diff --git a/error.txt b/error.txt deleted file mode 100644 index f36ab00..0000000 --- a/error.txt +++ /dev/null @@ -1,2 +0,0 @@ -[INFO] Connecting to SPARQL endpoint: http://host.docker.internal:7200/repositories/stringstothings/statements -[INFO] Loading named graph: https://example.org/taxonomy/ diff --git a/pyproject.toml b/pyproject.toml index 5bce31b..a879f6b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,6 +19,7 @@ dependencies = [ "python-multipart>=0.0.20", "rdflib>=7.1.4", "SPARQLWrapper>=2.0.0", + "rapidfuzz>=3.0.0", ] [dependency-groups] dev = [ diff --git a/src/strings2things/app/api/endpoints.py b/src/strings2things/app/api/endpoints.py index 527ccaa..5a37322 100644 --- a/src/strings2things/app/api/endpoints.py +++ b/src/strings2things/app/api/endpoints.py @@ -3,14 +3,9 @@ from fastapi import APIRouter, UploadFile, File, Form from fastapi.responses import Response from rdflib import Graph -from src.strings2things.app.core.rdf_transformer import RDFTransformer -from src.strings2things.app.core.ontology_manager import ( - OntologyManager, -) # Assume this exists -from src.strings2things.app.utils.rdf_utils import ( - parse_rdf, - serialize_rdf, -) # Also assume or create +from strings2things.app.core.rdf_transformer import RDFTransformer +from strings2things.app.core.ontology_manager import OntologyManager +from strings2things.app.utils.rdf_utils import parse_rdf, serialize_rdf import logging router = APIRouter() @@ -18,21 +13,38 @@ ontology_manager = OntologyManager() ontology_manager.load_ontologies() -transformer = RDFTransformer(ontology_manager.get_label_map()) +# Keep transformer as a base instance +base_label_map = ontology_manager.get_label_map() @router.post("/transform") async def transform_rdf( - file: UploadFile = File(...), serialization: str = Form("turtle") + file: UploadFile = File(...), + serialization: str = Form("turtle"), + fuzzy: bool = Form(False), # <-- new parameter + fuzzy_threshold: int = Form(90), # <-- configurable fuzzy matching threshold ) -> Response: """ Accepts an RDF file upload, transforms it using the label map, and returns the modified RDF graph in the requested format. + + Args: + file: The uploaded RDF file + serialization: Desired output RDF serialization (default: turtle) + fuzzy: Whether to use fuzzy matching (default: False) + threshold: Similarity threshold for fuzzy matching (0-100, default: 90) """ content = await file.read() try: input_graph = parse_rdf(content) + + transformer = RDFTransformer( + base_label_map, + fuzzy=fuzzy, + fuzzy_threshold=fuzzy_threshold, + ) + transformed_graph = transformer.transform(input_graph) serialized = serialize_rdf(transformed_graph, output_format=serialization) diff --git a/src/strings2things/app/core/rdf_transformer.py b/src/strings2things/app/core/rdf_transformer.py index e65a5f5..2248253 100644 --- a/src/strings2things/app/core/rdf_transformer.py +++ b/src/strings2things/app/core/rdf_transformer.py @@ -1,17 +1,48 @@ # app/core/rdf_transformer.py """ Transforms RDF graphs by replacing string literals with matching ontology IRIs. +Supports exact and fuzzy matching (RapidFuzz). """ from rdflib import Graph, Literal, URIRef from strings2things.app.core.transformation_log import TransformationLog +from rapidfuzz import process class RDFTransformer: - def __init__(self, label_map: dict[str, str]): + def __init__(self, label_map: dict[str, str], fuzzy: bool, fuzzy_threshold: int = 90): + """ + :param label_map: dict of {label -> IRI} + :param fuzzy_threshold: minimum score for fuzzy fallback + """ self.label_map = label_map + self.fuzzy = fuzzy + self.fuzzy_threshold = fuzzy_threshold self.log = TransformationLog() + def _find_match(self, label: str) -> str | None: + """ + Find an IRI for the given label. + First tries exact match, then (optionally) falls back to fuzzy. + """ + label = label.strip().lower() + + # Exact match first (cheap lookup) + iri = self.label_map.get(label) + if iri: + return iri + + # Fuzzy fallback + if self.fuzzy: + best = process.extractOne(label, self.label_map.keys()) + if best: + match, score, _ = best + if score >= self.fuzzy_threshold: + return self.label_map[match] + + return None + + def transform(self, input_graph: Graph) -> Graph: """ Replace matching string literals in the RDF graph with IRIs. @@ -20,18 +51,14 @@ def transform(self, input_graph: Graph) -> Graph: output_graph = Graph() for s, p, o in input_graph: - # if string matches object if isinstance(o, Literal) and isinstance(o.value, str): - label = o.value.strip().lower() - if label in self.label_map: - iri = URIRef(self.label_map[label]) + iri_str = self._find_match(o.value) + if iri_str: + iri = URIRef(iri_str) - # Retain original triple (to retain backward compatibility for now) + # Retain original triple (for backward compatibility) output_graph.add((s, p, o)) - output_graph.add( - (iri, URIRef("http://wwww.example.org/thingOf"), o) - ) - + output_graph.add((iri, URIRef("http://www.example.org/thingOf"), o)) output_graph.add((s, p, iri)) self.log.add_entry( @@ -39,10 +66,13 @@ def transform(self, input_graph: Graph) -> Graph: predicate=str(p), original_value=str(o), replacement_iri=str(iri), - reason="unambiguous match", + reason="exact match" + if o.value.strip().lower() in self.label_map + else f"fuzzy match (threshold={self.fuzzy_threshold})", ) continue + # If no match found → leave as-is output_graph.add((s, p, o)) self.log.add_entry( subject=str(s), @@ -52,7 +82,7 @@ def transform(self, input_graph: Graph) -> Graph: reason=( "not a string literal" if not isinstance(o, Literal) - else "no match in label map" + else "no match found" ), ) diff --git a/src/strings2things/app/core/transformation_log.py b/src/strings2things/app/core/transformation_log.py index e5f8a3e..22b2ecc 100644 --- a/src/strings2things/app/core/transformation_log.py +++ b/src/strings2things/app/core/transformation_log.py @@ -5,8 +5,9 @@ class TransformationLog: - def __init__(self): + def __init__(self, verbose: bool = True): self.entries = [] + self.verbose = verbose # control printing def add_entry( self, subject, predicate, original_value, replacement_iri, reason: str @@ -14,15 +15,27 @@ def add_entry( """ Record a transformation decision. """ - self.entries.append( - { - "subject": subject, - "predicate": predicate, - "original": original_value, - "replacement": replacement_iri, - "reason": reason, - } - ) + entry = { + "subject": subject, + "predicate": predicate, + "original": original_value, + "replacement": replacement_iri, + "reason": reason, + } + self.entries.append(entry) + + # 👇 Emit message immediately when adding entry + if self.verbose: + if replacement_iri: + print( + f"[TRANSFORM] Replaced '{original_value}' " + f"→ <{replacement_iri}> (subject: <{subject}>, predicate: <{predicate}>)" + ) + else: + print( + f"[TRANSFORM] No replacement for '{original_value}' " + f"(subject: <{subject}>, predicate: <{predicate}>, reason: {reason})" + ) def get_summary(self): """ diff --git a/tests/test_rdf_transformer.py b/tests/test_rdf_transformer.py index e272c2e..d94ca27 100644 --- a/tests/test_rdf_transformer.py +++ b/tests/test_rdf_transformer.py @@ -1,53 +1,70 @@ import pytest from rdflib import Graph, URIRef, Literal, Namespace from strings2things.app.core.rdf_transformer import RDFTransformer -from strings2things.app.core.transformation_log import