + incident response.

Method: Roslyn scan: audit-trail mechanism graded (SaveChanges interceptor/immutable AuditLog/[Audited] strong; bare IAuditable/AddAuditing weak). Deterministic.

Other · Domain Modelling — How much of the domain uses strongly-typed ids vs raw Guid/string/int — adoption curve, not all-or-nothing.

Method: Roslyn (DDD-gated): strongly-typed id adoption on domain entities/events; raw Guid/int/string ids counted versus wrapped types. Deterministic, adoption percentage.

Coverage: Population: id-like members by *Id/*Key NAME suffix; strongly-typed-ID shape then checked semantically — non-suffixed identifiers are not seen.

• `PanelTestAssignment.TestId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct TestId { Guid Value }`). — PanelTestAssignment.cs:8
• `PanelTestAssignment.PanelId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct PanelId { Guid Value }`). — PanelTestAssignment.cs:10
• `Accession.OrganizationId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct OrganizationId { Guid Value }`). — Accession.cs:31
• `Container.OrganizationId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct OrganizationId { Guid Value }`). — Container.cs:15
• `HealthcareOrganization.OrganizationId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct OrganizationId { Guid Value }`). — HealthcareOrganization.cs:25
• `HipaaAuditLog.OrganizationId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct OrganizationId { Guid Value }`). — HippaAuditLog.cs:27
• `Panel.OrganizationId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct OrganizationId { Guid Value }`). — Panel.cs:29
• `PatientRelationship.FromPatientId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct FromPatientId { Guid Value }`). — PatientRelationship.cs:9
• `PatientRelationship.ToPatientId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct ToPatientId { Guid Value }`). — PatientRelationship.cs:11
• `Patient.InternalId` is a raw `String` — give it a strongly-typed id (`readonly record struct InternalId { String Value }`). — Patient.cs:37
• `Patient.OrganizationId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct OrganizationId { Guid Value }`). — Patient.cs:40
• `Sample.ExternalId` is a raw `String` — give it a strongly-typed id (`readonly record struct ExternalId { String Value }`). — Sample.cs:20
• `Test.OrganizationId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct OrganizationId { Guid Value }`). — Test.cs:27
• `User.OrganizationId` is a raw `Guid` — give it a strongly-typed id (`readonly record struct OrganizationId { Guid Value }`). — User.cs:24

What to do

• Adopt strongly-typed ids across the domain — finish the migration or document the boundary; primitive ids invite transposed-argument bugs.

Other · Domain Modelling — Whether aggregates/entities carry the behaviour that protects their invariants, rather than being data bags driven by external services.

Method: Roslyn (DDD-gated): entity method BODIES classified mutator-vs-query — only methods that mutate the entity's own declared state count as invariant-protecting behaviour, so a getter/passthrough doesn't rescue an anemic class. Deterministic, exhaustive over domain-layer entities.

Coverage: Population: entities by name/base convention; rich-vs-anemic judged by classifying each method body mutator-vs-query — logic-bearing domain types outside the convention are invisible.

Other · Domain Modelling — Whether entities protect their state (private/init-only setters) instead of exposing public setters that bypass invariants. Softened when a rehydration framework (Marten/EF) is present.

Method: Roslyn (DDD-gated): public setters on entities detected; score softened when Marten/EF rehydration frameworks present. Deterministic, framework-aware.

Coverage: Population: entities by convention; encapsulation (setter shape) checked exhaustively within the set.

• `AccessionAttachment` exposes public setter(s) (Type). — AccessionAttachment.cs:13
• `HealthcareOrganization` exposes public setter(s) (KnownDomain). — HealthcareOrganization.cs:15

What to do

• Make entity setters private/init-only; change state only through methods that enforce the invariants (Marten/EF can bind via constructor or private setters).

Other · Domain Modelling — Whether the domain layer stays free of infrastructure dependencies (EF/Marten/HTTP/ASP.NET) — the clean-architecture dependency rule.

Method: Roslyn (DDD-gated): domain-layer types scanned for infrastructure usage in member SIGNATURES and inside method/accessor BODIES — resolved calls and object-creations into EF/Marten/HTTP/Mongo/Redis/message-bus types (not just a namespace allowlist). Deterministic, symbol-resolved, exhaustive over domain-layer bodies, DDD-native.

Coverage: Domain layer identified by NAMESPACE heuristic; infrastructure then resolved by symbol in member SIGNATURES and method/accessor BODIES — rename the layer and the check evaporates.

