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Ontology extraction tests (#560)
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tests/unit/test_extract/test_ontology/README.md
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# Ontology Extractor Unit Tests
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Comprehensive unit tests for the OntoRAG ontology extraction system.
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## Test Coverage
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### 1. `test_ontology_selector.py` - Auto-Include Properties Feature
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Tests the critical dependency resolution that automatically includes all properties related to selected classes.
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**Key Tests:**
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- `test_auto_include_properties_for_recipe_class` - Verifies Recipe class auto-includes `ingredients`, `method`, `produces`, `serves`
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- `test_auto_include_properties_for_ingredient_class` - Verifies Ingredient class auto-includes `food` property
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- `test_auto_include_properties_for_range_class` - Tests properties are included when class appears in range
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- `test_auto_include_adds_domain_and_range_classes` - Ensures related classes are added too
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- `test_multiple_classes_get_all_related_properties` - Tests combining multiple class selections
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- `test_no_duplicate_properties_added` - Ensures properties aren't duplicated
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### 2. `test_uri_expansion.py` - URI Expansion
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Tests that URIs are properly expanded using ontology definitions instead of constructed fallback URIs.
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**Key Tests:**
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- `test_expand_class_uri_from_ontology` - Class names expand to ontology URIs
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- `test_expand_object_property_uri_from_ontology` - Object properties use ontology URIs
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- `test_expand_datatype_property_uri_from_ontology` - Datatype properties use ontology URIs
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- `test_expand_rdf_prefix` - Standard RDF prefixes expand correctly
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- `test_expand_rdfs_prefix`, `test_expand_owl_prefix`, `test_expand_xsd_prefix` - Other standard prefixes
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- `test_fallback_uri_for_instance` - Entity instances get constructed URIs
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- `test_already_full_uri_unchanged` - Full URIs pass through
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- `test_dict_access_not_object_attribute` - **Critical test** verifying dict access works (not object attributes)
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### 3. `test_ontology_triples.py` - Ontology Triple Generation
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Tests that ontology elements (classes and properties) are properly converted to RDF triples with labels, comments, domains, and ranges.
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**Key Tests:**
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- `test_generates_class_type_triples` - Classes get `rdf:type owl:Class` triples
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- `test_generates_class_labels` - Classes get `rdfs:label` triples
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- `test_generates_class_comments` - Classes get `rdfs:comment` triples
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- `test_generates_object_property_type_triples` - Object properties get proper type triples
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- `test_generates_object_property_labels` - Object properties get labels
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- `test_generates_object_property_domain` - Object properties get `rdfs:domain` triples
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- `test_generates_object_property_range` - Object properties get `rdfs:range` triples
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- `test_generates_datatype_property_type_triples` - Datatype properties get proper type triples
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- `test_generates_datatype_property_range` - Datatype properties get XSD type ranges
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- `test_uses_dict_field_names_not_rdf_names` - **Critical test** verifying dict field names work
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- `test_total_triple_count_is_reasonable` - Validates expected number of triples
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### 4. `test_text_processing.py` - Text Processing and Segmentation
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Tests that text is properly split into sentences for ontology matching, including NLTK tokenization and TextSegment creation.
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**Key Tests:**
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- `test_segment_single_sentence` - Single sentence produces one segment
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- `test_segment_multiple_sentences` - Multiple sentences split correctly
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- `test_segment_positions` - Segment start/end positions are correct
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- `test_segment_complex_punctuation` - Handles abbreviations (Dr., U.S.A., Mr.)
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- `test_segment_question_and_exclamation` - Different sentence terminators
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- `test_segment_preserves_original_text` - Segments can reconstruct original
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- `test_text_segment_non_overlapping` - Segments don't overlap
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- `test_nltk_punkt_availability` - NLTK tokenizer is available
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- `test_unicode_text` - Handles unicode characters
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- `test_quoted_text` - Handles quoted text correctly
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### 5. `test_prompt_and_extraction.py` - LLM Prompt Construction and Triple Extraction
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Tests that the system correctly constructs prompts with ontology constraints and extracts/validates triples from LLM responses.
