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Okerew edited this page Sep 13, 2025 · 1 revision

DNALite API Documentation

Overview

The DNALite API is a Flask-based web service for storing, retrieving, listing, and deleting biological data (e.g., DNA, RNA, Protein sequences) using an SQLDNAEncoder. It provides RESTful endpoints for managing data in a structured manner.

Endpoints

1. Store Data

  • Endpoint: /store
  • Method: POST
  • Description: Stores biological data in the database.
  • Request Body: 
    {
  "data_name": "string",
  "data": "object"
}
  • Responses:
    • Success (201 Created): 
      {
  "message": "Data stored successfully"
}
    • Error (400 Bad Request): 
      {
  "error": "Missing required fields: data_name and data"
}
    • Error (500 Internal Server Error): 
      {
  "error": "Error message"
}

2. Retrieve Data

  • Endpoint: /retrieve/<data_name>
  • Method: GET
  • Description: Retrieves stored biological data by its name.
  • Path Parameter:
    • data_name: Name of the data to retrieve.
  • Responses:
    • Success (200 OK): 
      {
  "data": "object"
}
    • Error (404 Not Found): 
      {
  "message": "Data not found"
}
    • Error (500 Internal Server Error): 
      {
  "error": "Error message"
}

3. List Stored Data

  • Endpoint: /list
  • Method: GET
  • Description: Lists all stored data names.
  • Responses:
    • Success (200 OK): 
      [
  "data_name_1",
  "data_name_2",
  ...
]
    • Error (500 Internal Server Error): 
      {
  "error": "Error message"
}

4. Delete Data

  • Endpoint: /delete/<data_name>
  • Method: DELETE
  • Description: Deletes stored biological data by its name.
  • Path Parameter:
    • data_name: Name of the data to delete.
  • Responses:
    • Success (200 OK): 
      {
  "message": "Data deleted successfully"
}
    • Error (500 Internal Server Error): 
      {
  "error": "Error message"
}

5. Copy Database

  • Endpoint: /copy
  • Method: POST
  • Description: Copies the current database to a new database.
  • Request Body: 
    {
  "db_name": "string"
}
  • Responses:
    • Success (200 OK): 
      {
  "message": "Database copied to {db_name}"
}
    • Error (400 Bad Request): 
      {
  "error": "Missing required field: db_name"
}
    • Error (500 Internal Server Error): 
      {
  "error": "Error message"
}

Example Usage

1. Initialize the Flask App

from dnalite_api import create_app

app = create_app()

if __name__ == "__main__":
    app.run(debug=True)

2. Store Data

curl -X POST http://localhost:5000/store \
  -H "Content-Type: application/json" \
  -d '{"data_name": "example_dna", "data": {"sequence": "ATGC"}}'

3. Retrieve Data

curl -X GET http://localhost:5000/retrieve/example_dna

4. List Stored Data

curl -X GET http://localhost:5000/list

5. Delete Data

curl -X DELETE http://localhost:5000/delete/example_dna

6. Copy Database

curl -X POST http://localhost:5000/copy \
  -H "Content-Type: application/json" \
  -d '{"db_name": "new_database"}'

Dependencies

  • Flask: Web framework for building the API.
  • SQLDNAEncoder: Custom class for encoding and managing biological data in a database.

Error Handling

  • 400 Bad Request: Missing required fields in the request.
  • 404 Not Found: Data not found in the database.
  • 500 Internal Server Error: Unexpected errors during data operations.

Notes

  • The API is designed to be extensible for additional biological data types and operations.
  • Ensure the SQLDNAEncoder is properly initialized with a database connection.

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