• `AccessionAttachment` (domain layer) references `Microsoft.AspNetCore.Http` — an infrastructure concern (persistence/HTTP/web). — AccessionAttachment.cs:13
• `UploadAccessionAttachmentDto` (domain layer) references `Microsoft.AspNetCore.Http` — an infrastructure concern (persistence/HTTP/web). — UploadAccessionAttachmentDto.cs:3
• `Handler` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. (×28) — GetAccessionAttachmentList.cs:20, GetAccessionCommentView.cs:20, GetAccessionContactList.cs:19, …
• `Command` (domain layer) references `Microsoft.AspNetCore.Http` — an infrastructure concern (persistence/HTTP/web). — UploadAccessionAttachmentFile.cs:13
• `AccessionCommentRepository` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. — AccessionCommentRepository.cs:12
• `AccessionGenerator` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. — AccessionGenerator.cs:29
• `HealthcareOrganizationContactGenerator` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. — HealthcareOrganizationContactGenerator.cs:17
• `HealthcareOrganizationGenerator` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. — HealthcareOrganizationGenerator.cs:21
• `OrganizationGenerator` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. — OrganizationGenerator.cs:20
• `PanelTestGenerator` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. — PanelTestGenerator.cs:17
• `PatientGenerator` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. — PatientGenerator.cs:25
• `UserInfoGenerator` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. — UserInfoGenerator.cs:19
• `PanelRepository` (domain layer) uses `EF Core` inside a method body — infrastructure reached without it appearing in any signature. — PanelRepository.cs:13
• 37 further occurrence(s) are not listed individually; the score already reflects all 77.

What to do

• Invert domain→infrastructure dependencies: declare interfaces in the domain, implement them in infrastructure (Dependency Inversion).

Other · Domain Modelling — Whether repositories are per aggregate root (not per child entity) so the root's invariants can't be bypassed.

Method: Roslyn (DDD-gated): repository abstraction detection; repositories over non-aggregate-root entities flagged. Deterministic, DDD-native.

Coverage: Population: repositories + aggregate roots by NAME convention; per-root repository rule checked within the set.

Other · Domain Modelling — Whether clusters of primitives that travel together (a missing value object) are extracted — a low-weight suggestion, LLM-confirmed when configured.

Method: Roslyn (DDD-gated): primitive parameter clusters recurring three or more times across signatures extracted, then confirmed by language model when configured. Advisory, low-weight.

Other · Event-Driven — Whether event handlers stay asynchronous (no blocking remote HTTP/gRPC calls awaited inside a handler).

Method: Roslyn semantic scan (event-driven gated): event-handler bodies scanned for HTTP/gRPC invocations by resolved symbol type, not substring. Deterministic, semantic-resolved.

Other · Event-Driven — Whether commands have a single handler (one owner of the decision) and fan-out is modelled with events.

Method: Roslyn scan (event-driven gated): command-shaped messages identified by convention; handler count per command checked for the exactly-one rule. Deterministic, hard fact.

Other · Event-Driven — Whether events are named in the past tense (a clarity nudge — low weight).

Method: Roslyn scan (event-driven gated): domain and integration events checked for past-tense naming (-ed/-en suffix or irregular set). Naming nudge, low-weight advisory.

• `DomainEvent` reads as an instruction, not a fact that happened. Events describe something that already occurred — name them in the past tense (e.g. `OrderPlaced`, `PaymentCaptured`) so the ubiquitous language stays clear. — DomainEvent.cs:6

What to do

• Name events in the past tense — they record facts that already happened.

Other · Event-Driven — Whether state changes and message publishes are atomic (a transactional outbox) rather than a crash-unsafe dual write.

Method: Roslyn semantic scan (event-driven gated): event-handler methods scanned for DB-save plus bus-publish without a transactional outbox reference. Deterministic, semantic-resolved.

Other · Readiness — Whether retry-prone mutations (command handlers + message/event consumers) are idempotent so an at-least-once redelivery or client retry doesn't double-apply the effect — heuristic at-risk detection confirmed by language model, advisory.

Method: Roslyn heuristic (any mutation, ungated): command handlers and message/event consumers that mutate persistent state without a visible idempotency guard (exists/dedup check, upsert, idempotency-key/inbox, conditional/versioned write, fixed-value set) flagged as at-risk; each at-risk candidate then confirmed or cleared by a language model as genuinely non-idempotent versus naturally-idempotent. Advisory without a model (heuristic-only, degraded), per-candidate judged with one.