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**Key Tests:**
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- `test_build_extraction_variables_includes_text` - Prompt includes input text
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- `test_build_extraction_variables_includes_classes` - Prompt includes ontology classes
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- `test_build_extraction_variables_includes_properties` - Prompt includes properties
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- `test_validates_rdf_type_triple_with_valid_class` - Validates rdf:type against ontology
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- `test_rejects_rdf_type_triple_with_invalid_class` - Rejects invalid classes
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- `test_validates_object_property_triple` - Validates object properties
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- `test_rejects_unknown_property` - Rejects properties not in ontology
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- `test_parse_simple_triple_dict` - Parses triple from dict format
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- `test_filters_invalid_triples` - Filters out invalid triples
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- `test_expands_uris_in_parsed_triples` - Expands URIs using ontology
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- `test_creates_proper_triple_objects` - Creates Triple objects with Value subjects/predicates/objects
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### 6. `test_embedding_and_similarity.py` - Ontology Embedding and Similarity Matching
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Tests that ontology elements are properly embedded and matched against input text using vector similarity.
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**Key Tests:**
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- `test_create_text_from_class_with_id` - Text representation includes class ID
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- `test_create_text_from_class_with_labels` - Includes labels in text
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- `test_create_text_from_class_with_comment` - Includes comments in text
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- `test_create_text_from_property_with_domain_range` - Includes domain/range in property text
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- `test_normalizes_id_with_underscores` - Normalizes IDs (underscores to spaces)
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- `test_includes_subclass_info_for_classes` - Includes subclass relationships
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- `test_vector_store_api_structure` - Vector store has expected API
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- `test_selector_handles_text_segments` - Selector processes text segments
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- `test_merge_subsets_combines_elements` - Merging combines ontology elements
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- `test_ontology_element_metadata_structure` - Metadata structure is correct
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## Running the Tests
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### Run all ontology extractor tests:
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```bash
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cd /home/mark/work/trustgraph.ai/trustgraph
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pytest tests/unit/test_extract/test_ontology/ -v
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```
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### Run specific test file:
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```bash
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pytest tests/unit/test_extract/test_ontology/test_ontology_selector.py -v
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pytest tests/unit/test_extract/test_ontology/test_uri_expansion.py -v
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pytest tests/unit/test_extract/test_ontology/test_ontology_triples.py -v
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pytest tests/unit/test_extract/test_ontology/test_text_processing.py -v
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pytest tests/unit/test_extract/test_ontology/test_prompt_and_extraction.py -v
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pytest tests/unit/test_extract/test_ontology/test_embedding_and_similarity.py -v
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```
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### Run specific test:
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```bash
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pytest tests/unit/test_extract/test_ontology/test_ontology_selector.py::TestOntologySelector::test_auto_include_properties_for_recipe_class -v
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```
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### Run with coverage:
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```bash
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pytest tests/unit/test_extract/test_ontology/ --cov=trustgraph.extract.kg.ontology --cov-report=html
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```
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## Test Fixtures
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- `sample_ontology` - Complete Food Ontology with Recipe, Ingredient, Food, Method classes
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- `ontology_loader_with_sample` - Mock OntologyLoader with the sample ontology
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- `ontology_embedder` - Mock embedder for testing
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- `mock_embedding_service` - Mock service for generating deterministic embeddings
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- `vector_store` - InMemoryVectorStore for testing
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- `extractor` - Processor instance for URI expansion tests
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- `ontology_subset_with_uris` - OntologySubset with proper URIs defined
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- `sample_ontology_subset` - OntologySubset for testing triple generation
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- `text_processor` - TextProcessor instance for text segmentation tests
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- `sample_ontology_class` - Sample OntologyClass for testing
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- `sample_ontology_property` - Sample OntologyProperty for testing
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## Implementation Notes
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These tests verify the fixes made to address:
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1. **Disconnected graph problem** - Auto-include properties feature ensures all relevant relationships are available
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2. **Wrong URIs problem** - URI expansion using ontology definitions instead of constructed fallbacks
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3. **Dict vs object attribute problem** - URI expansion works with dicts (from `cls.__dict__`) not object attributes
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4. **Ontology visibility in KG** - Ontology elements themselves appear in the knowledge graph with proper metadata
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5. **Text segmentation** - Proper sentence splitting for ontology matching using NLTK
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