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Issue 1199 add sharing permisions to sample types #1953

Merged
merged 56 commits into from
Oct 10, 2024
Merged

Issue 1199 add sharing permisions to sample types #1953

merged 56 commits into from
Oct 10, 2024

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kdp-cloud
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  • Users are now able to set policies with permissions.
  • The current rules for viewing, editing and deleting should still remain the same.
  • There is also a upgrade job that adds policies to the existing sample types.

@kdp-cloud kdp-cloud added this to the 1.16.0 milestone Jul 10, 2024
@kdp-cloud kdp-cloud self-assigned this Jul 10, 2024
@kdp-cloud kdp-cloud linked an issue Jul 10, 2024 that may be closed by this pull request
Add sharing permissions to Sample Type #1199
Closed
@kdp-cloud kdp-cloud marked this pull request as ready for review July 10, 2024 19:09
@kdp-cloud
Add migration for sample_type_auth_lookup table
5793a5b
@kdp-cloud
Typo
53adc21
@kdp-cloud
Apply migration to schema
08424e2
@kdp-cloud
Implementation of acts_as_asset
45c905b
@kdp-cloud
Write upgrade task
089d33b
@kdp-cloud
Add missing routes
c91dd6c
@kdp-cloud
Keep Rubocop happy
edfb8f6
@kdp-cloud
Include the assets methods and routes
869abfa
@kdp-cloud
Add manage page
f025c5b
@kdp-cloud
Make sure contributors don't get a double permission when they're als…
8641699 
…o project member
@kdp-cloud
Can't access manage page of ISA-JSON compliant sample types
2bb4864
@kdp-cloud
Make sure user can't manage_update ISA-JSON compliant sample types
080a4c8
@kdp-cloud
Change is_isa_json_compliant
dcd8e57 
Add extra constraints to being ISA-JSON compliant like must have a
template id and must only be linked to ISA-JSON compliant
investigations.
@kdp-cloud
Remove comment out test
ff53254
@kdp-cloud
Convert into before_action
cadf689
@kdp-cloud
Add controller test for accessing the manage page
4a26951
@kdp-cloud
Change ISA-JSON compliant factories
2a824fc
@kdp-cloud
Add collections as resources
0777ba8
@kdp-cloud
Add has_content_blobs concern
a364e38
@kdp-cloud
Remove custom auth methods
bc3d9e7
@kdp-cloud
Fix controller tests
7a80dbc
@kdp-cloud
custom related investigations instead of association through studies
0aca7dd 
Since investigations can be associated through studies and assay. Better
write a custom related_investigations method.
@kdp-cloud
Skip action if is SampleType
2763620
@kdp-cloud kdp-cloud force-pushed the issue_1199_add_sharing_permisions_to_sample_types branch from 9c27d04 to 2a90c9b Compare July 24, 2024 13:01
@stuzart stuzart self-requested a review September 11, 2024 09:12
stuzart
stuzart requested changes Sep 11, 2024
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I think the main problem is the mixing of explicit permissions then being over-ruled by the old implicit permissions

I've not checked the tests as these may be affected by changes

app/controllers/sample_types_controller.rb Outdated Show resolved Hide resolved
app/models/sample_type.rb Outdated Show resolved Hide resolved
app/models/sample_type.rb Outdated Show resolved Hide resolved
lib/seek/acts_as_asset/content_blobs.rb Outdated Show resolved Hide resolved
lib/tasks/seek_upgrades.rake Outdated Show resolved Hide resolved
lib/tasks/seek_upgrades.rake Outdated Show resolved Hide resolved
lib/tasks/seek_upgrades.rake Outdated Show resolved Hide resolved
lib/tasks/seek_upgrades.rake Outdated Show resolved Hide resolved
lib/tasks/seek_upgrades.rake Show resolved Hide resolved
kdp-cloud and others added 9 commits September 30, 2024 13:33
@kdp-cloud
Remove redundant method
7b0a873 
Since  sharing permissions are set explicitly, linked samples should not
be revealed anymore
@kdp-cloud
Remove can_view and can_edit
fd57830 
Permissions are not overwritten anymore and are solely set through the
manual permissions
@kdp-cloud
Contributor already has manage permission
4c8d933
@kdp-cloud
Better reflect current policies
8f6a756
@kdp-cloud
Comment out tests about referring samples
2b1f044
@kdp-cloud
Merge branch 'main' into issue_1199_add_sharing_permisions_to_sample_…
b53d649 
…types
@kdp-cloud
Add missing end
4c43636
@kdp-cloud
Add Timecop gem to make test more reproduceable
a7f8449
@kdp-cloud
Make the deleting of the blob consistent
e824fcf 
Deleting blobs linked to sample types is done in the same manner as the
blobs linked to other assets.
@kdp-cloud kdp-cloud requested a review from stuzart October 2, 2024 12:38
stuzart
stuzart requested changes Oct 7, 2024
View reviewed changes
test/functional/samples_controller_test.rb Outdated Show resolved Hide resolved
test/functional/samples_controller_test.rb Outdated Show resolved Hide resolved
app/controllers/sample_types_controller.rb Outdated Show resolved Hide resolved
@kdp-cloud kdp-cloud merged commit f67c8d9 into seek4science:main Oct 10, 2024
11 checks passed
@kdp-cloud kdp-cloud linked an issue Nov 13, 2024 that may be closed by this pull request
Sample type sharing permission in DataHub #1523
Closed
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@stuzart stuzart stuzart approved these changes

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Labels
enhancement
Projects
DataHub
Status: Coded
SEEK 1.16.x
Status: Done
Milestone
1.16.0
Development

Successfully merging this pull request may close these issues.

Sample type sharing permission in DataHub Add sharing permissions to Sample Type
2 participants
@kdp-cloud @stuzart