Coverage: Population: retry-prone mutations — command handlers (CQRS write side) + message/event consumers (IConsumer/I*EventHandler) — that mutate persistent state; runs on any repo with mutations, not only event-driven ones. The at-risk subset (no obvious guard) is a HEURISTIC candidate set, each then LLM-JUDGED non-idempotent vs safe; a handler outside those conventions, or a guard the LLM can't confirm, is bounded by the sample. Degrades to heuristic-only when no model is configured.

• `Features.AuditPatientCreation.Handle` mutates persistent state (a repository write) with no idempotency guard, and the model confirms a re-run would double-apply it. A retry or at-least-once redelivery means it can run twice — add an exists/dedup check, an upsert, an idempotency-key/inbox, or a versioned write. — AuditPatientCreation.cs:24
• `Features.AuditPatientDeleted.Handle` mutates persistent state (a repository write) with no idempotency guard, and the model confirms a re-run would double-apply it. A retry or at-least-once redelivery means it can run twice — add an exists/dedup check, an upsert, an idempotency-key/inbox, or a versioned write. — AuditPatientDeleted.cs:23
• `Features.AuditPatientUpdate.Handle` mutates persistent state (a repository write) with no idempotency guard, and the model confirms a re-run would double-apply it. A retry or at-least-once redelivery means it can run twice — add an exists/dedup check, an upsert, an idempotency-key/inbox, or a versioned write. — AuditPatientUpdate.cs:24

What to do

• Make retry-prone mutations idempotent — guard each write with an exists/dedup check, an upsert, an idempotency-key/inbox, or a versioned write, so a re-run doesn't double-apply.

Other · Code Health — Unreviewed-generation residue: shipped members still throwing NotImplementedException, and placeholder string literals left in non-test, non-generated code. Scored as a quality signature, never as a claim about authorship.

Method: Roslyn syntax scan: NotImplementedException throws and placeholder string literals in non-test, non-generated shipped code. Deterministic, code-shape signature.

• A shipped member still throws NotImplementedException — generated scaffolding that was never completed. Implement it or remove the dead surface. — InfrastructureServiceExtension.cs:80

What to do

• Finish or delete NotImplementedException stubs and replace placeholder literals before shipping.

Other · Code Health — Unfinished work detected by code SHAPE, not keywords: members that only throw a "not implemented" exception, methods that take inputs and return a constant, async methods that never await, dead `if (false)` / `#if false` branches, and skeleton types most of whose members are holes. A real, objective slice of technical debt.

Method: Roslyn syntax scan: incompleteness by code shape (constant-returning methods, async-never-await, #if false branches, skeleton types), not keyword-gated. Deterministic, code-shape heuristic.

• `GetCancellationReasons` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. (×2) — PanelOrdersController.cs:98, TestOrdersController.cs:139
• `StopAsync` looks like it should compute a result but its body just returns a constant — a placeholder return that was never filled in. — MigrationHostedService.cs:48
• `AddWholeGenomeSequencing` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. — PanelTestGenerator.cs:102
• `AddOpticalGenomeMapping` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. — PanelTestGenerator.cs:189
• `AddTranscriptomeSequencing` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. — PanelTestGenerator.cs:256
• `AddCombinedSequencing` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. — PanelTestGenerator.cs:324
• `AddCombinedOgmWgsSequencing` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. — PanelTestGenerator.cs:392
• `AddCombinedOgmExternalDataAnalysis` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. — PanelTestGenerator.cs:460
• `AddBasicExomeSequencing` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. — PanelTestGenerator.cs:528
• `AddExpandedExomeSequencing` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. — PanelTestGenerator.cs:602
• `GetSuggestedMatchingRole` looks like it should compute a result but its body just returns a constant — a placeholder return that was never filled in. (×6) — RelationshipType.cs:271, RelationshipType.cs:277, RelationshipType.cs:283, …
• `OnCreated` takes parameters but its body is empty — it accepts inputs and does nothing. Either implement it or remove it. (×2) — CurrentUserFilterAttribute.cs:23, JobUserFilterAttribute.cs:14
• `ConvertToListAsync` is declared `async` but never awaits anything, so it runs synchronously while pretending to be asynchronous. Drop `async` or do the real async work. — IAsyncEnumerableExtensions.cs:5
• A line of code has been commented out rather than removed — dead weight that rots and confuses. Delete it (version control remembers). (×10) — AccessionAttachmentConfiguration.cs:31, AccessionAttachmentConfiguration.cs:32, AccessionAttachmentConfiguration.cs:33, …

What to do

• Finish or delete the unfinished stubs (NotImplementedException / empty / constant-returning bodies) — they are dead surface that looks live.
• Clear the softer debt: remove commented-out code and dead branches, re-enable or delete skipped tests, and replace blanket warning suppressions with targeted ones.

