PubMed MCP Server

"""Tests for the citation formatter module.""" import pytest from src.citation_formatter import CitationFormatter from src.models import Article, Author, CitationFormat, Journal, MeSHTerm class TestCitationFormatter: """Test the CitationFormatter class.""" @pytest.fixture def sample_article(self): """Create a sample article for testing.""" return Article( pmid="12345678", title="A Sample Research Article on Cancer Treatment", abstract="This is a sample abstract describing cancer treatment research.", authors=[ Author( last_name="Smith", first_name="John", initials="J", affiliation="University Hospital", ), Author( last_name="Doe", first_name="Jane", initials="J", ), Author(last_name="Johnson", first_name="Bob", initials="B"), ], journal=Journal( title="Journal of Cancer Research", iso_abbreviation="J Cancer Res", issn="1234-5678", volume="25", issue="3", pub_date="2023", ), pub_date="2023/03/15", doi="10.1000/example.doi", pmc_id="PMC1234567", article_types=["Journal Article", "Research Support"], mesh_terms=[ MeSHTerm(descriptor_name="Cancer", major_topic=True), MeSHTerm(descriptor_name="Treatment", major_topic=False), ], keywords=["cancer", "treatment", "research"], languages=["eng"], ) @pytest.fixture def minimal_article(self): """Create a minimal article for testing edge cases.""" return Article( pmid="87654321", title="Minimal Article", journal=Journal(title="Basic Journal"), ) def test_format_citation_apa(self, sample_article): """Test APA citation formatting.""" result = CitationFormatter.format_citation(sample_article, CitationFormat.APA) assert "Smith, J., Doe, J., & Johnson, B." in result assert "(2023)" in result assert "A Sample Research Article on Cancer Treatment" in result assert "*Journal of Cancer Research*" in result assert "*25*(3)" in result assert "https://doi.org/10.1000/example.doi" in result def test_format_citation_mla(self, sample_article): """Test MLA citation formatting.""" result = CitationFormatter.format_citation(sample_article, CitationFormat.MLA) assert "Smith, John, et al." in result assert '"A Sample Research Article on Cancer Treatment."' in result assert "*Journal of Cancer Research*" in result assert "vol. 25" in result assert "no. 3" in result assert "2023" in result assert "https://pubmed.ncbi.nlm.nih.gov/12345678/" in result def test_format_citation_chicago(self, sample_article): """Test Chicago citation formatting.""" result = CitationFormatter.format_citation(sample_article, CitationFormat.CHICAGO) assert "Smith, John, et al." in result assert '"A Sample Research Article on Cancer Treatment."' in result assert "*Journal of Cancer Research*" in result assert "25, no. 3" in result assert "(2023)" in result assert "https://doi.org/10.1000/example.doi" in result def test_format_citation_vancouver(self, sample_article): """Test Vancouver citation formatting.""" result = CitationFormatter.format_citation(sample_article, CitationFormat.VANCOUVER) assert "Smith J, Doe J, Johnson B." in result assert "A Sample Research Article on Cancer Treatment." in result assert "Journal of Cancer Research 2023;25(3)" in result assert "PMID: 12345678" in result def test_format_citation_bibtex(self, sample_article): """Test BibTeX citation formatting.""" result = CitationFormatter.format_citation(sample_article, CitationFormat.BIBTEX) assert "@article{" in result assert "title = {A Sample Research Article on Cancer Treatment}" in result assert "author = {John Smith and Jane Doe and Bob Johnson}" in result assert "journal = {Journal of Cancer Research}" in result assert "volume = {25}" in result assert "number = {3}" in result assert "year = {2023}" in result assert "doi = {10.1000/example.doi}" in result assert "pmid = {12345678}" in result def test_format_citation_endnote(self, sample_article): """Test EndNote citation formatting.""" result = CitationFormatter.format_citation(sample_article, CitationFormat.ENDNOTE) assert "%0 Journal Article" in result assert "%T A Sample Research Article on Cancer Treatment" in result assert "%A John Smith" in result assert "%A Jane Doe" in result assert "%A Bob Johnson" in result assert "%J Journal of Cancer Research" in result assert "%V 25" in result assert "%N 3" in result assert "%D 2023/03/15" in result assert "%R 10.1000/example.doi" in result assert "%M 12345678" in result def test_format_citation_ris(self, sample_article): """Test RIS citation formatting.""" result = CitationFormatter.format_citation(sample_article, CitationFormat.RIS) assert "TY - JOUR" in result assert "TI - A Sample Research Article on Cancer Treatment" in result assert "AU - John Smith" in result assert "AU - Jane Doe" in result assert "AU - Bob Johnson" in result assert "JO - Journal of Cancer Research" in result assert "VL - 25" in result assert "IS - 3" in result assert "PY - 2023" in result assert "DA - 2023/03/15" in result assert "DO - 10.1000/example.doi" in result assert "AN - 12345678" in result assert "ER - " in result def test_format_citation_unsupported_format(self, sample_article): """Test error handling for unsupported citation format.""" with pytest.raises(ValueError, match="Unsupported citation format"): CitationFormatter.format_citation(sample_article, "invalid_format") def