TransformationLog -EX = Namespace("http://example.org/") +EX = Namespace("http://example.org/ontology#") @pytest.fixture def label_map(): + # Ontology label map: canonical labels → IRIs return { - "geology": "http://example.org/ontology#Geology", - "biology": "http://example.org/ontology#Biology", + "geology": str(EX.Geology), + "biology": str(EX.Biology), + "physics": str(EX.Physics), } @pytest.fixture def input_graph(): g = Graph() - g.add((EX.subj1, EX.hasCategory, Literal("Geology"))) - g.add((EX.subj2, EX.hasCategory, Literal("UnknownLabel"))) - g.add((EX.subj3, EX.hasValue, URIRef("http://example.org/someIRI"))) + # Exact match example + g.add((EX.subj1, EX.hasCategory, Literal("geology"))) + + # Fuzzy match example (slightly misspelled) + g.add((EX.subj2, EX.hasCategory, Literal("biolgy"))) + + # Unknown label (should remain unchanged) + g.add((EX.subj3, EX.hasCategory, Literal("unknownlabel"))) + + # Non-literal value (should remain untouched) + g.add((EX.subj4, EX.hasValue, URIRef("http://example.org/someIRI"))) return g -def test_rdf_transformer(label_map, input_graph): - transformer = RDFTransformer(label_map) +def test_rdf_transformer_combined(label_map, input_graph): + # Initialize transformer with fuzzy matching enabled + transformer = RDFTransformer(label_map, fuzzy=True, fuzzy_threshold=90) output_graph = transformer.transform(input_graph) - # --- Check graph triples --- - # Original triple must remain - assert (EX.subj1, EX.hasCategory, Literal("Geology")) in output_graph + # --- 1. Check graph triples --- - # Transformed triple must be present - expected_iri = URIRef("http://example.org/ontology#Geology") - assert (EX.subj1, EX.hasCategory, expected_iri) in output_graph + # Exact match: literal replaced by IRI + assert (EX.subj1, EX.hasCategory, URIRef("http://example.org/ontology#Geology")) in output_graph - # UnknownLabel should remain unchanged (no IRI added) - assert (EX.subj2, EX.hasCategory, Literal("UnknownLabel")) in output_graph - assert len([t for t in output_graph.triples((EX.subj2, EX.hasCategory, None))]) == 1 + # Fuzzy match: literal replaced by IRI + assert (EX.subj2, EX.hasCategory, URIRef("http://example.org/ontology#Biology")) in output_graph - # Non-literals should remain untouched - assert (EX.subj3, EX.hasValue, URIRef("http://example.org/someIRI")) in output_graph + # Unknown label: literal remains unchanged + assert (EX.subj3, EX.hasCategory, Literal("unknownlabel")) in output_graph - # --- Check log entries --- + # Non-literals remain untouched + assert (EX.subj4, EX.hasValue, URIRef("http://example.org/someIRI")) in output_graph + + # --- 2. Check log entries --- log = transformer.log.entries - geology_log = next(e for e in log if e["original"] == "Geology") + + # Exact match log + geology_log = next(e for e in log if e["original"] == "geology") assert geology_log["replacement"] == "http://example.org/ontology#Geology" - assert geology_log["reason"] == "unambiguous match" + assert geology_log["reason"] == "exact match" + + # Fuzzy match log + biolgy_log = next(e for e in log if e["original"] == "biolgy") + assert biolgy_log["replacement"] == "http://example.org/ontology#Biology" + assert "fuzzy match" in biolgy_log["reason"] - unknown_log = next(e for e in log if e["original"] == "UnknownLabel") + # Unknown label log + unknown_log = next(e for e in log if e["original"] == "unknownlabel") assert unknown_log["replacement"] is None - assert unknown_log["reason"] == "no match in label map" + assert unknown_log["reason"] == "no match found" diff --git a/uv.lock b/uv.lock index a945a4d..d4482be 100644 --- a/uv.lock +++ b/uv.lock 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