* Better ETL accessors (soon to action, analysis group)

* Apply pre-commit after rebase

* Docstring

* Add analysis group to etl accessors

* No red lines usually means it's fine

---------

Co-authored-by: Michael Franklin <illusional@users.noreply.github.com>

* Deploy fixes

* Bump version

* PR clean-up

* Let the load method handle both dict / list requests

---------

Co-authored-by: Michael Franklin <illusional@users.noreply.github.com>

* Fixing etl-load function, removing wrong check.

* Fixing by-type key of etl-load.

* SET-68 Added initial 1-3 day buckets by processing times

* SET-74 SET-68 fixed queries and added collection site/processing chart

* minor null fix on ODD

* OurDNA Dashboard UI Enhancements (#908)

* SET-75 Fixed y-axis bug

* SET-73 added base for chart

* working cleanup

* SET-72 Added 24hr collection to process end time buckets tile

* Updated field for collection-lab

* testing WF identity

* testing WF identity

* Renamed workflow

* testing WF identity

* testing WF identity

* Renamed workflow

* final workflow

* organize imports

* add prettier check to linting workflow

* fix linting errors

* add working dir to frontend commands

* fix borked import organization in some files

* fix formatting commands so they get all files

they weren't working cos the glob was being processed by zsh rather than
prettier.

* fix ourdna dashboard linting error

* fix precommit problems

* fix some type errors

* bumping packages to patch vulns

* placing pin on dev only

* more upgrades

* fixed stale requirements-dev.txt

* final upgrades

* fixed pip-compile command

* Save test coverage and upload to sonarqube

* Pass linting

* Added pip-audit workflow

* added runs-on

* running only on dev reqs file

* added checkout repo action

* added requirements.txt back

* Save test coverage and upload to sonarqube

* Pass linting

* Refactor to have sonarqube be in the test.yaml file

* Test

* Rename

* More renaming

* Fix needs keyword

* Add Sonarqube condition

* add rough db schema for comments

* alter schema to simplify querying and allow for FTS

* add rough comment querying stack

* update to handle comment versions

* add scaffold for mutations

* add rough adding of comments to samples

* group comments into threads

* allow for comments on projects, sgs, samples, participants, assays

* move comment entity type to be an enum

* move comment querying to relevant entities and add loaders

* roll out adding of comments to all entities

* allow getting a comment by id, return comment when creating

* return created comment from add comment mutations

* add table methods to reply to and update comments

* add other mutations for comments, updating, replying deleting

* add family comments

* simplify code to add comments to entities, so it isn't needed on layers

* fix comment timestamps so that they are interpreted at UTC

* add assay ids to participant grid so that it can be filtered

* add viewer to graphql schema so that client can check user permission

* fix bug where a comment's thread wasn't returned when updating

* fix linting errors

* fix tests

* add big comment describing how comment query works

* update comment entity type to be named

* add tests for adding comments to entities

* add tests for comment actions like updating/deleting

* clean up tests, reduce duplication

* add tests for entity relatedness to comment tests

* update query for sample comments so that comments on parent samples work

previously, only comments on child samples appeared in the related
section

* fix copied code that wasn't updated

* Metamist Comments Frontend (#913)

* fix dark mode styling for sample page

* fix dark mode for analysis page

* basic setup for querying comments in the client

* rough initial layout for comments on projects

* remove default page padding and add it to pages that need it

* add viewer context so that components can access the current user

along with their permission

* update apollo

* add comment editing, adding to thread, and creating

* add error handling to viewer

* fix linting errors

* make sidebar sticky

* add comments to sample view

* change family, participant and analysis to not use modal

so that comments can be placed on the side of the page

* finish up styling and functionality for sidebar

* add comments to family view

* add commenting to participant view

* clean up discussion view

* refactor into a bunch of files

* performance fixes and comment link copying

* styling tweaks

* add ability to view comment version history

* Add deep linking for comments

* fix up syntax highlighting

* fix linting errors and deep linking of comments

* styling tweaks

* linting fixes

* add handling for subsamples to comments

this was causing problems in cases where there were comments on a parent
and child sample. The UI didn't handle changing between two discussion
sections of the same entity type - updated to distinguish between direct
and related comments better

* add comment deletion and restoration

* Comments and small refactors to make things more readable

* tweaks based on comments

* remove commented code

* Save test coverage and upload to sonarqube

* Pass linting

* Refactor to have sonarqube be in the test.yaml file

* Test

* Rename

* More renaming

* Fix needs keyword

* Add Sonarqube condition

* Output the execution report and upload to sonarqube

* Output the execution report and upload to sonarqube

* Run sonarqube not on main or dev

* Final changes to show unit test counts

* Only run scan on dev and main

* Update sonar-project.properties

* Update sonar-project.properties