🐛 Let Curator.from_tiledbsoma() validate and annotate all .obs columns
#2287
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Koncopd
reviewed
Dec 16, 2024
lamindb/_curate.py
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| @@ -1168,8 +1171,12 @@ def _check_save_keys(self): | |||
| with _open_tiledbsoma(self._experiment_uri, mode="r") as experiment: | |||
| experiment_obs = experiment.obs | |||
| self._n_obs = len(experiment_obs) | |||
| valid_obs_keys = [k for k in experiment_obs.keys() if k != "soma_joinid"] | |||
| valid_obs_keys = [ | |||
| k for k in experiment_obs.schema.names if k != "soma_joinid" | |||
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Please read from the saved schema here to avoid redundant requests, maybe they cache but let’s be careful anyways.
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You save the schema on the next line anyways.
|
Thank you for fixing, this is great, just one small thing here to correct. |
falexwolf
changed the title
.obs columns
falexwolf
changed the title
.obs columnsCurator.from_tiledbsoma() validate and annotate all .obs columns
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #2287 +/- ##
=======================================
Coverage 92.82% 92.82%
=======================================
Files 55 55
Lines 7202 7208 +6
=======================================
+ Hits 6685 6691 +6
Misses 517 517 ☔ View full report in Codecov by Sentry. |
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Fixes:
Curator.from_tiledbsoma()omits simple feature dtypes in the dataset #2285