"""Tests for PubMed module."""
from unittest.mock import MagicMock, patch
from biopython_mcp.modules import pubmed
class TestPubMedFetch:
"""Tests for pubmed_fetch function."""
@patch("biopython_mcp.modules.pubmed.httpx.Client")
def test_pubmed_fetch_success(self, mock_client_class: MagicMock) -> None:
"""Test successful PMC article fetch."""
mock_response = MagicMock()
mock_response.status_code = 200
mock_response.text = "<article>Test Article</article>"
mock_client = MagicMock()
mock_client.get.return_value = mock_response
mock_client.__enter__.return_value = mock_client
mock_client.__exit__.return_value = None
mock_client_class.return_value = mock_client
result = pubmed.pubmed_fetch("PMC123456", format="xml")
assert result["success"] is True
assert result["pmc_id"] == "PMC123456"
assert result["format"] == "xml"
assert "<article>" in result["content"]
@patch("biopython_mcp.modules.pubmed.httpx.Client")
def test_pubmed_fetch_not_found(self, mock_client_class: MagicMock) -> None:
"""Test PMC article not found."""
import httpx
mock_response = MagicMock()
mock_response.raise_for_status.side_effect = httpx.HTTPStatusError(
"404 Not Found", request=MagicMock(), response=MagicMock(status_code=404)
)
mock_client = MagicMock()
mock_client.get.return_value = mock_response
mock_client.__enter__.return_value = mock_client
mock_client.__exit__.return_value = None
mock_client_class.return_value = mock_client
result = pubmed.pubmed_fetch("PMC999999", format="xml")
assert result["success"] is False
assert "error" in result
@patch("biopython_mcp.modules.pubmed.httpx.Client")
def test_pubmed_fetch_timeout(self, mock_client_class: MagicMock) -> None:
"""Test PMC fetch timeout."""
import httpx
mock_client = MagicMock()
mock_client.get.side_effect = httpx.TimeoutException("Timeout")
mock_client.__enter__.return_value = mock_client
mock_client.__exit__.return_value = None
mock_client_class.return_value = mock_client
result = pubmed.pubmed_fetch("PMC123456", format="xml", timeout=1)
assert result["success"] is False
assert "timeout" in result["error"].lower()
@patch("biopython_mcp.modules.pubmed.httpx.Client")
def test_pubmed_fetch_invalid_format(self, mock_client_class: MagicMock) -> None:
"""Test that invalid format still returns content (no format validation)."""
mock_response = MagicMock()
mock_response.status_code = 200
mock_response.text = "<article>Test Article</article>"
mock_client = MagicMock()
mock_client.get.return_value = mock_response
mock_client.__enter__.return_value = mock_client
mock_client.__exit__.return_value = None
mock_client_class.return_value = mock_client
result = pubmed.pubmed_fetch("PMC123456", format="invalid")
# Function doesn't validate format - it just returns XML content
assert result["success"] is True
assert result["format"] == "invalid"
assert "<article>" in result["content"]
class TestGetPMCURL:
"""Tests for get_pmc_url function."""
def test_get_pmc_url_with_prefix(self) -> None:
"""Test URL generation with PMC prefix."""
url = pubmed.get_pmc_url("PMC123456")
assert url == "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC123456/"
def test_get_pmc_url_without_prefix(self) -> None:
"""Test URL generation without PMC prefix."""
url = pubmed.get_pmc_url("123456")
assert url == "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC123456/"
class TestGetDOIURL:
"""Tests for get_doi_url function."""
def test_get_doi_url(self) -> None:
"""Test DOI URL generation."""
url = pubmed.get_doi_url("10.1371/journal.pone.0012345")
assert url == "https://doi.org/10.1371/journal.pone.0012345"
class TestPubMedReview:
"""Tests for pubmed_review function."""
@patch("biopython_mcp.database")
def test_pubmed_review_full_format(self, mock_database: MagicMock) -> None:
"""Test review generation with full format."""
