Y25-640 - Integrate model extensions and remove much API v1 code

[sabrine33]

Closes #5306 and #5136

• Removes model extensions from API v1, integrating them into the Rails models where appropriate
• Removes a significant amount (but not all) of API v1 code and tests

[codecov]

Codecov Report

❌ Patch coverage is 93.33333% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 82.54%. Comparing base (a4f03a7) to head (c24e0c7).

Files with missing lines	Patch %	Lines
app/models/plate.rb	83.33%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5309      +/-   ##
===========================================
- Coverage    84.96%   82.54%   -2.43%     
===========================================
  Files         1496     1313     -183     
  Lines        33967    32370    -1597     
  Branches      3622     3590      -32     
===========================================
- Hits         28861    26720    -2141     
- Misses        4259     4833     +574     
+ Partials       847      817      -30     

Flag	Coverage Δ
javascript	76.31% <ø> (ø)
ruby	82.39% <93.33%> (-2.43%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
• 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

[StephenHulme]

Line diff summary:

Path                                            │ Lines │ Graph
────────────────────────────────────────────────┼───────┼───────
.rubocop_todo.yml                               │   188 │ ❇️⛔
.ruby-version                                   │     2 │ ❇️⛔
Gemfile.lock                                    │    14 │ ❇️⛔
app/api/core/                                   │   566 │ ⛔⛔⛔
app/api/core/endpoint/                          │   112 │ ⛔
app/api/core/endpoint/basic_handler/            │     2 │ ❇️⛔
app/api/core/io/                                │     4 │ ⛔
app/api/core/io/base/json_formatting_behaviour/ │     2 │ ❇️⛔
app/api/core/service/                           │   222 │ ⛔⛔
app/api/                                        │     1 │ ⛔
app/api/endpoints/                              │   919 │ ⛔⛔⛔⛔⛔
app/api/endpoints/tube/                         │    11 │ ⛔
app/api/io/active_record/                       │    19 │ ⛔
app/api/io/                                     │  1376 │ ⛔⛔⛔⛔⛔⛔⛔
app/api/io/endpoints/uuids/                     │    14 │ ⛔
app/api/io/transfer/                            │   132 │ ⛔
app/api/io/tube/                                │    17 │ ⛔
app/api/model_extensions/                       │   497 │ ⛔⛔⛔
app/controllers/                                │     2 │ ⛔
app/middleware/api/                             │   329 │ ⛔⛔
app/models/accession_service/                   │     2 │ ❇️⛔
app/models/                                     │   354 │ ❇️⛔
app/models/extensions/                          │   200 │ ❇️
app/models/submission/                          │    15 │ ❇️⛔
app/models/transfer/                            │    12 │ ❇️⛔
app/validators/                                 │    11 │ ❇️⛔
config/                                         │     3 │ ⛔
features/api/                                   │  4201 │ ⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔
features/api/illumina_b/                        │   583 │ ⛔⛔⛔
features/api/npg/                               │    28 │ ⛔
features/api/pulldown/                          │   749 │ ⛔⛔⛔⛔
features/api/sample_manifests/                  │   364 │ ⛔⛔
features/api/searches/                          │   777 │ ⛔⛔⛔⛔
features/api/tag_qc/                            │   666 │ ⛔⛔⛔⛔
features/api/uk10k/                             │  1165 │ ⛔⛔⛔⛔⛔⛔
features/api/users/                             │    29 │ ⛔
features/submission/                            │   114 │ ⛔
features/support/                               │    63 │ ⛔
features/support/step_definitions/              │    30 │ ❇️⛔
lib/                                            │     4 │ ❇️⛔
spec/api/                                       │  2922 │ ⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔⛔
spec/api/core/                                  │    57 │ ⛔
spec/factories/                                 │     2 │ ❇️⛔
spec/models/                                    │     4 │ ❇️⛔
spec/                                           │     2 │ ⛔
spec/requests/                                  │    28 │ ⛔
spec/support/                                   │     1 │ ❇️

[BenTopping]

Are you planning to do a post-standup on this PR? Happy to take a look through this week although I think it will be tricky to discern anything given the size of the PR.

Also wondering whether this needs code review as it was pair programmed?

[StephenHulme]

Yes, that's the plan, hopefully this week (Thurs or Fri), otherwise early next week.

I think the biggest value in reviewing will be asking diffiult questions about things we haven't thought about, as well as knowledge-sharing about what we have learnt about Sequencescape. There's a fair amount of v1 functionality coming out, but probably less value in removing code to be removed.

[andrewsparkes]

Looks good. Lots of work, well done.