test_format_multiple_citations(self, sample_article, minimal_article): """Test formatting multiple citations.""" articles = [sample_article, minimal_article] result = CitationFormatter.format_multiple_citations(articles, CitationFormat.APA) assert len(result) == 2 assert "Smith, J., Doe, J., & Johnson, B." in result[0] assert "Minimal Article" in result[1] def test_clean_text(self): """Test text cleaning functionality.""" dirty_text = "<p>Sample text with <b>HTML</b> tags and extra spaces</p>" clean_text = CitationFormatter._clean_text(dirty_text) assert clean_text == "Sample text with HTML tags and extra spaces" assert "<" not in clean_text assert ">" not in clean_text def test_clean_text_empty(self): """Test text cleaning with empty input.""" assert CitationFormatter._clean_text("") == "" assert CitationFormatter._clean_text(None) == "" def test_format_authors_apa_many_authors(self): """Test APA author formatting with many authors.""" authors = [f"Author {i}" for i in range(25)] # More than 20 authors result = CitationFormatter._format_authors_apa(authors) assert "... & Author 24" in result # Should truncate and show last author def test_format_authors_apa_single_author(self): """Test APA author formatting with single author.""" authors = ["John Smith"] result = CitationFormatter._format_authors_apa(authors) assert result == "Smith, J." def test_format_authors_apa_two_authors(self): """Test APA author formatting with two authors.""" authors = ["John Smith", "Jane Doe"] result = CitationFormatter._format_authors_apa(authors) assert result == "Smith, J., & Doe, J." def test_format_authors_apa_empty(self): """Test APA author formatting with empty list.""" result = CitationFormatter._format_authors_apa([]) assert result == "" def test_minimal_article_formatting(self, minimal_article): """Test formatting with minimal article data.""" result = CitationFormatter.format_citation(minimal_article, CitationFormat.APA) assert "Minimal Article" in result assert "Basic Journal" in result assert "https://pubmed.ncbi.nlm.nih.gov/87654321/" in result def test_article_without_doi_apa(self, minimal_article): """Test APA formatting when DOI is not available.""" result = CitationFormatter.format_citation(minimal_article, CitationFormat.APA) assert "https://pubmed.ncbi.nlm.nih.gov/87654321/" in result assert "doi.org" not in result def test_article_without_doi_mla(self, minimal_article): """Test MLA formatting when DOI is not available.""" result = CitationFormatter.format_citation(minimal_article, CitationFormat.MLA) assert "https://pubmed.ncbi.nlm.nih.gov/87654321/" in result def test_bibtex_citation_key_generation(self, sample_article): """Test BibTeX citation key generation.""" result = CitationFormatter.format_citation(sample_article, CitationFormat.BIBTEX) # Should include author last name, year, and first word of title assert "@article{smith2023a," in result def test_ris_page_range_formatting(self): """Test RIS page range formatting.""" article = Article( pmid="12345678", title="Test Article", journal=Journal(title="Test Journal", pages="123-456"), ) result = CitationFormatter.format_citation(article, CitationFormat.RIS) assert "SP - 123" in result assert "EP - 456" in result def test_ris_single_page_formatting(self): """Test RIS single page formatting.""" article = Article( pmid="12345678", title="Test Article", journal=Journal(title="Test Journal", pages="123"), ) result = CitationFormatter.format_citation(article, CitationFormat.RIS) assert "SP - 123" in result assert "EP -" not in result def test_vancouver_author_limit(self): """Test Vancouver style author limiting to 6 authors.""" authors = [ Author(last_name=f"Author{i}", first_name=f"First{i}", initials=f"F{i}") for i in range(10) ] article = Article( pmid="12345678", title="Test Article", authors=authors, journal=Journal(title="Test Journal"), ) result = CitationFormatter.format_citation(article, CitationFormat.VANCOUVER) assert "et al" in result # Should only show first 6 authors assert "Author5 F5" in result assert "Author6 F6" not in result def test_edge_case_empty_fields(self): """Test handling of articles with empty or None fields.""" article = Article( pmid="12345678", title="", # Empty title abstract=None, authors=[], # No authors journal=Journal(title=""), # Empty journal pub_date=None, doi=None, ) # Should not crash with empty fields result = CitationFormatter.format_citation(article, CitationFormat.APA) assert isinstance(result, str) def test_special_characters_in_title(self): """Test handling of special characters in titles.""" article = Article( pmid="12345678", title="Special Characters: α, β, γ & More!", journal=Journal(title="Test Journal"), ) result = CitationFormatter.format_citation(article, CitationFormat.APA) assert "Special Characters: α, β, γ & More!" in result def test_long_author_names(self): """Test handling of very long author names.""" article = Article( pmid="12345678", title="Test Article", authors=[ Author( last_name="VeryLongLastNameThatExceedsNormalLength", first_name="ExtremelyLongFirstNameThatIsUnusuallyVerbose", initials="E.L.", ) ], journal=Journal(title="Test Journal"), ) result = CitationFormatter.format_citation(article, CitationFormat.APA) assert "VeryLongLastNameThatExceedsNormalLength" in result