BioMCP

"""Tests for domain handlers module.""" import pytest from biomcp.constants import DEFAULT_TITLE from biomcp.domain_handlers import ( ArticleHandler, TrialHandler, VariantHandler, get_domain_handler, ) class TestArticleHandler: """Test ArticleHandler class.""" def test_format_pubmed_article(self): """Test formatting a PubMed article.""" article = { "pmid": "12345", "title": "Test Article Title", "abstract": "This is a test abstract that is longer than 200 characters. " * 5, "pub_year": "2023", "journal": "Test Journal", "authors": ["Smith J", "Doe J", "Johnson A", "Williams B"], } result = ArticleHandler.format_result(article) assert result["id"] == "12345" assert result["title"] == "Test Article Title" assert len(result["snippet"]) == 203 # 200 + "..." assert result["snippet"].endswith("...") assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/12345/" assert result["metadata"]["year"] == "2023" assert result["metadata"]["journal"] == "Test Journal" assert len(result["metadata"]["authors"]) == 3 # Only first 3 def test_format_preprint_article(self): """Test formatting a preprint article.""" preprint = { "doi": "10.1101/2023.01.01.12345", "id": "biorxiv-123", "title": "Preprint Title", "abstract": "Short abstract", "url": "https://www.biorxiv.org/content/10.1101/2023.01.01.12345", "pub_year": "2023", "source": "bioRxiv", "authors": ["Author A", "Author B"], } result = ArticleHandler.format_result(preprint) assert result["id"] == "10.1101/2023.01.01.12345" assert result["title"] == "Preprint Title" assert result["snippet"] == "Short abstract..." assert ( result["url"] == "https://www.biorxiv.org/content/10.1101/2023.01.01.12345" ) assert result["metadata"]["source"] == "bioRxiv" def test_format_article_missing_fields(self): """Test formatting article with missing fields.""" article = { "pmid": "67890", # Missing title, abstract, etc. } result = ArticleHandler.format_result(article) assert result["id"] == "67890" assert ( result["title"] == DEFAULT_TITLE ) # Should use default for missing title assert result["snippet"] == "" # Empty when no abstract assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/67890/" def test_format_article_with_date_field(self): """Test formatting article with date field instead of pub_year.""" article = { "pmid": "123", "title": "Test", "date": "2023-05-15", } result = ArticleHandler.format_result(article) assert result["metadata"]["year"] == "2023" def test_format_article_title_normalization(self): """Test that article title whitespace is normalized.""" article = { "pmid": "123", "title": " Test Article\n\nWith Extra Spaces ", } result = ArticleHandler.format_result(article) assert result["title"] == "Test Article With Extra Spaces" class TestTrialHandler: """Test TrialHandler class.""" def test_format_trial_api_v2(self): """Test formatting trial with API v2 structure.""" trial = { "protocolSection": { "identificationModule": { "nctId": "NCT12345", "briefTitle": "Brief Title", "officialTitle": "Official Title", }, "statusModule": { "overallStatus": "RECRUITING", "startDateStruct": {"date": "2023-01-01"}, "primaryCompletionDateStruct": {"date": "2024-12-31"}, }, "descriptionModule": { "briefSummary": "This is a brief summary of the trial." }, "designModule": { "phases": ["PHASE3"], }, } } result = TrialHandler.format_result(trial) assert result["id"] == "NCT12345" assert result["title"] == "Brief Title" assert "brief summary" in result["snippet"] assert result["url"] == "https://clinicaltrials.gov/study/NCT12345" assert result["metadata"]["status"] == "RECRUITING" assert result["metadata"]["phase"] == "PHASE3" assert result["metadata"]["start_date"] == "2023-01-01" assert result["metadata"]["primary_completion_date"] == "2024-12-31" def test_format_trial_legacy_flat(self): """Test formatting trial with legacy flat structure.""" trial = { "NCT Number": "NCT67890", "Study Title": "Legacy Trial Title", "Brief Summary": "Legacy summary", "Study Status": "COMPLETED", "Phases": "Phase 2", "Start Date": "2022-01-01", "Completion Date": "2023-12-31", } result = TrialHandler.format_result(trial) assert result["id"] == "NCT67890" assert result["title"] == "Legacy Trial Title" assert result["snippet"].startswith("Legacy summary") assert result["url"] == "https://clinicaltrials.gov/study/NCT67890" assert result["metadata"]["status"] == "COMPLETED" assert result["metadata"]["phase"] == "Phase 