Maturity · Maturity — Whether the repo and its projects have a README, and whether it's substantive and current.

Method: Filesystem scan: README presence, word count, and headings for depth; git history for staleness. Exhaustive across root and project dirs, deterministic.

What to do

• Add an 'Architecture' / 'How it works' section to the root README — the high-level shape.
• Add a README to the 8 of 8 project(s) that lack one — worth up to 2 pts.

Maturity · Maturity — Whether key decisions (ADRs) and the high-level shape (C4/diagrams) are written down.

Method: Filesystem scan: ADR folder/naming conventions or content, plus Mermaid/PlantUML/C4/architecture.md discovery. Exhaustive, deterministic.

• No Architecture Decision Records found — decisions aren't captured for future maintainers.

What to do

• Start an ADR log (docs/adr/) recording significant decisions and their rationale.

Maturity · Maturity — Whether the repo is organised deliberately — src/test separation and consistent project naming.

Method: Filesystem scan: src/test folder separation and namespace-prefix consistency (majority RootNamespace agreement). Exhaustive across projects, deterministic.

• Projects aren't grouped under a src/ folder — production and tooling code are mixed at the root.
• Test projects aren't grouped under a tests/ folder — the test surface isn't separable from production code at a glance.

What to do

• Group production code under src/ (or split deliberately, e.g. backend/ + frontend/) so production and tooling code aren't mixed at the root.
• Group test projects under tests/ (or test/, spec/) so the test surface is discoverable and CI can scope it.

Maturity · Maturity — Whether the README actually describes the code that exists (LLM-judged, advisory).

Method: Judged by language model at low temperature: README accuracy versus actual projects, within a disclosed tolerance. Advisory, not a measured number.

• The README mentions running migrations in the 'boundary' project.

What to do

• Reconcile the README with reality: The README mentions running migrations in the 'boundary' project..

Readiness · Readiness — Whether an automated pipeline builds and tests every change.

Method: Filesystem scan: CI workflow files (.github/workflows, .gitlab-ci.yml, etc.) for build and test stages. Exhaustive, deterministic.

Readiness · Readiness — Whether the code is diagnosable in production — structured logging, tracing/metrics, health checks.

Method: Filesystem/Roslyn scan: structured-logging frameworks (Serilog, NLog), OpenTelemetry, and health-check endpoint patterns. Exhaustive, deterministic.

• Only 2/3 service-like projects use logging (pure contract/DTO projects are excluded — they have nothing to log).

What to do

• Extend structured logging to the remaining service-like projects so the whole executable surface is diagnosable in production.

Readiness · Readiness — Whether SAST, secret/dependency scanning and performance benchmarking are wired in (presence, not runtime).

Method: Filesystem/Roslyn scan: CodeQL, Dependabot, secret-scanning, and BenchmarkDotNet presence in pipelines and projects. Exhaustive, deterministic.

• No static application security testing (CodeQL / security analyzers / codehealth) detected.

What to do

• Add a SAST step (e.g. CodeQL) or a security analyzer package.
• Enable Dependabot/Renovate or a dependency-review gate.
• Add gitleaks/trufflehog in CI to block PRs that introduce committed secrets.

Readiness · Readiness — Whether releases are automated and safely reversible (probes, rolling updates, approval gates) — from manifests/pipeline files, not the live environment.

Method: Filesystem scan: deployment manifests/IaC (K8s YAML, Helm, Terraform) for rolling updates, probes, approval gates, migration hooks. Exhaustive, deterministic.

• Deployment automation exists but no readiness/liveness probes, rolling-update strategy, lifecycle hooks or migration job were evidenced — a bad release is harder to detect and reverse.

What to do

• Add readiness/liveness probes and a rolling-update (or blue/green) strategy so a bad release is caught and rolled back automatically.
• Add an approval/environment gate (required reviewers / protection rules) before production promotion.

Readiness · Readiness — Whether disaster recovery is planned and codified — backups, geo-recovery, RTO/RPO, persistence guarantees — from IaC + container manifests + docs, never the live cloud.

Method: Filesystem scan: disaster recovery, backup, geo-recovery, RTO/RPO, persistence guarantees from IaC, manifests, and docs. Exhaustive, deterministic, never a live environment.

