diff options
Diffstat (limited to 'tests/unit')
| -rw-r--r-- | tests/unit/test_llm.py | 132 |
1 files changed, 68 insertions, 64 deletions
diff --git a/tests/unit/test_llm.py b/tests/unit/test_llm.py index 7b8a970..8fbaba6 100644 --- a/tests/unit/test_llm.py +++ b/tests/unit/test_llm.py @@ -1,10 +1,9 @@ -# pylint: disable=unused-argument -"""Test cases for procedures defined in llms module""" -from dataclasses import dataclass +"""Test cases for procedures defined in llms """ +# pylint: disable=C0301 import pytest -from gn3.llms.process import get_gnqa +from gn3.llms.process import fetch_pubmed from gn3.llms.process import parse_context - +from gn3.llms.process import format_bibliography_info @pytest.mark.unit_test @@ -36,67 +35,72 @@ def test_parse_context(): assert parsed_result == expected_result - -@dataclass(frozen=True) -class MockResponse: - """mock a response object""" - text: str - - def __getattr__(self, name: str): - return self.__dict__[f"_{name}"] - - -class MockGeneNetworkQAClient: - """mock the GeneNetworkQAClient class""" - - def __init__(self, session, api_key): - pass - - def ask(self, query, auth_token): - """mock method for ask query""" - # Simulate the ask method - return MockResponse("Mock response"), "F400995EAFE104EA72A5927CE10C73B7" - - def get_answer(self, task_id): - """mock get_answer method""" - return MockResponse("Mock answer"), 1 - - -def mock_filter_response_text(text): - """ method to simulate the filterResponseText method""" - return {"data": {"answer": "Mock answer for what is a gene", "context": {}}} - - -def mock_parse_context(context, get_info_func, format_bib_func): - """method to simulate the parse context method""" - return [] - - @pytest.mark.unit_test -def test_get_gnqa(monkeypatch): - """test for process.get_gnqa functoin""" - monkeypatch.setattr( - "gn3.llms.process.GeneNetworkQAClient", - MockGeneNetworkQAClient - ) +def test_format_bib_info(): + """Test for formatting bibliography info """ + mock_fahamu_bib_info = [ + { + "author": "J.m", + "firstName": "john", + "title": "Genes and aging", + "year": 2013, + "doi": "https://Articles.com/12231" + }, + "2019-Roy-Evaluation of Sirtuin-3 probe quality and co-expressed genes", + "2015 - Differential regional and cellular distribution of TFF3 peptide in the human brain.txt"] + expected_result = [ + "J.m.Genes and aging.2013.https://Articles.com/12231 ", + "2019-Roy-Evaluation of Sirtuin-3 probe quality and co-expressed genes", + "2015 - Differential regional and cellular distribution of TFF3 peptide in the human brain" + ] - monkeypatch.setattr( - 'gn3.llms.process.filter_response_text', - mock_filter_response_text - ) - monkeypatch.setattr( - 'gn3.llms.process.parse_context', - mock_parse_context - ) + assert all((format_bibliography_info(data) == expected + for data, expected + in zip(mock_fahamu_bib_info, expected_result))) - query = "What is a gene" - auth_token = "test_token" - result = get_gnqa(query, auth_token) - expected_result = ( - "F400995EAFE104EA72A5927CE10C73B7", - 'Mock answer for what is a gene', - [] - ) +@pytest.mark.unit_test +def test_fetching_pubmed_info(monkeypatch): + """Test for fetching and populating pubmed data with pubmed info""" + def mock_load_file(_filename, _dir_path): + return { + "12121": { + "Abstract": "items1", + "Author": "A1" + } + } + # patch the module with the mocked function + + monkeypatch.setattr("gn3.llms.process.load_file", mock_load_file) + expected_results = [ + { + "title": "Genes", + "year": "2014", + "doi": "https/article/genes/12121", + "doc_id": "12121", + "pubmed": { + "Abstract": "items1", + "Author": "A1" + } + }, + { + "title": "Aging", + "year": "2014", + "doc_id": "12122" + } + ] - assert result == expected_result + data = [{ + "title": "Genes", + "year": "2014", + "doi": "https/article/genes/12121", + "doc_id": "12121", + }, + { + "title": "Aging", + "year": "2014", + "doc_id": "12122" + }] + + assert (fetch_pubmed(data, "/pubmed.json", "data/") + == expected_results) |