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* initial animalv2 model declarations * implement initial feedback items * help text cleanup and TODO removals * dose_group_id added * updated animalv2 migration file * fixed ruff formatting issue on animalv2 migration file --------- Co-authored-by: Tom Feiler <tom.feiler@icf.com> Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
* initial animalv2 model declarations * implement initial feedback items * help text cleanup and TODO removals * dose_group_id added * updated animalv2 migration file * fixed ruff formatting issue on animalv2 migration file * add animal_version flag to assessment * enable basic UI functionality for animalv2 experiments can we CRUD an Experiment; next step is to do a sub-object in htmx style. * update experiment form to match mockup layout * enable UI functionality for animalv2 chemicals first sub-object in htmx style * animalv2 tests first checkin model tests (and a model update after finding a typo) * additional animalv2 tests * enable UI functionality for animalv2 animalgroups * enable (partial) UI functionality for animalv2 treatments note, dosegroups are not yet implemented for treatments. * enable integrated subform UI functionality for dose groups associated with a treatment * run `make format` * implemented most feedback from draft PR still having ruff-related formatting issues; resolving that before merging this into bioassay-v2. * intentional format error introduction troubleshooting ruff/CICD issues on my side * removing intentional formatting errors * switch test fixture back to animalv1 to avoid breaking existing integration tests * implement endpoint UI * implement observationtime UI * implement DataExtraction UI * move away from mutable argument default * updated fixtures file with new animalv2 fields * add additional test coverage for animalv2 modeled after epiv2. Not complete; hit hour cap. * Update Animal V2 HTMX viewsets (#1048) * update templates to new htmx pattern * bring forward crud_url change * fix some url issues * condense htmx viewset urls * fix template issues * merge with main, use common templates * fix data extraction url * format * html format * fix animalv2 test helper * add formset handling to shared _object_edit_row template * fix study detail merge * indent * cleanup after merge * fix spacing diff * remove old template artifact * fix migrations * update comments * improve layout * use smarter clone method name * rename context variable * fix htmx style editing for experiment updates --------- Co-authored-by: Andy Shapiro <shapiro.andy@epa.gov> Co-authored-by: Andy Shapiro <shapiromatron@gmail.com> * change url from ani-bioassay to animal-bioassay * move logic out of is_valid and into clean where possible * remove extrajs from experiment form template note - used only when initially creating experiment. When editing/associating sub-objects, template is not even used. * various minor reformatting/cleanup fixes As per code review, stuff like: * switching multiline imports back to single line where ruff allows * backing out of unneeded reformatting changes * comment cleanups * etc. (I think my ruff must have been misconfigured at some point, introducing some of these errors) * switch from hastext/safe to optional table row for comment display * convert handcoded colgroup html to use the bs4 templatetag * remove DoseGroupFormHelper and similars and switch to a common generic version * collapse various aniv2 migrations into single cleaned up ones * change v2_timepoints from prop to method and switch to standard Django get approach * rework FormsetConfiguration as dataclass; add type hints and explanatory comments * fix migrations * htmx updates * fix tests * update test_forms * cleanup type annotations and add TODO to comments * add a feature flag * review comments * review JS --------- Co-authored-by: Tom Feiler <tom.feiler@icf.com> Co-authored-by: Andy Shapiro <shapiromatron@gmail.com> Co-authored-by: Andy Shapiro <shapiro.andy@epa.gov> Co-authored-by: Matt Munns <mmunns16@gmail.com> Co-authored-by: casey1173 <caseyhansen1999@gmail.com>
* added study level value schema and migration * added admin view and sample fixture value * added CRUDL operations * added animalv2 htmx and views unit tests * updated table display and test case for update * fix htmx_alert * htmx updates * update test * update lists * show values on study detail page * few more comments from final review * fix new test --------- Co-authored-by: Berkowitz <55586@icf.com> Co-authored-by: Casey Hansen <42587248+caseyhans@users.noreply.github.com> Co-authored-by: casey1173 <caseyhansen1999@gmail.com> Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
# Conflicts: # pyproject.toml
* animalv2 api Implements API for all of the animalv2 model, including study level values. Includes test coverage. * adding aniv2 studylevelvalues to test fixture seeing if this fixes the test in github env * add migrations * poe format * reorder content types in fixture * reduce content being returned by serializer * cleanup some of boilerplate code --------- Co-authored-by: Andy Shapiro <shapiro.andy@epa.gov>
* add guidelines and guideline profiles * add obvervations to models * update experiment and observation model * add observation UI and logic * Add experiment observations tab to sidebar * update assessment form and toxrefdb text * Add tests * lint changes * move Observation model from vocab to animalv2 * make enable observations false * biome format * minor edits to observation checks * create a vocab.Guideline table * refine vocab app; remove api for guidelines * revert vocab changes * use foreign key for guidelines * remove ExperimentFilterList * whoops; undo delete * remove sidebar link * add line to observations page * refactor animalv2 observations * format * fix djhtml on windows * use standard manager class --------- Co-authored-by: 63080 <63080_icfcorp> Co-authored-by: Andy Shapiro <shapiro.andy@epa.gov> Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
Shared permission class that allows reads for any authenticated user and writes for users who are team members or PMs on any assessment.
- Add UpdateModelMixin and DestroyModelMixin to Endpoint viewset - Set http_method_names = METHODS_NO_PUT (PATCH only, no PUT) - Add perform_update/perform_destroy with logging and cache busting - Fix EndpointSerializer.validate to use self.instance.animal_group on update - Skip name/name_term requirement on partial updates not touching those fields - Add EndpointSerializer.update for nested groups/effects on PATCH
- Add ReferenceCreateSerializer for creating manual references - Add CreateModelMixin to ReferenceViewSet with serializer switching - Automatically links new references to the assessment's manual-import Search - Enables two-step workflow: create reference, then create study from reference_id
- Add SpeciesViewSet with full CRUD and IsTeamMemberOrHigher permissions - Expand StrainViewSet from LIST-only to full CRUD ModelViewSet - Both use METHODS_NO_PUT (PATCH only, no PUT) - Register species endpoint at /assessment/api/species/
- Add ObservationSerializer for the Observation model - Add ObservationViewSet with EditPermissionsCheckMixin pattern - Register at /animalv2/api/observation/
- Add CreateModelMixin to DoseUnitsViewSet - Add IsTeamMemberOrHigher permission class
- Add GuidelineSerializer and GuidelineProfileSerializer - Add GuidelineViewSet and GuidelineProfileViewSet with IsTeamMemberOrHigher perms - Register at /vocab/api/guideline/ and /vocab/api/guideline-profile/
- AnimalClient: add update_endpoint, delete_endpoint - LiteratureClient: add create_reference - AssessmentClient: add list_species, create_species, list_strains, create_strain, create_dose_units - VocabClient: add list_guidelines, create_guideline, list_guideline_profiles, create_guideline_profile
Tests for: endpoint update/delete, reference creation, species/strain/dose-units CRUD, observation CRUD, and guideline/guideline-profile CRUD.
- Fix EndpointSerializer partial update validation: use existing instance values for fields not in PATCH data instead of hardcoded defaults - Fix Observation test: use Term.objects.first() since Observation.endpoint is a FK to Term, not to animalv2.Endpoint - Disable pagination on Guideline/GuidelineProfile viewsets (small lookup tables that should return flat lists)
…ation test, hopefully.
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This is for work concerning updating the bioassay code with the latest HAWC code and merging the bioassay code into main after testing.