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"""Unit tests for PubMed tool."""
from unittest.mock import AsyncMock, MagicMock
import pytest
from src.tools.pubmed import PubMedTool
# Sample PubMed XML response for mocking
SAMPLE_PUBMED_XML = """<?xml version="1.0" ?>
<PubmedArticleSet>
<PubmedArticle>
<MedlineCitation>
<PMID>12345678</PMID>
<Article>
<ArticleTitle>Metformin in Alzheimer's Disease: A Systematic Review</ArticleTitle>
<Abstract>
<AbstractText>Metformin shows neuroprotective properties...</AbstractText>
</Abstract>
<AuthorList>
<Author>
<LastName>Smith</LastName>
<ForeName>John</ForeName>
</Author>
</AuthorList>
<Journal>
<JournalIssue>
<PubDate>
<Year>2024</Year>
<Month>01</Month>
</PubDate>
</JournalIssue>
</Journal>
</Article>
</MedlineCitation>
</PubmedArticle>
</PubmedArticleSet>
"""
class TestPubMedTool:
"""Tests for PubMedTool."""
@pytest.mark.asyncio
async def test_search_returns_evidence(self, mocker):
"""PubMedTool should return Evidence objects from search."""
# Mock the HTTP responses
mock_search_response = MagicMock()
mock_search_response.json.return_value = {"esearchresult": {"idlist": ["12345678"]}}
mock_search_response.raise_for_status = MagicMock()
mock_fetch_response = MagicMock()
mock_fetch_response.text = SAMPLE_PUBMED_XML
mock_fetch_response.raise_for_status = MagicMock()
mock_client = AsyncMock()
mock_client.get = AsyncMock(side_effect=[mock_search_response, mock_fetch_response])
mock_client.__aenter__ = AsyncMock(return_value=mock_client)
mock_client.__aexit__ = AsyncMock(return_value=None)
mocker.patch("httpx.AsyncClient", return_value=mock_client)
# Act
tool = PubMedTool()
results = await tool.search("metformin alzheimer")
# Assert
assert len(results) == 1
assert results[0].citation.source == "pubmed"
assert "Metformin" in results[0].citation.title
assert "12345678" in results[0].citation.url
@pytest.mark.asyncio
async def test_search_empty_results(self, mocker):
"""PubMedTool should return empty list when no results."""
mock_response = MagicMock()
mock_response.json.return_value = {"esearchresult": {"idlist": []}}
mock_response.raise_for_status = MagicMock()
mock_client = AsyncMock()
mock_client.get = AsyncMock(return_value=mock_response)
mock_client.__aenter__ = AsyncMock(return_value=mock_client)
mock_client.__aexit__ = AsyncMock(return_value=None)
mocker.patch("httpx.AsyncClient", return_value=mock_client)
tool = PubMedTool()
results = await tool.search("xyznonexistentquery123")
assert results == []
def test_parse_pubmed_xml(self):
"""PubMedTool should correctly parse XML."""
tool = PubMedTool()
results = tool._parse_pubmed_xml(SAMPLE_PUBMED_XML)
assert len(results) == 1
assert results[0].citation.source == "pubmed"
assert "Smith John" in results[0].citation.authors
@pytest.mark.asyncio
async def test_search_preprocesses_query(self, mocker):
"""Test that queries are preprocessed before search."""
mock_search_response = MagicMock()
mock_search_response.json.return_value = {"esearchresult": {"idlist": []}}
mock_search_response.raise_for_status = MagicMock()
mock_client = AsyncMock()
mock_client.get = AsyncMock(return_value=mock_search_response)
mock_client.__aenter__ = AsyncMock(return_value=mock_client)
mock_client.__aexit__ = AsyncMock(return_value=None)
mocker.patch("httpx.AsyncClient", return_value=mock_client)
tool = PubMedTool()
await tool.search("What drugs help with Long COVID?")
# Verify call args
call_args = mock_client.get.call_args
params = call_args[1]["params"]
term = params["term"]
# "what" and "help" should be stripped
assert "what" not in term.lower()
assert "help" not in term.lower()
# "long covid" should be expanded
assert "PASC" in term or "post-COVID" in term
@pytest.mark.asyncio
async def test_rate_limiting_enforced(self, mocker):
"""PubMedTool should enforce rate limiting between requests."""
from unittest.mock import patch
mock_search_response = MagicMock()
mock_search_response.json.return_value = {"esearchresult": {"idlist": []}}
mock_search_response.raise_for_status = MagicMock()
mock_client = AsyncMock()
mock_client.get = AsyncMock(return_value=mock_search_response)
mock_client.__aenter__ = AsyncMock(return_value=mock_client)
mock_client.__aexit__ = AsyncMock(return_value=None)
mocker.patch("httpx.AsyncClient", return_value=mock_client)
tool = PubMedTool()
# Reset last request time to ensure rate limit is triggered
tool._last_request_time = 0.0
# Mock time to control elapsed time
with patch("asyncio.get_running_loop") as mock_loop:
loop_mock = MagicMock()
loop_mock.time.side_effect = [0.0, 0.1] # Only 0.1s elapsed, need 0.34s
mock_loop.return_value = loop_mock
# Mock sleep to verify it's called
with patch("asyncio.sleep") as mock_sleep:
await tool.search("test query")
# Should sleep for at least (0.34 - 0.1) = 0.24 seconds
mock_sleep.assert_called_once()
call_arg = mock_sleep.call_args[0][0]
assert call_arg >= 0.24
@pytest.mark.asyncio
async def test_api_key_included_in_params(self, mocker):
"""PubMedTool should include API key in params when provided."""
