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Project setup - Branch DEV

Please note: the Python major version for below task has to match. I.e You may use virtual-env3.6 in combination with python3.12. But virtual-env2.7 is not compatible to use. Thus it is not recommend to use virtualenv or phython in command line without version. The recommend version is Python 3.12

1. Create a virtual env on linux system

virtualenv-<version> -p /usr/bin/python3.12 .agent-env

2. Activate venv

source .agent-env/bin/activate

3. Install depencies

pip<version> install -r requirements.txt

4. Set the environment values for the database connection

  • rename .env-template to .env
  • set the values like DB_HOST, DB_PORT, DB_SERVICE_NAME, DB_USER, DB_PASSWORD

5. Start project

python<version> main.py

TESTING FLASK APPLICATION

Create a step-by-step guide for developers and testers to verify the /samples BrAPI endpoint manually.

Objective

To validate the /samples endpoint with different query parameter combinations.

Pre-requisites

  • Application Setup: The application must be running locally or on a test server.
  • Environment: Ensure all necessary environment variables are set up in the .env file.
  • Tools:
    • API Testing Tool: Use tools like Postman or cURL.
    • Sample Data: Prepare valid and invalid data for testing.
  • Dependencies: Install the extension with dependencies and run your test suite:
    • $ pip install pytest-flask
    • $ pytest

Endpoint Details

  • Endpoint URL:
  • HTTP Method: GET
  • Parameters:
    • pageSize: Number of records per page (integer).
    • currentPage or page: Page number (integer).
    • Other filter parameters based on column names in the mv_brapi_samples table.

Testing Steps

Verify Basic Connectivity - Use a browser or REST client to send a GET request to /genotyping/brapi/v2/samples. - Expected: A JSON response with metadata and result.data fields.

Example:

- Send a GET request to the endpoint using Postman or cURL
- Bash: curl -X GET : <http://localhost:&lt;port&gt;/genotyping/brapi/v2/samples>

Tests

1. Simple Test
    - Test with a single parameter: page=1.
    - Verify:
        - Status code = 200.
        - Response JSON includes currentPage = 1.
    - Example:
        - bash
        - curl -X GET : <http://localhost:&lt;port&gt;/genotyping/brapi/v2/samples?page=1>'

2. Complex Test
    - Test with multiple parameters: page=1, pageSize=5, and sampleType=DNA.
    - Verify:
        - Status code = 200.
        - Response JSON includes pageSize = 5 and a filtered dataset matching the sampleType.
    - Example:
        - bash
        - curl -X GET : ‘<http://localhost:&lt;port&gt;/genotyping/brapi/v2/samples?page=1&pageSize=5&sampleType=DNA>'

Database Validation - Run queries directly on the database to ensure the API results align with the mv_brapi_samples table.

Test Scenarios

Scenario Parameters Expected Outcome
Basic Test page=1 200, first page of results.
Multiple Parameters page=1&pageSize=5&sampleType=DNA 200, paginated and filtered results.
Invalid Page Number page=-1 400 or a safe default (page=0).
Excessive Page Size pageSize=10000 200, limited to server-defined max size (e.g., 1000).
No Results Found sampleType=XYZ 200, empty result.data.
SQL Injection Prevention Malicious input in parameters 400 or sanitized query preventing SQL injection.

Test Cases

Test Case ID Test Case Description Steps to Execute Expected Result Actual Result Status (Pass/Fail)
TC001 Test the /samples endpoint - Simple Query 1. Send a GET request to /samples endpoint with minimal params. Response status: 200, Response contains sample data with valid metadata and pagination info. Response status: 200, Valid metadata and pagination info found. Pass
TC002 Test the /samples endpoint - Complex Query 1. Send a GET request with detailed query parameters to /samples. Response status: 200, Response contains filtered and relevant data according to the parameters. Response status: 200, Filtered and relevant data found. Pass
TC003 Test Sample Retrieval by Reference ID (Simple Query) 1. Send a GET request to /samples/{referenceId}. Response status: 200, Correct sample details retrieved for the given reference ID. Response status: 200, Correct details retrieved. Pass
TC004 Verify /samples Endpoint with Live Log & Response 1. Log the call and ensure proper response format and metadata. Logs should capture all response details, proper metadata, pagination, and sample information in JSON format. Logs captured response with valid metadata and details. Pass

Summary of Test Results

  • Total Test Cases Executed: 4
  • Total Test Cases Passed: 4
  • Total Test Cases Failed: 0

Conclusion

The manual testing of the /samples endpoint for the BrAPI project has been successful. All test cases passed, and the API is verified for correctness, logging, and data handling capabilities.