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Assorted fixes for starting materials in collections #1167

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Merged
merged 6 commits into from
May 14, 2025
Merged

Assorted fixes for starting materials in collections #1167

merged 6 commits into from
May 14, 2025

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ml-evs
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@ml-evs ml-evs commented May 2, 2025 •
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Some fixes to allow starting materials to appear in collections in the UI, plus some assorted fixes to the item graph to better show starting materials.

  • Refactor summary endpoint so that starting materials can be requested when called from collection table
  • Add a default search index of date for all items and use it by default when returning inventory (rather than implicitly using ctime
  • Update the item graph endpoint so ignore collections by default, which are a frequent cause of errors
  • Some tweaks for logging and cleaning up MongoDB connections

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cypress bot commented May 2, 2025 •
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datalab    Run #3286

Run Properties:  status check passed Passed #3286  •  git commit b28a3510be ℹ️: Merge 1fe19fb9e5160db15ad9b6d110185f73c64614ed into 1964ba51ce18b92264f91798d5fe...
Project datalab
Branch Review ml-evs/item-summary
Run status status check passed Passed #3286
Run duration 07m 53s
Commit git commit b28a3510be ℹ️: Merge 1fe19fb9e5160db15ad9b6d110185f73c64614ed into 1964ba51ce18b92264f91798d5fe...
Committer Matthew Evans
View all properties for this run ↗︎
Test results
Tests that failed  Failures 0
Tests that were flaky  Flaky 0
Tests that did not run due to a developer annotating a test with .skip  Pending 0
Tests that did not run due to a failure in a mocha hook  Skipped 0
Tests that passed  Passing 504
View all changes introduced in this branch ↗︎

@ml-evs ml-evs force-pushed the ml-evs/item-summary branch 3 times, most recently from 55fa8f6 to 34b0ca3 Compare May 4, 2025 14:45
@ml-evs ml-evs added refactoring For issues/PRs that refactor existing code/features Python labels May 14, 2025
@ml-evs ml-evs force-pushed the ml-evs/item-summary branch from a95ec89 to 2157df8 Compare May 14, 2025 12:08
@ml-evs ml-evs changed the title Fixes for starting materials in collections Assorted fixes for starting materials in collections May 14, 2025
ml-evs added 4 commits May 14, 2025 13:28
@ml-evs
Add starting materials to item graph when requested, remove collectio…
8fb3d3c 
…n nodes by default

Update graph test case to remove collections

- Revert to previous behaviour where starting materials are hidden unless connected or requested

- Add simple separate test module for item graph
@ml-evs
Use PEP 639 SPDX license in pyproject
8a8feea
@ml-evs
Use atexit to register MongoClient destructor to suppress warnings …
cd9a204 
…in test
@ml-evs
Separate root logger and access log format for more concise logging
1fe19fb
@ml-evs ml-evs force-pushed the ml-evs/item-summary branch from 2157df8 to 1fe19fb Compare May 14, 2025 12:28
@ml-evs ml-evs marked this pull request as ready for review May 14, 2025 12:37
BenjaminCharmes
BenjaminCharmes approved these changes May 14, 2025
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Works very well !

@ml-evs ml-evs merged commit 61b917c into main May 14, 2025
23 of 29 checks passed
@ml-evs ml-evs deleted the ml-evs/item-summary branch May 14, 2025 13:26
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codecov bot commented May 14, 2025 •
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Codecov Report

❌ Patch coverage is 75.60976% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 70.94%. Comparing base (1964ba5) to head (1fe19fb).
⚠️ Report is 98 commits behind head on main.

Files with missing lines Patch % Lines
pydatalab/src/pydatalab/routes/v0_1/graphs.py 55.55% 4 Missing ⚠️
pydatalab/src/pydatalab/logger.py 76.92% 3 Missing ⚠️
pydatalab/src/pydatalab/routes/v0_1/items.py 83.33% 2 Missing ⚠️
pydatalab/src/pydatalab/mongo.py 83.33% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #1167      +/-   ##
==========================================
- Coverage   71.22%   70.94%   -0.29%     
==========================================
  Files          64       64              
  Lines        4240     4271      +31     
==========================================
+ Hits         3020     3030      +10     
- Misses       1220     1241      +21
Files with missing lines Coverage Δ
pydatalab/src/pydatalab/routes/v0_1/collections.py 70.45% <100.00%> (ø)
pydatalab/src/pydatalab/mongo.py 81.08% <83.33%> (+1.08%) ⬆️
pydatalab/src/pydatalab/routes/v0_1/items.py 82.63% <83.33%> (-0.96%) ⬇️
pydatalab/src/pydatalab/logger.py 84.84% <76.92%> (-1.95%) ⬇️
pydatalab/src/pydatalab/routes/v0_1/graphs.py 77.27% <55.55%> (-19.56%) ⬇️
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@BenjaminCharmes BenjaminCharmes BenjaminCharmes approved these changes

@jdbocarsly jdbocarsly Awaiting requested review from jdbocarsly jdbocarsly is a code owner

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