feat!: authorization support for some (mostly "Bento Public") endpoints #529

davidlougheed · 2024-08-07T20:37:34Z

No description provided.

…eacon

codecov · 2024-08-07T20:43:20Z

Codecov Report

Attention: Patch coverage is 98.25784% with 10 lines in your changes missing coverage. Please review.

Project coverage is 89.43%. Comparing base (0346ef7) to head (a7b7a5f).
Report is 74 commits behind head on develop.

Files with missing lines	Patch %	Lines
chord_metadata_service/chord/views_search.py	90.00%	2 Missing ⚠️
chord_metadata_service/discovery/utils.py	98.14%	1 Missing and 1 partial ⚠️
chord_metadata_service/patients/api_views.py	96.29%	1 Missing and 1 partial ⚠️
chord_metadata_service/phenopackets/summaries.py	85.71%	1 Missing and 1 partial ⚠️
chord_metadata_service/authz/permissions.py	95.65%	1 Missing ⚠️
chord_metadata_service/discovery/fields.py	91.66%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #529      +/-   ##
===========================================
+ Coverage    88.63%   89.43%   +0.80%     
===========================================
  Files          131      134       +3     
  Lines         4830     5094     +264     
  Branches       714      748      +34     
===========================================
+ Hits          4281     4556     +275     
+ Misses         395      386       -9     
+ Partials       154      152       -2

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… use)

test: test refactoring + testing of more discovery responses

… data type

…middleware

davidlougheed · 2024-08-20T19:28:13Z

@v-rocheleau still work to be done, but requesting an initial look at this code

…d-scope-class refact(discovery)!: introduce container class for discovery scope

v-rocheleau

Small questions, otherwise looks good!

v-rocheleau · 2024-09-09T16:55:47Z

chord_metadata_service/patients/api_views.py

+    discovery: DiscoveryConfig,
+    request: DrfRequest,
+    dt_permissions: DataTypeDiscoveryPermissions,
+    queryset: QuerySet,
+    scope_repr: str,  # We pass disc


discovery and scope_repr arguments are derived from the same ValidatedDiscoveryScope instance.
Might be better to replace those 2 params with a single ValidatedDiscoveryScope param, otherwise someone could theoretically pass a discovery and scope_repr that don't belong together.

this was to avoid having to deal with EmptyConfig type in two places, since scopes can return empty configs. but yeah, i agree this also isn't the best (and the comment is truncated/unfinished)

chord_metadata_service/phenopackets/summaries.py

chord_metadata_service/experiments/summaries.py

v-rocheleau

LGTM!

davidlougheed added 9 commits August 5, 2024 17:09

feat(authz): add authz submodule + middleware class

3ad923b

fix(discovery): some type hinting/exports for model lookup related code

84253b5

refact: initial (partial) authz porting

a069a0d

feat!: permissions for public filtering endpoint + consolidate with b…

6aa9aef

…eacon

test: replace some status codes with constants

e92c136

lint(discovery): properly mark None as allowed for discovery param

204dc4f

chore(authz): allow more authz-enabled endpoints

44f4c9a

refact(authz): more work on authz support for public endpoints

6313fd7

more work on authz impl

2a12a9e

davidlougheed added 16 commits August 7, 2024 16:53

chore: clean up unneeded diff

4a1ff24

fix(discovery): handle UUID errors from discovery get

db0766d

lint(authz): rm unused helper functions (might be reverted for future…

003a61c

… use)

refact: discovery overview 403

cddfb75

test: test refactoring + testing of more discovery responses

lint(chord): rm unused code

5eea18d

test(chord): more testing of API error cases

3b16614

refact(chord): simplify some code in views_data_types

b21c250

refact!(chord): tweaks and tests for dataset data type summary

79905ff

lint

dcf77bd

perf(chord): parallelize dataset data type summary response

f78ec9b

refact: consolidate permissions defs to authz module

fb36b65

feat(chord): handle dataset not existing/validation error for dataset…

21f8d0f

… data type

chore: CORS config

920b156

feat: true counts even with 0 individuals with query data perms

1155a16

Merge remote-tracking branch 'origin/develop' into feat/partial-auth-…

0d1c7f6

…middleware

fix: rm project and dataset from public search query params

cf58ae8

davidlougheed requested a review from v-rocheleau August 20, 2024 19:27

davidlougheed added 2 commits August 27, 2024 11:13

Merge branch 'develop' into feat/partial-auth-middleware

469f38d

test: test more authz conditions + refact some endpoint tests

619fbaf

davidlougheed added 14 commits September 4, 2024 12:16

chore(discovery): clean up un-needed get_discovery_scope variable

d4a2b73

test(discovery): fix name of helper fn for test discovery configs

f513614

chore(discovery): clean up exception-handling response logic

4347195

chore(chord): handle dataset fetching errs for summary endpoint

9ab2fdd

chore(chord): consistent error handling for not founds/bad reqs

5f2fd6f

lint(chord): rm dead code

74c3bb7

refact(chord): use scope obj in 2 more places

98426f8

chore(discovery): ValidatedDiscoveryScope - check dataset parent project

155d9ec

Merge pull request #531 from bento-platform/refact/discovery/validate…

248d77c

…d-scope-class refact(discovery)!: introduce container class for discovery scope

refact(discovery): rm pointless async getter for scope discovery config

86c53f4

refact(discovery): use scope instead of 3 params in summary stats

95b3ca7

refact: enforce scope in summary endpoints + restructure stats code

a10ffe4

test(discovery): implement subtests in more places

16dfb7c

refact(discovery): factor out scoping public model querysets

6c60dfe

davidlougheed requested a review from v-rocheleau September 4, 2024 21:31

davidlougheed added 3 commits September 4, 2024 17:36

fix: address testing inside container issue

4333aee

lint(chord): clean up imports

0b39b6b

test(discovery): filtering public individuals by dataset

b046774

davidlougheed marked this pull request as ready for review September 5, 2024 15:42

davidlougheed added 5 commits September 5, 2024 13:24

refact(discovery): better + compound types for optional discovery config

59f5dec

fix(discovery): handle missing permissions case for public-search-fields

22a7154

chore: clarifying comment [no ci]

cf3219a

test(chord): invalid DATS dataset update

99f2bea

test(experiments): experiment summary scoping

80a3e45

v-rocheleau requested changes Sep 9, 2024

View reviewed changes

davidlougheed added 2 commits September 9, 2024 14:28

fix: summaries select_related

250edb5

refact(discovery): handle empty discovery config better for /public

a7b7a5f

v-rocheleau approved these changes Sep 9, 2024

View reviewed changes

davidlougheed merged commit 72437c0 into develop Sep 9, 2024
7 checks passed

davidlougheed deleted the feat/partial-auth-middleware branch September 9, 2024 19:23

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feat!: authorization support for some (mostly "Bento Public") endpoints #529

feat!: authorization support for some (mostly "Bento Public") endpoints #529

davidlougheed commented Aug 7, 2024

codecov bot commented Aug 7, 2024 •

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davidlougheed commented Aug 20, 2024

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v-rocheleau Sep 9, 2024

davidlougheed Sep 9, 2024

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feat!: authorization support for some (mostly "Bento Public") endpoints #529

feat!: authorization support for some (mostly "Bento Public") endpoints #529

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davidlougheed commented Aug 7, 2024

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davidlougheed commented Aug 20, 2024

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