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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

Commits on Jul 24, 2024

  1. Add migration for sample_type_auth_lookup table

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    kdp-cloud committed Jul 24, 2024
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  2. Typo

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    kdp-cloud committed Jul 24, 2024
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  3. Apply migration to schema

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    kdp-cloud committed Jul 24, 2024
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  4. Implementation of acts_as_asset

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    kdp-cloud committed Jul 24, 2024
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  5. Write upgrade task

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    kdp-cloud committed Jul 24, 2024
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  6. Add missing routes

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    kdp-cloud committed Jul 24, 2024
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  7. Keep Rubocop happy

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    kdp-cloud committed Jul 24, 2024
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  8. Include the assets methods and routes

    @kdp-cloud
    kdp-cloud committed Jul 24, 2024
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  9. Add manage page

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    kdp-cloud committed Jul 24, 2024
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  10. Make sure contributors don't get a double permission when they're als… 

    …o project member
    @kdp-cloud
    kdp-cloud committed Jul 24, 2024
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  11. Can't access manage page of ISA-JSON compliant sample types

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    kdp-cloud committed Jul 24, 2024
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  12. Make sure user can't manage_update ISA-JSON compliant sample types

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    kdp-cloud committed Jul 24, 2024
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  13. Change is_isa_json_compliant 

    Add extra constraints to being ISA-JSON compliant like must have a
template id and must only be linked to ISA-JSON compliant
investigations.
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  14. Remove comment out test

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    kdp-cloud committed Jul 24, 2024
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  15. Convert into before_action

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    kdp-cloud committed Jul 24, 2024
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  16. Add controller test for accessing the manage page

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    kdp-cloud committed Jul 24, 2024
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  17. Change ISA-JSON compliant factories

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    kdp-cloud committed Jul 24, 2024
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  18. Add collections as resources

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    kdp-cloud committed Jul 24, 2024
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  19. Add has_content_blobs concern

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  20. Remove custom auth methods

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    kdp-cloud committed Jul 24, 2024
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  21. Fix controller tests

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  22. custom related investigations instead of association through studies 

    Since investigations can be associated through studies and assay. Better
write a custom related_investigations method.
    @kdp-cloud
    kdp-cloud committed Jul 24, 2024
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  23. Skip action if is SampleType

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    kdp-cloud committed Jul 24, 2024
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  24. Fix sample type tests

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    kdp-cloud committed Jul 24, 2024
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  25. Add policy and discussion_links to schema

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    kdp-cloud committed Jul 24, 2024
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  26. Fix some more tests

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    kdp-cloud committed Jul 24, 2024
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  27. Add permissions partial

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    kdp-cloud committed Jul 24, 2024
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  28. Update sharing policies and tags

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    kdp-cloud committed Jul 24, 2024
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  29. Add manage sample type button to show page

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  30. Write controller test for managing sample types

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  31. Reuse attributes

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    kdp-cloud committed Jul 24, 2024
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  32. Test for isa_study sample type permissions

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    kdp-cloud committed Jul 24, 2024
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  33. Simplify isa assays controller test

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    kdp-cloud committed Jul 24, 2024
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  34. Test for isa_assay sample type permissions

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    kdp-cloud committed Jul 24, 2024
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  35. Typo

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    kdp-cloud committed Jul 24, 2024
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  36. Update policies before linking to sample types

    @kdp-cloud
    kdp-cloud committed Jul 24, 2024
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Commits on Sep 30, 2024

  1. Remove redundant method 

    Since  sharing permissions are set explicitly, linked samples should not
be revealed anymore
    @kdp-cloud
    kdp-cloud committed Sep 30, 2024
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  2. Remove can_view and can_edit 

    Permissions are not overwritten anymore and are solely set through the
manual permissions
    @kdp-cloud
    kdp-cloud committed Sep 30, 2024
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  3. Contributor already has manage permission

    @kdp-cloud
    kdp-cloud committed Sep 30, 2024
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  4. Better reflect current policies

    @kdp-cloud
    kdp-cloud committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. Comment out tests about referring samples

    @kdp-cloud
    kdp-cloud committed Oct 1, 2024
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  2. Merge branch 'main' into issue_1199_add_sharing_permisions_to_sample_… 

    …types
    @kdp-cloud
    kdp-cloud authored Oct 1, 2024
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  3. Add missing end

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    kdp-cloud committed Oct 1, 2024
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  4. Add Timecop gem to make test more reproduceable

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    kdp-cloud committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. Make the deleting of the blob consistent 

    Deleting blobs linked to sample types is done in the same manner as the
blobs linked to other assets.
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    kdp-cloud committed Oct 2, 2024
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  2. Revert "Add Timecop gem to make test more reproduceable" 

    This reverts commit a7f8449.
    @kdp-cloud
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  3. Use ActiveSupport's Testing TimeHelpers

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    kdp-cloud committed Oct 2, 2024
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Commits on Oct 8, 2024

  1. Fix sample_controller_test 

    Add a contributor to the sample types in the test fixes the failing
tests regarding sample type links with referring samples linked to it.
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    kdp-cloud committed Oct 8, 2024
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  2. Revert "Use ActiveSupport's Testing TimeHelpers" 

    This reverts commit c88d4d2.
    @kdp-cloud
    kdp-cloud committed Oct 8, 2024
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Commits on Oct 9, 2024

  1. Rearrange before_actions

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    kdp-cloud committed Oct 9, 2024
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  2. Remove obsolete referring samples logic

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    kdp-cloud committed Oct 9, 2024
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  3. Change tests to something more useful.

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    kdp-cloud committed Oct 9, 2024
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Commits on Oct 10, 2024

  1. Remove the destroy method to fall back to the default -> Fixes the fa… 

    …iling API test
    @kdp-cloud
    kdp-cloud committed Oct 10, 2024
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  2. Fix check_no_created_samples

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    kdp-cloud committed Oct 10, 2024
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  3. Reorder before_action check_isa_json_compliance

    @kdp-cloud
    kdp-cloud committed Oct 10, 2024
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  4. clean up

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    kdp-cloud committed Oct 10, 2024
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