"""Tests for PubMed module."""
import tempfile
from pathlib import Path
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.",
}
with tempfile.TemporaryDirectory() as tmpdir:
result = pubmed.pubmed_review(
query="test query",
path="test",
filename="review.md",
obsidian_vault=tmpdir,
max_results=2,
)
assert result["status"] == "success"
assert "filepath" in result
# Verify file was created
filepath = Path(result["filepath"])
assert filepath.exists()
assert filepath.suffix == ".md"
# Read and verify content
content = filepath.read_text()
assert content.startswith("---") # YAML frontmatter
assert "# Literature Review:" in content
assert "Test Article 1" in content
assert result["articles_written"] == 1
assert "file_size_kb" in result
@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",
}
with tempfile.TemporaryDirectory() as tmpdir:
result = pubmed.pubmed_review(
query="test",
path="test",
filename="review.md",
obsidian_vault=tmpdir,
)
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,
}
with tempfile.TemporaryDirectory() as tmpdir:
result = pubmed.pubmed_review(
query="test",
path="test",
filename="review.md",
obsidian_vault=tmpdir,
)
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_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}
with tempfile.TemporaryDirectory() as tmpdir:
result = pubmed.pubmed_review(
query="test query",
path="research",
filename="literature_review.md",
obsidian_vault=tmpdir,
)
assert result["status"] == "success"
assert "filepath" in result
# Read and verify content
filepath = Path(result["filepath"])
content = filepath.read_text()
# Verify Obsidian YAML frontmatter is present
assert content.startswith("---")
assert "title: Literature Review" in content
assert "tags: [literature-review, pubmed, biopython-mcp]" in content
assert "status: complete" in content
# Verify file is in correct location
assert "research" in str(filepath)