mock_search_response = MagicMock()
mock_search_response.json.return_value = {"esearchresult": {"idlist": []}}
mock_search_response.raise_for_status = MagicMock()
mock_client = AsyncMock()
mock_client.get = AsyncMock(return_value=mock_search_response)
mock_client.__aenter__ = AsyncMock(return_value=mock_client)
mock_client.__aexit__ = AsyncMock(return_value=None)
mocker.patch("httpx.AsyncClient", return_value=mock_client)
# Test with API key
tool = PubMedTool(api_key="test-api-key-123")
await tool.search("test query")
# Verify API key was included in params
call_args = mock_client.get.call_args
params = call_args[1]["params"]
assert "api_key" in params
assert params["api_key"] == "test-api-key-123"
# Test without API key
tool_no_key = PubMedTool(api_key=None)
mock_client.get.reset_mock()
await tool_no_key.search("test query")
call_args = mock_client.get.call_args
params = call_args[1]["params"]
assert "api_key" not in params
@pytest.mark.asyncio
async def test_handles_429_rate_limit(self, mocker):
"""PubMedTool should raise RateLimitError on 429 response."""
import httpx
from src.utils.exceptions import RateLimitError
mock_response = MagicMock()
mock_response.status_code = 429
mock_response.raise_for_status.side_effect = httpx.HTTPStatusError(
"Rate limit", request=MagicMock(), response=mock_response
)
mock_client = AsyncMock()
mock_client.get = AsyncMock(return_value=mock_response)
mock_client.__aenter__ = AsyncMock(return_value=mock_client)
mock_client.__aexit__ = AsyncMock(return_value=None)
mocker.patch("httpx.AsyncClient", return_value=mock_client)
tool = PubMedTool()
with pytest.raises(RateLimitError, match="rate limit exceeded"):
await tool.search("test query")
@pytest.mark.asyncio
async def test_handles_500_server_error(self, mocker):
"""PubMedTool should raise SearchError on 500 response."""
import httpx
from src.utils.exceptions import SearchError
mock_response = MagicMock()
mock_response.status_code = 500
mock_response.raise_for_status.side_effect = httpx.HTTPStatusError(
"Server error", request=MagicMock(), response=mock_response
)
mock_client = AsyncMock()
mock_client.get = AsyncMock(return_value=mock_response)
mock_client.__aenter__ = AsyncMock(return_value=mock_client)
mock_client.__aexit__ = AsyncMock(return_value=None)
mocker.patch("httpx.AsyncClient", return_value=mock_client)
tool = PubMedTool()
with pytest.raises(SearchError, match="PubMed search failed"):
await tool.search("test query")
@pytest.mark.asyncio
async def test_handles_network_timeout(self, mocker):
"""PubMedTool should handle network timeout errors."""
import httpx
from src.utils.exceptions import SearchError
mock_client = AsyncMock()
mock_client.get = AsyncMock(side_effect=httpx.TimeoutException("Timeout"))
mock_client.__aenter__ = AsyncMock(return_value=mock_client)
mock_client.__aexit__ = AsyncMock(return_value=None)
mocker.patch("httpx.AsyncClient", return_value=mock_client)
tool = PubMedTool()
# Should be retried by tenacity, but eventually raise SearchError
with pytest.raises(SearchError):
await tool.search("test query")
def test_parse_empty_xml(self):
"""PubMedTool should handle empty XML gracefully."""
tool = PubMedTool()
empty_xml = '<?xml version="1.0" ?><PubmedArticleSet></PubmedArticleSet>'
results = tool._parse_pubmed_xml(empty_xml)
assert results == []
def test_parse_malformed_xml(self):
"""PubMedTool should raise SearchError on malformed XML."""
from src.utils.exceptions import SearchError
tool = PubMedTool()
malformed_xml = "<not>valid</xml>"
with pytest.raises(SearchError, match="Failed to parse PubMed XML"):
tool._parse_pubmed_xml(malformed_xml)
def test_parse_article_without_abstract(self):
"""PubMedTool should skip articles without abstracts."""
tool = PubMedTool()
xml_no_abstract = """<?xml version="1.0" ?>
<PubmedArticleSet>
<PubmedArticle>
<MedlineCitation>
<PMID>12345678</PMID>
<Article>
<ArticleTitle>Test Article</ArticleTitle>
</Article>
</MedlineCitation>
</PubmedArticle>
</PubmedArticleSet>
"""
results = tool._parse_pubmed_xml(xml_no_abstract)
# Should return empty list because article has no abstract
assert results == []
def test_parse_article_without_title(self):
"""PubMedTool should skip articles without titles."""
tool = PubMedTool()
xml_no_title = """<?xml version="1.0" ?>
<PubmedArticleSet>
<PubmedArticle>
<MedlineCitation>
<PMID>12345678</PMID>
<Article>
<Abstract>
<AbstractText>Some abstract text</AbstractText>
</Abstract>
</Article>
</MedlineCitation>
</PubmedArticle>
</PubmedArticleSet>
"""
results = tool._parse_pubmed_xml(xml_no_title)
# Should return empty list because article has no title
assert results == []
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