feat: add rdf_reader

Author: ChenZiHong-Gavin

graphgen/models/reader/rdf_reader.py

@@ -0,0 +1,48 @@
+from typing import Any, Dict, List
+
+import rdflib
+from rdflib import Literal
+from rdflib.util import guess_format
+
+from graphgen.bases.base_reader import BaseReader
+
+
+class RDFReader(BaseReader):
+    """
+    Reader for RDF files that extracts triples and represents them as dictionaries.
+    """
+
+    def read(self, file_path: str) -> List[Dict[str, Any]]:
+        g = rdflib.Graph()
+        fmt = guess_format(file_path)
+        try:
+            g.parse(file_path, format=fmt)
+        except Exception as e:
+            raise ValueError(f"Cannot parse RDF file {file_path}: {e}") from e
+
+        docs: List[Dict[str, Any]] = []
+        text_col = self.text_column
+
+        for subj in set(g.subjects()):
+            literals = []
+            props = {}
+            for _, pred, obj in g.triples((subj, None, None)):
+                pred_str = str(pred)
+                if isinstance(obj, Literal):
+                    literals.append(str(obj))
+                props.setdefault(pred_str, []).append(str(obj))
+
+            text = " ".join(literals).strip()
+            if not text:
+                raise ValueError(
+                    f"Subject {subj} has no literal values; "
+                    f"missing '{text_col}' for text column."
+                )
+
+            doc = {"id": str(subj), text_col: text, "properties": props}
+            docs.append(doc)
+
+        if not docs:
+            raise ValueError("RDF file contains no valid documents.")
+
+        return self.filter(docs)

requirements.txt

@@ -24,6 +24,9 @@ leidenalg
 igraph
 python-louvain
 
+# KG
+rdflib
+
 # Bioinformatics
 biopython