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362 add and edit attributes in sample types #2032

Merged
merged 49 commits into from
Nov 14, 2024
Merged

362 add and edit attributes in sample types #2032

merged 49 commits into from
Nov 14, 2024

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kdp-cloud
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@kdp-cloud kdp-cloud commented Oct 21, 2024 •
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  • Adds possibility to add new optional attribute to an existing sample type
  • Makes the title of a sample attribute editable.
  • If the title of an attribute is updated, the JSON metadata values of all samples that are linked to the sample type are also updated as a background job.

Closes #1257
Closes #1258
Closes #362

@kdp-cloud
Add sample metadata updater module
cfd7789
@kdp-cloud
Add Sample Metadata upater job
133718f
@kdp-cloud
Add after_action for updating the sample json metadata
9c5aec7
@kdp-cloud
Skip if sample metadata keys correspond with sample attribute titles
90ac8b4
@kdp-cloud
Remove add new attribute constraint
037521b
@kdp-cloud
Don't start job if there are samples
caeab80
@kdp-cloud
typo
8ce597b
@kdp-cloud
Make unit editable
d78ea79
@kdp-cloud
Fix sample types controller test
fd18c8b 
add attribute button is still visible, even when the sample type has
samples.
@kdp-cloud
test for adding new attribute
36e355a
@kdp-cloud
linting
f894152
@kdp-cloud
Add UpdateSampleMetadataTest
fd3a532
@kdp-cloud
Add test
a631ae3 
Checks if the sample metadata keys (attribute title) has changed after
the job ran.
@kdp-cloud
Fix the Sample metadata updater
662fbdf 
Pass a Hash describing wich attributes have a different title.
@kdp-cloud
Check user
f4a59ac
@kdp-cloud
Change allow_name_change?
8b20eaf 
User should only be able to change the sample type attribute's title if
the user has editing permission to all samples.
@kdp-cloud
Add explaination
4a079c1 
Add explaination to why changing the attribute's name is prohibited
@kdp-cloud
Fix test
2547489
@kdp-cloud
Change existing title constraints test
928ffc4 
Add new scenario's where tests should fail or succeed
@kdp-cloud
Add test for changing name of attribute.
d44fafc
@kdp-cloud
Allow adding optional attribute to existing sample type
3cb7b13
@kdp-cloud kdp-cloud self-assigned this Oct 21, 2024
This was linked to issues Oct 21, 2024
Allow editing of Attributes in existing Sample Types #1258
Closed
Add and edit attributes #362
Closed
@kdp-cloud kdp-cloud marked this pull request as ready for review October 22, 2024 15:40
fbacall
fbacall reviewed Oct 23, 2024
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Flagged a few issues, mostly around concurrency

lib/seek/samples/sample_type_editing_constraints.rb Outdated Show resolved Hide resolved
app/jobs/update_sample_metadata_job.rb Outdated Show resolved Hide resolved
app/views/isa_studies/_sample_types_form.html.erb Outdated Show resolved Hide resolved
lib/seek/samples/sample_type_editing_constraints.rb Outdated Show resolved Hide resolved
lib/seek/samples/sample_metadata_updater.rb Outdated Show resolved Hide resolved
app/controllers/sample_types_controller.rb Show resolved Hide resolved
lib/seek/samples/sample_metadata_updater.rb Outdated Show resolved Hide resolved
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I added a locking mechanism, locking the sample type and its linked samples while the background job is running. Creating new samples in this sample type is now prohibited as well.

fbacall
fbacall reviewed Nov 13, 2024
View reviewed changes
app/models/sample_type.rb Outdated Show resolved Hide resolved
app/models/sample.rb Outdated Show resolved Hide resolved
app/controllers/samples_controller.rb Outdated Show resolved Hide resolved
app/jobs/update_sample_metadata_job.rb Show resolved Hide resolved
test/functional/sample_types_controller_test.rb Outdated Show resolved Hide resolved
@kdp-cloud kdp-cloud merged commit 96a68df into seek4science:main Nov 14, 2024
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@fbacall fbacall fbacall approved these changes

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