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Improved reports with tables #624

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@gaurav gaurav commented Dec 11, 2025 •
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This PR adds some additional reports that generate tables that can be used in publications and GitHub. Previous reports were generated as detailed JSON and TSV files; this PR gets rid of those detailed TSVs and replaces them with the tables we are generating for the Babel paper. The final step will be in #628, but if we can generate the tables here, that's all we need for now.

WIP. Should be merged after PR #594.

gaurav and others added 30 commits December 14, 2025 01:33
@gaurav
Added snakemake-executor-plugin-slurm.
fb53454 
# Conflicts:
#	uv.lock

diff --git c/uv.lock i/uv.lock
index d667353..df33f81 100644
--- c/uv.lock
+++ i/uv.lock
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@gaurav
Added a prefix table report.
bb0f066
@gaurav
Removed hack needed to run script locally.
84ea1e7
@gaurav
Improving generate_curie_report.
81c148f
@gaurav
Tweaked memory requirements.
48ed891
@gaurav
Improved the cliques_leaders report.
0bce139
@gaurav
Increased memory requirements for generate_curie_report.
7f4adba
@gaurav
Reduced variables in generate_curie_report.
aedae17
@gaurav
Fixed SQL query.
9ab5ebc
@gaurav
Attempt at reorganizing the Biolink type query in generate_curie_report.
0edf7d5
@gaurav
Fixed queries.
e110416
@gaurav
Moved inner query into a temporary table.
177db49
@gaurav
Attempt to get clique lookups to work in limited memory.
44f2faf
@gaurav
Removed index we can't build.
744e3bf
@gaurav
Started work on an improved clique leader report.
a442dc7
@gaurav
First stab at generate_cliques_table.
2c106d5
@gaurav
Added totals to clique report.
8bae8fa
@gaurav
Fixed some keys.
6136ba0
@gaurav
Rewrote Biolink-type query with a suggestion from ChatGPT.
74f9c36
@gaurav
Fix typo.
f4b858a
@gaurav
Fix set issue.
0b3f68b
@gaurav
Fix second table name.
6b4f508
@gaurav
Fixed some issues.
51671df
@gaurav
Maybe fix the SQL query?
23aa44c
@gaurav
Fixed filename for Taxon.
37d23b8
@gaurav
Fixed dictionary name.
b672525
@gaurav
Rearranged queries for generate_curie_report.
a423e6e
@gaurav
Let's try really reducing memory on generate_curie_report.
ddce865
@gaurav
Filled in missing filename.
b704c51
@gaurav
Fixed totals.
273cc22
@gaurav gaurav changed the base branch from master to 35-run-distribute-hatteras December 14, 2025 06:34
This was referenced Dec 14, 2025
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2 participants

@gaurav