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Release - ETL acessors, pip audit, Sonarqube & Metamist comments #928
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* 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
dancoates
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dancoates
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* 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
dancoates
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dancoates
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Release - Metamist comments
Release - ETL acessors, pip audit, Sonarqube & Metamist comments
Sep 16, 2024
dancoates
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* Update sonar-project.properties * Update sonar-project.properties
nevoodoo
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nevoodoo
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Sep 16, 2024
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This is a release that combines the previous release and new release. The previous release needed to be re-merged so that it wouldn't be a squash merge to avoid dev history getting out of sync.