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@mlin mlin commented Nov 7, 2025

@jahilton noticed that the builder's summary pivot table didn't include spatial datasets, making it incomplete and also discrepant with the total_cell_count shown in the same report (which did count spatial). This diff includes spatial in the pivot table, breaking it out by collection.

Revised example summary:

                 label      value
 census_schema_version      2.4.0
     census_build_date 2025-11-04
dataset_schema_version      7.0.0
      total_cell_count  217768036
     unique_cell_count  125463259
                                             unique count                                       
attribute                                          assays cell types      cells datasets tissues
organism           collection                                                                   
callithrix_jacchus census_data                          1         40    2275451       27      33
homo_sapiens       census_data                         37        898  158982719     1086     417
                   census_spatial_sequencing            2        228    3042411      361      49
macaca_mulatta     census_data                          2         54    7010229       19      29
mus_musculus       census_data                         16        473   43653561      172     101
                   census_spatial_sequencing            2         67    2645566      179       6
pan_troglodytes    census_data                          1         25     158099        1       1

(2275451+158982719+3042411+7010229+43653561+2645566+158099=217768036)

AFAIK this particular report was only used internally, but it was good to explore this because it does raise the question of whether the census_obj​​["census_info"]["summary"], census_obj["census_info"]["summary_cell_counts"], and other census_info tables should similarly count the spatial and non-spatial collections separately for each organism, instead of lumping them together as they do now. A separate issue we can file @brianraymor

@mlin mlin marked this pull request as ready for review November 7, 2025 08:07
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codecov bot commented Nov 7, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.63%. Comparing base (7d3ab1b) to head (c7800f8).
⚠️ Report is 1 commits behind head on main.

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@@           Coverage Diff           @@
##             main    #1440   +/-   ##
=======================================
  Coverage   91.63%   91.63%           
=======================================
  Files          75       75           
  Lines        5844     5844           
=======================================
  Hits         5355     5355           
  Misses        489      489           
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I don't think I have looked at this file before 😅

I think I am okay with this code not being tested since AFAICT it's just for display at build time.

If there are equivalent statistics in census_summary I would like a follow up issue opened that removes this code and uses that instead.

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mlin commented Nov 8, 2025

Agreed, filed #1442

@mlin mlin merged commit c0245da into main Nov 8, 2025
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@mlin mlin deleted the mlin/builder-summary-spatial-pivot branch November 8, 2025 04:54
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5 participants