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Feature/genome group categories#91

Merged
bilalebi merged 7 commits intomainfrom
feature/genome_group_categories
Apr 13, 2026
Merged

Feature/genome group categories#91
bilalebi merged 7 commits intomainfrom
feature/genome_group_categories

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@EbiArnie
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@EbiArnie EbiArnie commented Mar 25, 2026

Changes

This PR introduces /genome_group_categories endpoint

For now, we're mocking the order and display_name of genome group categories (top level/tabs in the UI)
This will be adressed in a later PR once we have the data ready
The genome groups' info is coming from the DB as desired

Example

Query

http://127.0.0.1:8000/api/metadata/genome_group_categories

Response

{
  "group_categories": [
    {
      "display_name": "External projects",
      "type": "project",
      "groups": [
        {
          "group_id": 12,
          "title": "Vertebrate Genomes Project (VGP)",
          "description": "The Vertebrate Genomes Project (VGP) is an international effort to generate near error-free, high-quality reference genome assemblies for all ~70,000 extant vertebrate species, advancing biology, conservation, and disease research.",
          "rank": 1,
          "genomes_count": 399
        },
        {
          "group_id": 13,
          "title": "Biodiversity Genomics Europe (BGE)",
          "description": "The ERGA-BGE project accelerates genomic science across Europe by generating high-quality reference genomes for biodiversity, supporting conservation, monitoring, and research as part of the Biodiversity Genomics Europe and Earth BioGenome initiatives.",
          "rank": 2,
          "genomes_count": 63
        },
        {
          "group_id": 14,
          "title": "Ancient Environmental Genomics Initiative for Sustainability (AEGIS)",
          "description": "AEGIS is a global research consortium using ancient environmental DNA and genomics to uncover past adaptations and genetic diversity, guiding development of climate-resilient crops and sustainable food systems under climate change.",
          "rank": 3,
          "genomes_count": 79
        }
      ]
    }
  ]
}

EbiArnie and others added 4 commits March 25, 2026 17:15
- This is unfinished code for the new genome group category endpoint
- DB adaptor changes and tests are done and work
- Schema objects are missing
- API endpoint and test is there, but can not work without the schema
  objects
- Logic to transform from model to schema may be incorrect.
@bilalebi bilalebi marked this pull request as ready for review April 2, 2026 17:49
@bilalebi bilalebi requested review from azangru and veidenberg April 2, 2026 17:49
@bilalebi bilalebi self-assigned this Apr 2, 2026
Comment thread src/api/resources/routes.py Outdated
Comment thread src/api/schemas/genome.py Outdated
Comment thread src/api/models/logic.py Outdated
Comment thread src/api/resources/routes.py Outdated
@bilalebi bilalebi merged commit 5a8ce66 into main Apr 13, 2026
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4 participants