Samplesheet tool by alneberg · Pull Request #995 · NationalGenomicsInfrastructure/genomics-status

alneberg · 2026-04-29T07:23:42Z

I think the python part is now ready to look at. I will review the javascript code myself again before I give a go ahead for a real review.

Documentation to come as well....

…n app

alneberg · 2026-05-18T08:49:17Z

I've looked at demux_sample_info.py and flowcells.py so far. Found a small bug on stage: The link to the "Setup LIMS Step ID" in the metadata section is wrong (https://genomics-status-stage.scilifelab.se/ngi-lims-stage.scilifelab.se/clarity/work-complete/1300155)

Thank you! This should be fixed now.

Co-authored-by: Anandashankar Anil <aanil@users.noreply.github.com>

…sheet

Co-authored-by: Anandashankar Anil <aanil@users.noreply.github.com>

aanil

👍 Nice! Looks functional to me.

alneberg added 30 commits November 14, 2025 10:10

AI start of samplesheet editor

7c5f5ea

Basic table for samplesheet editor

efbb060

Added some metadata and links to projects for samplesheet editor

d9c422b

Draft structure of a sample_info_demux document in test data

036d147

Added a draft post api resource for submitting sample info from LIMS

ade83c2

Moved samplesheet to demux_sample_info

b6e9b03

Removed the test data from the sample info get method and use the new db

eaca6ad

Draft page for demux sample info editing

adc117c

Made calculated samples table with customizable columns

ceeb9ea

Draft for editing demux sample info

3591356

Moved things around

0f3cd11

Added a first bulk edit method

1f4441b

Bulk action for RC 2 as well

5fb5182

Track changes for demux sample info

2c9035d

Use flowcell id instead of document id to find demux_sample_info

dbf26ab

Use tabs instead of view mode

9b6b577

Prettier navbar links and collapsed column configuration

834ca0d

Moved version history into a tab

56fdabd

possible to add samples sort of

ecb1abe

Move the add sample into the edit dialogue

d848207

Some kind of edit functionality for samples

a5a8902

renamed two fields in the database

d385c4d

Changed some field names in the thest_data json

cf025f2

Split up the post method to allow for sample type classification

a7ad52b

Very fragile attempt to implement the calculation stage

fd013c7

started with project type specific demux settings

761bba5

Moved configuration file to a separate directory and load it from mai…

72573b9

…n app

Ruff fix

a552797

AI generated tests

4de9804

New format of the sample classification patterns.json

4885423

aanil reviewed May 12, 2026

View reviewed changes

Comment thread status/demux_sample_info.py Outdated

alneberg added 2 commits May 18, 2026 10:22

Removed a loop through a dictionary, thanks to review comment

6798fea

Use the same LIMS URI as the other pages on genstat

a93c390

alneberg and others added 5 commits May 18, 2026 11:11

Removed unused project id variable due to review comment

71edd1f

Removed some duplicated code thanks to review comment

f850a74

Cleaner fetching of demux_sample_info document

b847f91

Remove unnecessary step.

00b9793

Co-authored-by: Anandashankar Anil <aanil@users.noreply.github.com>

Split up the nested dictionary editing to two functions

23242a0

ssjunnebo approved these changes May 18, 2026

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alneberg removed the WIP Work in progress label May 19, 2026