Enable soft deletion of items

[ml-evs]

By default, delete will now simply set a flag _deleted on the database entry, so that it can be restored in future. This is important for e.g., labelled samples and maintaining old relationships to samples.

[cypress]

datalab    Run #2853

Run Properties:   Failed #2853  •  a024a3c012 ℹ️: Merge 8a9caa20a2dd871bc458207f239fa3bddefe5bdc into f5bc9dddcb761c5b2c61704d1a1c...

Project	datalab
Branch Review	ml-evs/delete-sample-rework
Run status	Failed #2853
Run duration	08m 08s
Commit	a024a3c012 ℹ️: Merge 8a9caa20a2dd871bc458207f239fa3bddefe5bdc into f5bc9dddcb761c5b2c61704d1a1c...
Committer	Matthew Evans
View all properties for this run ↗︎

---

Test results
Failures	69
Flaky	0
Pending	0
Skipped	0
Passing	78
View all changes introduced in this branch ↗︎

---

Tests for review

  batchSampleFeature.cy.js • 7 failed tests • End-to-end tests (firefox)

View Output

Test		Artifacts
Batch sample creation > modifies some data in the first sample		Screenshots
Batch sample creation > modifies some data in the second sample		Screenshots
Batch sample creation > checks the copied samples		Screenshots
Batch sample creation > checks the created samples		Screenshots
Batch sample creation > uses the template id, name, date, copyFrom, and components		Screenshots
Batch sample creation > plays with the number of rows		Screenshots
Batch cell creation > creates a batch of cells using the template id, name, date, copyFrom, and components		Screenshots

  editPage.cy.js • 8 failed tests • End-to-end tests (firefox)

View Output

Test		Artifacts
Edit Page > Checks editing the sample edit page		Screenshots
Edit Page > adds a chemical formula to component1		Screenshots
Edit Page > adds some synthesis information		Screenshots
Edit Page > deletes synthesis components and re-adds them		Screenshots
Edit Page > tries to add a non-numeric value into quantity		Screenshots
Edit Page > Add some blocks to the sample and checks unsaved warning behavior		Screenshots
Edit Page > Uploads an XRD file, makes an XRD block and checks that the plot works		Screenshots
Edit Page > Uploads a fake PNG image, make a Media block and checks that the image is shown		Screenshots

  equipment.cy.js • 3 failed tests • End-to-end tests (firefox)

View Output

Test		Artifacts
Equipment table page > Checks if one of the equipment items is in the database		Screenshots
Equipment table page > Deletes an item		Screenshots
Equipment edit page > modifies some data in a sample		Screenshots

  sampleTablePage.cy.js • 5 failed tests • End-to-end tests (firefox)

View Output

Test		Artifacts
Advanced sample creation features > deletes the first sample and makes sure the copy is still there		Screenshots
Advanced sample creation features > modifies some data in the second sample		Screenshots
Advanced sample creation features > checks the edit page of the copied sample		Screenshots
Advanced sample creation features > copies the copied sample, this time with additional components		Screenshots
Advanced sample creation features > checks the edit page of the copied sample with components		Screenshots

  batchSampleFeature.cy.js • 7 failed tests • End-to-end tests (chrome)

View Output

Test		Artifacts
Batch sample creation > modifies some data in the first sample		Test Replay Screenshots
Batch sample creation > modifies some data in the second sample		Test Replay Screenshots
Batch sample creation > checks the copied samples		Test Replay Screenshots
Batch sample creation > checks the created samples		Test Replay Screenshots
Batch sample creation > uses the template id, name, date, copyFrom, and components		Test Replay Screenshots
Batch sample creation > plays with the number of rows		Test Replay Screenshots
Batch cell creation > creates a batch of cells using the template id, name, date, copyFrom, and components		Test Replay Screenshots

The first 5 failed specs are shown, see all 12 specs in Cypress Cloud.

[codecov]

Codecov Report

Attention: Patch coverage is 81.66667% with 11 lines in your changes missing coverage. Please review.

Project coverage is 68.35%. Comparing base (39be3fb) to head (bcd033f).

Files with missing lines	Patch %	Lines
pydatalab/pydatalab/mongo.py	60.00%	4 Missing ⚠️
pydatalab/pydatalab/permissions.py	72.72%	3 Missing ⚠️
pydatalab/pydatalab/routes/v0_1/graphs.py	81.81%	2 Missing ⚠️
pydatalab/pydatalab/routes/v0_1/items.py	90.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #831      +/-   ##
==========================================
+ Coverage   68.22%   68.35%   +0.12%     
==========================================
  Files          62       62              
  Lines        3909     3953      +44     
==========================================
+ Hits         2667     2702      +35     
- Misses       1242     1251       +9     

Files with missing lines	Coverage Δ
pydatalab/pydatalab/models/items.py	96.77% <100.00%> (ø)
pydatalab/pydatalab/models/traits.py	97.87% <100.00%> (+0.37%)	⬆️
pydatalab/pydatalab/routes/v0_1/graphs.py	94.59% <81.81%> (-2.24%)	⬇️
pydatalab/pydatalab/routes/v0_1/items.py	82.80% <90.00%> (+0.15%)	⬆️
pydatalab/pydatalab/permissions.py	84.31% <72.72%> (-0.14%)	⬇️
pydatalab/pydatalab/mongo.py	76.62% <60.00%> (-3.66%)	⬇️

[ml-evs]

Have tried to rebase this too, but needs more time in the oven. Will revisit for the next release cycle.