refact!: define a "scopeable model" base class + modelviewset scoping #536

davidlougheed · 2024-09-10T14:41:25Z

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codecov · 2024-09-10T14:44:36Z

Codecov Report

Attention: Patch coverage is 95.76720% with 24 lines in your changes missing coverage. Please review.

Project coverage is 92.71%. Comparing base (9f12712) to head (3488176).
Report is 86 commits behind head on develop.

Files with missing lines	Patch %	Lines
chord_metadata_service/chord/ingest/views.py	82.05%	5 Missing and 2 partials ⚠️
chord_metadata_service/restapi/api_renderers.py	82.92%	5 Missing and 2 partials ⚠️
chord_metadata_service/experiments/api_views.py	92.50%	2 Missing and 1 partial ⚠️
chord_metadata_service/authz/permissions.py	83.33%	1 Missing and 1 partial ⚠️
chord_metadata_service/chord/export/views.py	89.47%	1 Missing and 1 partial ⚠️
chord_metadata_service/phenopackets/api_views.py	92.85%	1 Missing and 1 partial ⚠️
chord_metadata_service/chord/export/cbioportal.py	92.85%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #536      +/-   ##
===========================================
+ Coverage    92.04%   92.71%   +0.66%     
===========================================
  Files          115      116       +1     
  Lines         4237     4391     +154     
  Branches       376      386      +10     
===========================================
+ Hits          3900     4071     +171     
+ Misses         249      229      -20     
- Partials        88       91       +3

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…odel-base-class # Conflicts: # chord_metadata_service/phenopackets/api_views.py

…odel-base-class # Conflicts: # chord_metadata_service/chord/tests/test_api.py # chord_metadata_service/discovery/api_views.py # chord_metadata_service/discovery/utils.py # chord_metadata_service/experiments/api_views.py # chord_metadata_service/phenopackets/api_views.py

test: add more tests / fix test issues

…odel-base-class

v-rocheleau

Final requests I think, looks good!

chord_metadata_service/authz/viewset.py

chord_metadata_service/experiments/api_views.py

chord_metadata_service/patients/models.py

chord_metadata_service/phenopackets/api_views.py

chord_metadata_service/restapi/api_views.py

chord_metadata_service/resources/tests/test_api.py

chord_metadata_service/authz/viewset.py

gsfk

Working well for me so far.

gsfk · 2025-01-15T20:46:05Z

post-approval comment: behaviour when mismatching projects & datasets is not always consistent. If I manage to request a project_id and and an incorrect dataset_id (from another project, say), I get a mix of behaviours:

/api/public_rules returns a sensible error message
/api/individuals returns "Forbidden"

working now, thanks

v-rocheleau

LGTM! Nice work

v-rocheleau · 2025-01-15T20:51:01Z

chord_metadata_service/restapi/exception_handler.py

refact: define a "scopeable model" base class + modelviewset scoping

09f4cfc

davidlougheed added 23 commits September 10, 2024 11:21

refact: define common top-level (data type model) scope filters

5cac2ff

Merge remote-tracking branch 'origin/develop' into refact/scopeable-m…

1fd3ea6

…odel-base-class # Conflicts: # chord_metadata_service/phenopackets/api_views.py

refact(discovery): constant for instance ValidatedDiscoveryScope

8bcff91

chore(discovery): allow specifying data type for authz repr of scope

843cabf

refact: start working on auth systems for model viewsets

a60a418

chore: remove authorized dataset filters (CanDIG legacy code)

827bd4f

fix: proper permissions for schema endpoints

c811bbd

more work on scoped models

65cc1f7

test: work on tests

c07b471

fix(phenopackets): issues with biosample batch / csv rendering

cc1235e

chore(patients): enable authz for individuals API

43f0c3f

more authz functionality impl

0368ad7

test: add more tests / fix test issues

fix!: only enable GET/POST list endpoints (biosample batch viewset)

a21afde

test: individual phenopackets responses

1d884dd

refact: authz fn name change

8af3867

refact(restapi): create base class for Bento CSV renderers

d435acd

chore: allow override of checked permission for POST-query-data reqs

3b3b991

chore: cache scope for repeated request scope gets

7068623

test: fix forbidden phenopackets attachment test

f5dc770

refact: create authz base modelviewset

a90b779

add TODOs

44f1031

Merge remote-tracking branch 'origin/develop' into refact/scopeable-m…

44427c1

…odel-base-class

davidlougheed changed the title ~~[WIP] refact: define a "scopeable model" base class + modelviewset scoping~~ refact: define a "scopeable model" base class + modelviewset scoping Nov 27, 2024

davidlougheed added 3 commits November 27, 2024 11:37

lint

721c9c9

test(experiments): fix wrong method for experiment batch tests

6a0c306

test: fix test helper

e04f552

davidlougheed changed the title ~~refact: define a "scopeable model" base class + modelviewset scoping~~ refact!: define a "scopeable model" base class + modelviewset scoping Nov 27, 2024

davidlougheed added 7 commits January 9, 2025 13:26

test(experiments): scoping tests for /api/experiments

42ad69a

fix(experiments): bad prefetch for exp result scoping

b3c1d46

test(experiments): experiment result scoping tests

cd42615

refact(chord): async queryset dataset id grouping + comment

b2f2dc1

chore(deps): update lockfile

673ca39

chore(authz): finish docstring

4846699

refact: include list mixin with generic scoped model viewset

bf223b8

davidlougheed requested a review from v-rocheleau January 9, 2025 18:54

refact: rm unused candig code

0a3eaa0

davidlougheed marked this pull request as ready for review January 9, 2025 18:57

davidlougheed added 2 commits January 9, 2025 16:31

chore: log public individuals search + queried fields

4619d1f

chore(authz): error log if permission_from_request is unimpl

a764f8a

davidlougheed requested a review from gsfk January 14, 2025 19:05

v-rocheleau requested changes Jan 15, 2025

View reviewed changes

davidlougheed added 6 commits January 15, 2025 14:11

chore(deps): update lockfile

ca27822

chore(authz): add get_queryset not impl to override + test

e428a90

chore: commenting for batch API viewsets

637b40d

chore: cleaner individual model scope filters + tests

4902a9c

chore: make permission_classes explicit for search overview

68d4af9

fix(patients): model scope filters

95e0b72

gsfk approved these changes Jan 15, 2025

View reviewed changes

davidlougheed added 3 commits January 15, 2025 14:43

test(authz): test obj_is_in_request_scope exception branch

6fe09af

test(authz): request_has_data_type_permissions tests

9c1afc2

refact!: handle scope exceptions with DRF exc handler

c91d084

davidlougheed requested a review from v-rocheleau January 15, 2025 20:31

lint

3488176

v-rocheleau approved these changes Jan 15, 2025

View reviewed changes

chord_metadata_service/restapi/exception_handler.py

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v-rocheleau Jan 15, 2025

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Nice!

davidlougheed reacted with hooray emoji

davidlougheed merged commit c23a2ca into develop Jan 15, 2025
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davidlougheed deleted the refact/scopeable-model-base-class branch January 15, 2025 20:55

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refact!: define a "scopeable model" base class + modelviewset scoping #536

refact!: define a "scopeable model" base class + modelviewset scoping #536

davidlougheed commented Sep 10, 2024

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v-rocheleau Jan 15, 2025

refact!: define a "scopeable model" base class + modelviewset scoping #536

refact!: define a "scopeable model" base class + modelviewset scoping #536

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