Merge remote-tracking branch 'origin/main' into fix/733-explanation-premises

CHANGELOG.md

@@ -20,6 +20,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Fixes `VectorStore.update_vectors`/`delete_vectors` to delegate to the active backend store instead of only mutating in-memory state, correcting existing behavior for all non-`inmemory` backends
   - 25 unit and integration tests in `tests/vector_store/test_sqlite_vec_store.py` covering init, add, search, get, update, delete, read-only mode, and stats
 
+### Fixed
+
+- **Missing `shacl` optional-dependency extra** (#736) by @Sameer6305
+  - `pip install semantica[shacl]` referenced no matching extra in `pyproject.toml`, so `pyshacl` was never installed despite being documented as the fix in `ontology_validator.py`'s `ImportError` message, the Explorer API, the healthcare cookbook notebook, and the changelog
+  - Added `shacl = ["pyshacl>=0.25.0"]` to `[project.optional-dependencies]` and folded `shacl` into the `all` extra
+
+- **`NodeEmbedder` `AttributeError` masked in `ContextGraph.analyze_graph_with_kg`** (#734) by @Sameer6305
+  - `analyze_graph_with_kg()` called a non-existent `NodeEmbedder.generate_embeddings()`, and the surrounding broad `except Exception` swallowed the resulting `AttributeError`, silently returning `{"error": "Graph analysis failed due to an internal error"}` from `get_causal_chain()`'s supporting analytics and `get_decision_insights()`
+  - Rewired the call site to the real `NodeEmbedder.compute_embeddings(graph_store, node_labels, relationship_types)` API, deriving `node_labels`/`relationship_types` from `self.node_type_index`/`self.edge_type_index`
+  - Added a dedicated `except AttributeError` branch that logs distinctly and re-raises, so a broken internal method call surfaces as a diagnosable error instead of being indistinguishable from a legitimately empty analysis result
+
 ---
 
 ## [0.5.1] - 2026-06-29

pyproject.toml

@@ -116,6 +116,9 @@ llm-all = [
 # ---- Document Parsing ----
 parse-docling = ["docling>=2.107.0"]
 
+# ---- SHACL Validation ----
+shacl = ["pyshacl>=0.25.0"]
+
 # ---- Database Connectors ----
 db-snowflake = ["snowflake-connector-python>=4.6.0", "cryptography>=49.0.0"]
 db-arrow = ["pyarrow>=24.0.0"]
@@ -234,8 +237,8 @@ explorer-lite = [
 
 # Everything (cross-platform — gpu excluded; install semantica[gpu] separately on Linux)
 all = [
-  "semantica[dev,viz,infra,cloud,monitoring,watch,llm-all,models-huggingface,split-all,graph-all,vectorstore-all,parse-docling,ingest-parquet,ingest-arrow,explorer]",
-  "semantica[dev,viz,infra,cloud,monitoring,watch,llm-all,models-huggingface,split-all,graph-all,vectorstore-all,parse-docling,ingest-parquet,ingest-arrow,agno]"
+  "semantica[dev,viz,infra,cloud,monitoring,watch,llm-all,models-huggingface,split-all,graph-all,vectorstore-all,parse-docling,ingest-parquet,ingest-arrow,shacl,explorer]",
+  "semantica[dev,viz,infra,cloud,monitoring,watch,llm-all,models-huggingface,split-all,graph-all,vectorstore-all,parse-docling,ingest-parquet,ingest-arrow,shacl,agno]"
 ]
 
 # ---------------- ENTRYPOINTS ----------------

semantica/context/context_graph.py

@@ -2214,12 +2214,26 @@ class ContextGraph:
             
             # Node embeddings
             if "node_embedder" in self.kg_components:
-                embeddings = self.kg_components["node_embedder"].generate_embeddings(kg_graph)
-                analysis["node_embeddings"] = embeddings
+                node_labels = list(self.node_type_index.keys())
+                relationship_types = list(self.edge_type_index.keys())
+                if node_labels:
+                    embeddings = self.kg_components["node_embedder"].compute_embeddings(
+                        graph_store=self,
+                        node_labels=node_labels,
+                        relationship_types=relationship_types,
+                    )
+                    analysis["node_embeddings"] = embeddings
             
             self.logger.info("Completed comprehensive graph analysis")
             return analysis
             
+        except AttributeError as e:
+            # A broken internal method call (e.g. calling a method that doesn't
+            # exist on one of the kg_components) is a programming error, not a
+            # legitimate empty-analysis result. Log it distinctly and re-raise
+            # rather than masking it under the generic message below.
+            self.logger.error(f"Graph analysis failed due to a broken internal method call: {e}")
+            raise
         except Exception as e:
             self.logger.error(f"Failed to analyze graph with KG: {e}")
             return {"error": "Graph analysis failed due to an internal error"}