# Mock search result
mock_database.entrez_search.return_value = {
"success": True,
"ids": ["12345", "67890"],
"total_found": 2,
}
# Mock summary result
mock_database.entrez_summary.return_value = {
"success": True,
"summaries": [
{
"Id": "12345",
"Title": "Test Article 1",
"AuthorList": [{"LastName": "Smith", "Initials": "J"}],
"FullJournalName": "Test Journal",
"PubDate": "2024",
"ArticleIds": {"pmc": "PMC123", "doi": "10.1234/test"},
}
],
}
# Mock fetch result for abstract
mock_database.entrez_fetch.return_value = {
"success": True,
"data": "Test abstract content.",
}
result = pubmed.pubmed_review(
query="test query",
output_path="/tmp/test.md",
format="full",
max_results=2,
)
assert result["status"] == "success"
assert "content" in result
assert isinstance(result["content"], str)
assert result["content"].startswith("---") # YAML frontmatter
assert "# Literature Review:" in result["content"]
assert "Test Article 1" in result["content"]
assert result["articles_written"] == 1
assert result["filepath"] == "/tmp/test.md"
assert "file_size_kb" in result
@patch("biopython_mcp.database")
def test_pubmed_review_invalid_output_path(self, mock_database: MagicMock) -> None:
"""Test review with invalid output path."""
result = pubmed.pubmed_review(query="test", output_path="/tmp/test.txt", format="full")
assert result["status"] == "error"
assert result["error_type"] == "validation_error"
assert ".md" in result["message"]
@patch("biopython_mcp.database")
def test_pubmed_review_invalid_format(self, mock_database: MagicMock) -> None:
"""Test review with invalid format."""
result = pubmed.pubmed_review(query="test", output_path="/tmp/test.md", format="invalid")
assert result["status"] == "error"
assert result["error_type"] == "validation_error"
@patch("biopython_mcp.database")
def test_pubmed_review_search_failure(self, mock_database: MagicMock) -> None:
"""Test review when search fails."""
mock_database.entrez_search.return_value = {
"success": False,
"error": "Search failed",
}
result = pubmed.pubmed_review(query="test", output_path="/tmp/test.md")
assert result["status"] == "error"
assert result["error_type"] == "query_error"
@patch("biopython_mcp.database")
def test_pubmed_review_no_results(self, mock_database: MagicMock) -> None:
"""Test review when no articles found."""
mock_database.entrez_search.return_value = {
"success": True,
"ids": [],
"total_found": 0,
}
result = pubmed.pubmed_review(query="test", output_path="/tmp/test.md")
assert result["status"] == "error"
assert result["error_type"] == "query_error"
assert "No articles found" in result["message"]
@patch("biopython_mcp.database")
def test_pubmed_review_minimal_format(self, mock_database: MagicMock) -> None:
"""Test review generation with minimal format."""
mock_database.entrez_search.return_value = {
"success": True,
"ids": ["12345"],
"total_found": 1,
}
mock_database.entrez_summary.return_value = {
"success": True,
"summaries": [
{
"Id": "12345",
"Title": "Test Article",
"PubDate": "2024",
"ArticleIds": {"doi": "10.1234/test"},
}
],
}
result = pubmed.pubmed_review(query="test", output_path="/tmp/test.md", format="minimal")
assert result["status"] == "success"
assert result["format"] == "minimal"
assert "content" in result
assert "Test Article" in result["content"]
@patch("biopython_mcp.database")
def test_pubmed_review_summary_format(self, mock_database: MagicMock) -> None:
"""Test review generation with summary format."""
mock_database.entrez_search.return_value = {
"success": True,
"ids": ["12345"],
"total_found": 1,
}
mock_database.entrez_summary.return_value = {
"success": True,
"summaries": [
{
"Id": "12345",
"Title": "Test abstract Article",
"PubDate": "2024",
"ArticleIds": {"pmc": "PMC123"},
}
],
}
mock_database.entrez_fetch.return_value = {
"success": True,
"data": "First sentence. Second sentence.",
}
result = pubmed.pubmed_review(query="test", output_path="/tmp/test.md", format="summary")
assert result["status"] == "success"
assert result["format"] == "summary"
assert "content" in result
assert "Test abstract Article" in result["content"]
assert "First sentence" in result["content"]
@patch("biopython_mcp.database")
def test_pubmed_review_obsidian_frontmatter(self, mock_database: MagicMock) -> None:
"""Test that Obsidian YAML frontmatter is included in content."""
mock_database.entrez_search.return_value = {
"success": True,
"ids": ["12345"],
"total_found": 1,
}
mock_database.entrez_summary.return_value = {
"success": True,
"summaries": [
{
"Id": "12345",
"Title": "Test Article",
"PubDate": "2024",
"FullJournalName": "Test Journal",
"ArticleIds": {},
}
],
}
mock_database.entrez_fetch.return_value = {"success": False}
result = pubmed.pubmed_review(query="test query", output_path="/tmp/test.md")
assert result["status"] == "success"
assert "content" in result
# Verify Obsidian YAML frontmatter is present
assert result["content"].startswith("---")
assert "title: Literature Review" in result["content"]
assert "tags: [literature-review, pubmed, biopython-mcp]" in result["content"]
assert "status: complete" in result["content"]
