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"""Test cases for procedures defined in llms """
# pylint: disable=C0301
# pylint: disable=W0613
from datetime import datetime, timedelta
from unittest.mock import patch
from unittest.mock import MagicMock
import pytest
from gn3.llms.process import fetch_pubmed
from gn3.llms.process import parse_context
from gn3.llms.process import format_bibliography_info
from gn3.llms.errors import LLMError
from gn3.api.llm import clean_query
from gn3.api.llm import is_verified_anonymous_user
from gn3.api.llm import is_valid_address
from gn3.api.llm import check_rate_limiter
FAKE_NOW = datetime(2025, 1, 1, 12, 0, 0)
@pytest.mark.unit_test
def test_parse_context():
"""test for parsing doc id context"""
def mock_get_info(doc_id):
return f"Info for {doc_id}"
def mock_format_bib(doc_info):
return f"Formatted Bibliography: {doc_info}"
parsed_result = parse_context({
"doc1": [{"text": "Summary 1"}, {"text": "Summary 2"}],
"doc2": [{"text": "Summary 3"}, {"text": "Summary 4"}],
}, mock_get_info, mock_format_bib)
expected_result = [
{
"doc_id": "doc1",
"bibInfo": "Formatted Bibliography: Info for doc1",
"comboTxt": "\tSummary 1\tSummary 2",
},
{
"doc_id": "doc2",
"bibInfo": "Formatted Bibliography: Info for doc2",
"comboTxt": "\tSummary 3\tSummary 4",
},
]
assert parsed_result == expected_result
@pytest.mark.unit_test
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"
]
assert all((format_bibliography_info(data) == expected
for data, expected
in zip(mock_fahamu_bib_info, expected_result)))
@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"
}
]
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)
@pytest.mark.unit_test
def test_clean_query():
"""Test function for cleaning up query"""
assert clean_query("!what is genetics.") == "what is genetics"
assert clean_query("hello test?") == "hello test"
assert clean_query(" hello test with space?") == "hello test with space"
@pytest.mark.unit_test
def test_is_verified_anonymous_user():
"""Test function for verifying anonymous user metadata"""
assert is_verified_anonymous_user({}) is False
assert is_verified_anonymous_user({"Anonymous-Id" : "qws2121dwsdwdwe",
"Anonymous-Status" : "verified"}) is True
@pytest.mark.unit_test
def test_is_valid_address() :
"""Test function checks if is a valid ip address is valid"""
assert is_valid_address("invalid_ip") is False
assert is_valid_address("127.0.0.1") is True
@patch("gn3.api.llm.datetime")
@patch("gn3.api.llm.db.connection")
@patch("gn3.api.llm.is_valid_address", return_value=True)
@pytest.mark.unit_test
def test_first_time_visitor(mock_is_valid, mock_db_conn, mock_datetime):
"""Test rate limiting for first-time visitor"""
mock_datetime.utcnow.return_value = FAKE_NOW
mock_datetime.strptime = datetime.strptime # keep real one
mock_datetime.strftime = datetime.strftime # keep real one
# Set up DB mock
mock_conn = MagicMock()
mock_cursor = MagicMock()
mock_conn.__enter__.return_value = mock_conn
mock_conn.cursor.return_value = mock_cursor
mock_cursor.fetchone.return_value = None
mock_db_conn.return_value = mock_conn
result = check_rate_limiter("127.0.0.1", "test/llm.db", "Chromosome x")
assert result is True
mock_cursor.execute.assert_any_call("""
INSERT INTO Limiter(identifier, tokens, expiry_time)
VALUES (?, ?, ?)
""", ("127.0.0.1", 4, "2025-01-01 12:24:00"))
@patch("gn3.api.llm.datetime")
@patch("gn3.api.llm.db.connection")
@patch("gn3.api.llm.is_valid_address", return_value=True)
@pytest.mark.unit_test
def test_visitor_at_limit(mock_is_valid, mock_db_conn, mock_datetime):
"""Test rate limiting for Visitor at limit"""
mock_datetime.utcnow.return_value = FAKE_NOW
mock_datetime.strptime = datetime.strptime # keep real one
mock_datetime.strftime = datetime.strftime
mock_conn = MagicMock()
mock_cursor = MagicMock()
mock_conn.__enter__.return_value = mock_conn
mock_conn.cursor.return_value = mock_cursor
fake_expiry = (FAKE_NOW + timedelta(minutes=10)).strftime("%Y-%m-%d %H:%M:%S")
mock_cursor.fetchone.return_value = (0, fake_expiry) #token returned are 0
mock_db_conn.return_value = mock_conn
with pytest.raises(LLMError) as exc_info:
check_rate_limiter("127.0.0.1", "test/llm.db", "Chromosome x")
# assert llm error with correct message is raised
assert exc_info.value.args == ('Rate limit exceeded. Please try again later.', 'Chromosome x')
@patch("gn3.api.llm.datetime")
@patch("gn3.api.llm.db.connection")
@patch("gn3.api.llm.is_valid_address", return_value=True)
@pytest.mark.unit_test
def test_visitor_with_tokens(mock_is_valid, mock_db_conn, mock_datetime):
"""Test rate limiting for user with valid tokens"""
mock_datetime.utcnow.return_value = FAKE_NOW
mock_datetime.strptime = datetime.strptime # Use real versions
mock_datetime.strftime = datetime.strftime
mock_conn = MagicMock()
mock_cursor = MagicMock()
mock_conn.__enter__.return_value = mock_conn
mock_conn.cursor.return_value = mock_cursor
fake_expiry = (FAKE_NOW + timedelta(minutes=10)).strftime("%Y-%m-%d %H:%M:%S")
mock_cursor.fetchone.return_value = (3, fake_expiry) # Simulate 3 tokens
mock_db_conn.return_value = mock_conn
results = check_rate_limiter("127.0.0.1", "test/llm.db", "Chromosome x")
assert results is True
mock_cursor.execute.assert_any_call("""
UPDATE Limiter
SET tokens = tokens - 1
WHERE identifier = ? AND tokens > 0
""", ("127.0.0.1",))
@patch("gn3.api.llm.datetime")
@patch("gn3.api.llm.db.connection")
@patch("gn3.api.llm.is_valid_address", return_value=True)
@pytest.mark.unit_test
def test_visitor_token_expired(mock_is_valid, mock_db_conn, mock_datetime):
"""Test rate limiting for expired tokens"""
mock_datetime.utcnow.return_value = FAKE_NOW
mock_datetime.strptime = datetime.strptime
mock_datetime.strftime = datetime.strftime
mock_conn = MagicMock()
mock_cursor = MagicMock()
mock_conn.__enter__.return_value = mock_conn
mock_conn.cursor.return_value = mock_cursor
fake_expiry = (FAKE_NOW - timedelta(minutes=10)).strftime("%Y-%m-%d %H:%M:%S")
mock_cursor.fetchone.return_value = (3, fake_expiry) # Simulate 3 tokens
mock_db_conn.return_value = mock_conn
result = check_rate_limiter("127.0.0.1", "test/llm.db", "Chromosome x")
assert result is True
mock_cursor.execute.assert_any_call("""
UPDATE Limiter
SET tokens = ?, expiry_time = ?
WHERE identifier = ?
""", (4, "2025-01-01 12:24:00", "127.0.0.1"))
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