feat: add organism images

[Smeds]

Description

This pull-request will make it possible to display organism images

Select workflow page

Assembly Table page

Organism Table page

Please feel free to make updates to formatting. And if someone could create a better looking missing_image file.

Related Issue

Handle issue #937

[Smeds]

I will add an screenshot of the information popup on monday

[Smeds]

[Smeds]

@NoopDog It would be great if we could have this looked at during this week. We said that for Genomic Informatics we would have the site in beta stage, and it would be nice to have some changes added between alpha and beta.

[NoopDog]

@Smeds can you provide some instructions how to run this to get the images?

[Smeds]

@Smeds can you provide some instructions how to run this to get the images?

@NoopDog To build everything you will have to follow these commands

#Fetch images
npm run fetch-ga2-organism-images
# add image information to intermediate files
npm run build-ga2-from-ncbi
# create final json files with image information
npm run build-ga2-db

[Smeds]

@NoopDog Did you manage to run the commands?

[Smeds]

@NoopDog we will do a short demo if GenomeArk on the next VGP meeting on Friday. Do you think someone could look at this feature before that?

[Smeds]

@NoopDog Have you had time to test the performance?

[MillenniumFalconMechanic]

LGTM!

[Copilot]

Pull request overview

This PR adds organism image display functionality to the GA2 catalog, allowing organism avatars to be shown on the Select workflow, Assembly Table, and Organism Table pages. The implementation includes:

• Scripts to fetch images from Wikimedia Commons and store them in an S3 bucket
• Integration of image metadata (URL, credit, license, source) into the build pipeline
• React components to display organism images as thumbnails and full-size with attribution
• Database schema updates to include image-related fields

Key Changes

• Python build scripts to fetch and process organism images from Wikimedia Commons
• TypeScript build updates to include image metadata in catalog entities
• React OrganismAvatar component with thumbnail and full-size display modes
• Configuration updates to add organism image columns to tables

Reviewed changes

Copilot reviewed 22 out of 30 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
site-config/ga2/category.ts	Adds organism avatar category keys and labels (contains typo)
site-config/ga2/local/index/organism/columnDefs.ts	Defines organism image column configuration (contains typo)
site-config/ga2/local/index/genome/columnDefs.ts	Defines organism image column for genome table (contains typo)
catalog/py_package/catalog_build/build.py	Adds image path mapping logic (has duplicate assignment)
catalog/ga2/build/py/select_images_for_organism.py	Interactive tool to select organism images from Wikimedia
catalog/ga2/build/py/fetch_images_from_bucket.py	Downloads images from S3-compatible storage
catalog/ga2/build/ts/build-catalog.ts	Integrates image data into catalog build
app/components/Entity/components/OrganismAvatar/*	React component for displaying organism images
app/apis/catalog/ga2/entities.ts	Adds ImageData interface and image fields

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Smeds]

I'm test building everything now