2" def test_format_trial_legacy_simple(self): """Test formatting trial with legacy simple structure.""" trial = { "nct_id": "NCT11111", "brief_title": "Simple Trial", "overall_status": "ACTIVE", "phase": "PHASE1", } result = TrialHandler.format_result(trial) assert result["id"] == "NCT11111" assert result["title"] == "Simple Trial" assert result["metadata"]["status"] == "ACTIVE" assert result["metadata"]["phase"] == "PHASE1" def test_format_trial_missing_title(self): """Test formatting trial with missing brief title.""" trial = { "protocolSection": { "identificationModule": { "nctId": "NCT99999", "officialTitle": "Only Official Title", }, } } result = TrialHandler.format_result(trial) assert result["id"] == "NCT99999" assert result["title"] == "Only Official Title" def test_format_trial_empty_phases(self): """Test formatting trial with empty phases array.""" trial = { "protocolSection": { "identificationModule": {"nctId": "NCT123"}, "designModule": {"phases": []}, } } result = TrialHandler.format_result(trial) assert result["metadata"]["phase"] == "" class TestVariantHandler: """Test VariantHandler class.""" def test_format_variant_complete(self): """Test formatting variant with complete data.""" variant = { "_id": "chr7:g.140453136A>T", "dbnsfp": { "genename": "BRAF", "hgvsp": ["BRAF:p.V600E"], }, "dbsnp": { "rsid": "rs121913529", "gene": {"symbol": "BRAF"}, }, "clinvar": { "rcv": { "clinical_significance": "Pathogenic", } }, "cadd": { "consequence": "missense_variant", }, } result = VariantHandler.format_result(variant) assert result["id"] == "chr7:g.140453136A>T" assert result["title"] == "BRAF BRAF:p.V600E" assert "Pathogenic" in result["snippet"] assert "rs121913529" in result["url"] assert result["metadata"]["gene"] == "BRAF" assert result["metadata"]["rsid"] == "rs121913529" assert result["metadata"]["clinical_significance"] == "Pathogenic" assert result["metadata"]["consequence"] == "missense_variant" def test_format_variant_gene_list(self): """Test formatting variant when gene is a list.""" variant = { "_id": "rs123", "dbnsfp": {"genename": ["GENE1", "GENE2"]}, } result = VariantHandler.format_result(variant) assert result["metadata"]["gene"] == "GENE1" def test_format_variant_clinvar_list(self): """Test formatting variant when clinvar RCV is a list.""" variant = { "_id": "rs456", "clinvar": { "rcv": [ {"clinical_significance": "Pathogenic"}, {"clinical_significance": "Likely pathogenic"}, ] }, } result = VariantHandler.format_result(variant) assert result["metadata"]["clinical_significance"] == "Pathogenic" def test_format_variant_minimal(self): """Test formatting variant with minimal data.""" variant = { "_id": "chr1:g.12345A>G", } result = VariantHandler.format_result(variant) assert result["id"] == "chr1:g.12345A>G" assert result["title"] == "chr1:g.12345A>G" assert "Unknown" in result["snippet"] assert result["url"] == "" def test_format_variant_hgvsp_list(self): """Test formatting variant when HGVS protein is a list.""" variant = { "_id": "rs789", "dbnsfp": { "genename": "TP53", "hgvsp": ["TP53:p.R175H", "TP53:p.R175C"], }, } result = VariantHandler.format_result(variant) assert result["title"] == "TP53 TP53:p.R175H" def test_format_variant_no_rsid_url(self): """Test variant URL generation without rsID.""" variant = { "_id": "chr2:g.234567C>T", } result = VariantHandler.format_result(variant) assert result["url"] == "" class TestGetDomainHandler: """Test get_domain_handler function.""" def test_get_article_handler(self): """Test getting article handler.""" handler = get_domain_handler("article") assert handler == ArticleHandler def test_get_trial_handler(self): """Test getting trial handler.""" handler = get_domain_handler("trial") assert handler == TrialHandler def test_get_variant_handler(self): """Test getting variant handler.""" handler = get_domain_handler("variant") assert handler == VariantHandler def test_get_invalid_handler(self): """Test getting handler for invalid domain.""" with pytest.raises(ValueError) as exc_info: get_domain_handler("invalid") assert "Unknown domain: invalid" in str(exc_info.value) def test_get_handler_case_sensitive(self): """Test that domain names are case sensitive.""" # Should work with lowercase handler = get_domain_handler("article") assert handler == ArticleHandler # Should fail with uppercase with pytest.raises(ValueError): get_domain_handler("ARTICLE")