amr-portal

A portal for viewing antimicrobial resistance (AMR) data

Local setup

git clone https://github.com/Ensembl/amr-portal.git
cd amr-portal

Backend

1. Install requirements

cd backend
python -m venv venv
source venv/bin/activate
pip install -r requirements.txt

2. Create a .env File

# .env
DUCKDB_PATH=path/to/duckdb/file.duckdb

Or

export DUCKDB_PATH=path/to/duckdb/file.duckdb

# make sure you're in the *root directory*
cd ..
uvicorn backend.main:app --reload

Swagger UI: http://localhost:8000/docs

For production use:

uvicorn backend.main:app --host 0.0.0.0 --port 8000 --workers 4

For testing:

Create a .env.test file in the project root with the following content:

DUCKDB_PATH=path/to/test_data.duckdb

Then run:

TESTING=true pytest backend/

API Calls Examples

/filters-config

curl -X 'GET' \
  'http://localhost:8000/filters-config' \
  -H 'accept: application/json'

/amr-records

Fetching Phenotype data

curl -X 'POST' \
  'http://localhost:8000/amr-records' \
  -H 'accept: application/json' \
  -H 'Content-Type: application/json' \
  -d '{
  "selected_filters": [
    { "category": "phenotype-genus", "value": "Streptococcus" },
    { "category": "phenotype-Antibiotic_abbreviation", "value": "OXA" },
    { "category": "phenotype-Antibiotic_abbreviation", "value": "AMK" }
  ],
  "view_id": 1,
  "order_by": {
    "category": "phenotype-collection_date",
    "order": "DESC"
  }
}'

Fetching Genotype data

curl -X 'POST' \
  'http://localhost:8000/amr-records' \
  -H 'accept: application/json' \
  -H 'Content-Type: application/json' \
  -d '{
  "selected_filters": [
    { "category": "genotype-Contig_id", "value": "CQKJ01000001.1" },
    { "category": "genotype-Contig_id", "value": "DAFBZU010000245.1" }
  ],
  "view_id": 2,
  "order_by": {
    "category": "genotype-Contig_id",
    "order": "DESC"
  }
}'

/download

Download data in the current page in CSV format

curl -X 'POST' \
  'http://localhost:8000/amr-records/download' \
  -H 'Content-Type: application/json' \
  -d '{
  "selected_filters": [
    { "category": "phenotype-genus", "value": "Streptococcus" },
    { "category": "phenotype-Antibiotic_abbreviation", "value": "OXA" },
    { "category": "phenotype-Antibiotic_abbreviation", "value": "AMK" }
  ],
  "view_id": 1,
  "order_by": {
    "category": "phenotype-collection_date",
    "order": "DESC"
  }
}'

Download all matches in JSON format

curl -X 'POST' \
  'http://localhost:8000/amr-records/download?scope=all&file_format=json' \
  -H 'Content-Type: application/json' \
  -d '{
  "selected_filters": [
    { "category": "phenotype-genus", "value": "Streptococcus" }
  ],
  "view_id": 1,
  "order_by": {
    "category": "phenotype-collection_date",
    "order": "DESC"
  }
}'

Frontend

Prerequisite: need to have Node installed. As a rule of thumb, always use the latest LTS version of Node.

cd frontend
npm install
npm run dev

Production build

Frontend

cd frontend
npm install
npm run build

This will create a dist directory containing a static html file and all the assets that it loads.

Further details

The frontend combines a static site built with Eleventy with islands of interactivity built with web components and Lit. For more details about the build setup, see frontend/eleventy.config.js, and the documentation in the docs/decisions directory.