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 DBHOST, DBPORT, DBSERVICENAME, DBUSER, DBPASSWORD

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:
  • Local:
  • Test Server: Replace < port > with the port number (e.g., http://test-server:5000/samples)
• 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 mvbrapisamples 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 mvbrapisamples 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.