[DEVSU-2860] apicalls to react query

[kttkjl]

Migrates API calls across the application from ad-hoc api.get() calls to react-query, establishing a centralized, auto-generated query layer.

Query infrastructure (app/queries/)

• queryKeys.ts — auto-generated from the OpenAPI spec via scripts/generateQueryKeys.ts; defines a typed, nested registry of all API route keys
• get.ts — auto-generated react-query hooks (e.g. useReportSummaryAnalystComments, useReportSignatures) built on a shared useAuthedQuery wrapper that gates requests on the presence of an auth token

Code generation scripts (scripts/)

• generateQueryKeys.ts — fetches the OpenAPI spec and emits queryKeys.ts
• generateQueryHooks.ts — reads queryKeys.ts and emits a hook for every key entry in get.ts

Migration scope

• ReportView subcomponents — AnalystComments, GenomicSummary, RapidSummary, Settings, TumourSummary, MutationBurden, Appendices, PatientInformation, KbMatches, and more
• Shared components — SignatureCard, TumourSummaryEdit, UserSettingsDialog, AddEditVariantText
• Top-level views — ReportsView, ReportsSearchView, MyReportsView, TemplateView, PrintView, PatientsView
• Single source of truth for report (ReportView/index.tsx, ReportContext)

Report data is now fetched once at the ReportView level and distributed via context, removing duplicated fetch logic in child components
ReportContext types updated to reflect the full ReportType

Other

• Removed useSignatures hook (superseded by generated hooks)
• tsx added as a dev dependency for running the generation scripts (pinned to ^3.14.0 for Node 16 compatibility; upgrade to ^4.x planned with Node 20 migration)
• Fixed AnalystComments test — queries were silently disabled due to missing SecurityContext.Provider (no auth token → enabled: false)

Future tasks

• the linked useQuery calls in rapidSummary view can probably use the new hooks
• update the build process to node 20 for up-to-date libraries (74 vulns atm)

[kttkjl]

Hooks all in, would probably need to revamp the usage of useContext(ReportContext) into useReport

but that useReport also coincides with the auto-generated API hooks, would probably rename useReport into useReportContext in the next commits while deprecating useContext(ReportContext)

[kttkjl]

Downgrading tsx to v3 for now, will make a ticket probably to migrate to node 20

[github-actions]

Test Results

    1 files  ±0    28 suites  ±0   5m 5s ⏱️ +11s
145 tests ±0  145 ✔️ ±0  0 💤 ±0  0 ❌ ±0 
142 runs  ±0  142 ✔️ ±0  0 💤 ±0  0 ❌ ±0 

Results for commit 1696853. ± Comparison against base commit 08c04b3.

[github-actions]

Test Results

    1 files  ±0    28 suites  ±0   4m 56s ⏱️ -10s
145 tests ±0  145 ✔️ ±0  0 💤 ±0  0 ❌ ±0 
142 runs  ±0  142 ✔️ ±0  0 💤 ±0  0 ❌ ±0 

Results for commit 03d2f19. ± Comparison against base commit 80ec189.

♻️ This comment has been updated with latest results.

[kttkjl]

useReport API call and useReport with the context is probably confusing when importing ...

[bnguyen-bcgsc]

In Tumour Summary, if I make changes and click save, the changes don't show up until I refresh the page