• A persistence guard (data volume / purge-protection) was found, but no backup, geo-recovery or RTO/RPO controls were evidenced — a volume that survives a container recreate is not a tested restore from catastrophic loss.

What to do

• Codify backups + geo-recovery in IaC and document RTO/RPO and the restore procedure — a persistence guard alone is not disaster recovery.

Readiness · Readiness — Whether outbound HTTP calls are wrapped in resilience (retry/timeout/circuit-breaker) so a failing dependency doesn't cascade.

Method: Roslyn scan: Polly resilience markers (Retry, CircuitBreaker, Timeout) on outbound HTTP invocations. Computed per type, deterministic.

• The app makes outbound HTTP calls but no resilience handler was detected (Polly / AddStandardResilienceHandler / circuit-breaker). A slow or failing dependency will cascade — add timeouts, retries with back-off, and a circuit breaker.

What to do

• Add `AddStandardResilienceHandler()` (or Polly policies) to your HttpClient registrations so a flaky dependency can't take the app down.

Readiness · Readiness — Whether EF Core schema changes go through versioned migrations rather than the un-evolvable EnsureCreated().

Method: Roslyn scan: EF Core DbContext for a versioned migrations directory versus bare EnsureCreated usage. Exhaustive per project, deterministic.

Other · Security — Transport security, security headers, secure cookies, input validation, middleware order and crypto hygiene (presence, not runtime).

Method: Roslyn plus filesystem scan: HSTS/security headers, secure cookies, input validation, middleware order, weak crypto (MD5/SHA1/DES); HTTPS-metadata context-aware. Deterministic.

• No Content-Security-Policy / X-Frame-Options / X-Content-Type-Options configuration found — defense in depth, even when a reverse proxy could set them. (−2.0 on this card.)

What to do

• Add security response headers (Content-Security-Policy, X-Frame-Options, X-Content-Type-Options) — defense in depth, even when a reverse proxy could set them.

Other · Code Health — Whether the code avoids sync-over-async (deadlock-prone blocking on tasks) and async void.

Method: Roslyn syntax scan: async methods scanned for .Wait()/.GetAwaiter().GetResult() and async-void outside event handlers. Deterministic, hard fact per invocation.

• Blocking on a Task with `.Wait()`/`.GetAwaiter().GetResult()` can deadlock (and wastes a thread). Make the caller `async` and `await` instead. — PeakLimsDbContext.cs:173

What to do

• Sync-over-async (deadlock risk)

Other · Code Health — Whether async methods accept a CancellationToken so work can be cancelled (adoption curve).

Method: Roslyn scan: every async method (excluding framework-fixed overrides/Blazor handlers) checked for CancellationToken parameter presence. Deterministic, adoption percentage.

• Only 148/308 async methods accept a CancellationToken, so requests can't be cancelled cleanly under load or on client disconnect. In Blazor Server circuits and other short-write hosts, omitting it can be an accepted convention — judge against your hosting model.
• No CancellationToken parameter — work can't be cancelled cleanly on disconnect/shutdown. (×25) — AccessionAttachmentsController.cs:23, AccessionAttachmentsController.cs:53, AccessionAttachmentsController.cs:66, …

What to do

• Thread a CancellationToken through async methods so work stops promptly on cancellation.

Other · Code Health — Whether exceptions are handled rather than silently swallowed or rethrown with lost stack traces.

Method: Roslyn syntax scan: every catch clause counted; empty catches and bare rethrows flagged. Population is all catch clauses, not estimated. Deterministic, hard fact.

Other · Code Health — Whether log calls use message templates (queryable) rather than interpolated strings.

Method: Roslyn syntax scan: every log call-site counted; interpolated-string first-argument violations flagged. Population is all log calls, not estimated. Deterministic.

Other · Code Health — Whether nullable reference types are enabled and not undermined by heavy `!` suppression.

Method: Roslyn compiler-options scan: NullableContextOptions per project; null-forgiving (!) suppression density per 1k syntax nodes. Deterministic, adoption plus suppression penalty.

• 1/4 projects enable <Nullable>enable</Nullable>. NRTs catch a whole class of null-deref bugs at compile time.
• ~0.1 `!` suppressions per 1k syntax nodes — each one tells the compiler to trust you about null, suppressing the very safety NRTs provide.

What to do

• Enable <Nullable>enable</Nullable> across all projects and resolve warnings rather than suppressing with `!`.