Graph access via SPARQL
This commit is contained in:
94
backend/app/graph_export.py
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94
backend/app/graph_export.py
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@@ -0,0 +1,94 @@
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from __future__ import annotations
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from typing import Any
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def edge_retrieval_query(*, edge_limit: int, include_bnodes: bool) -> str:
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bnode_filter = "" if include_bnodes else "FILTER(!isBlank(?s) && !isBlank(?o))"
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return f"""
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SELECT ?s ?p ?o
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WHERE {{
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?s ?p ?o .
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FILTER(!isLiteral(?o))
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FILTER(?p NOT IN (
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<http://www.w3.org/2000/01/rdf-schema#label>,
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<http://www.w3.org/2004/02/skos/core#prefLabel>,
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<http://www.w3.org/2004/02/skos/core#altLabel>
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))
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{bnode_filter}
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}}
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LIMIT {edge_limit}
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"""
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def graph_from_sparql_bindings(
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bindings: list[dict[str, Any]],
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*,
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node_limit: int,
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include_bnodes: bool,
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) -> tuple[list[dict[str, object]], list[dict[str, object]]]:
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"""
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Convert SPARQL JSON results bindings into:
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nodes: [{id, termType, iri, label}]
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edges: [{source, target, predicate}]
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IDs are assigned densely (0..N-1) based on first occurrence in bindings.
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"""
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node_id_by_key: dict[tuple[str, str], int] = {}
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node_meta: list[tuple[str, str]] = [] # (termType, iri)
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out_edges: list[dict[str, object]] = []
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def term_to_key_and_iri(term: dict[str, Any]) -> tuple[tuple[str, str], tuple[str, str]] | None:
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t = term.get("type")
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v = term.get("value")
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if not t or v is None:
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return None
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if t == "literal":
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return None
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if t == "bnode":
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if not include_bnodes:
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return None
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# SPARQL JSON uses bnode identifiers without the "_:" prefix; we normalize to "_:id".
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return (("bnode", str(v)), ("bnode", f"_:{v}"))
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# Default to "uri".
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return (("uri", str(v)), ("uri", str(v)))
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def get_or_add(term: dict[str, Any]) -> int | None:
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out = term_to_key_and_iri(term)
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if out is None:
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return None
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key, meta = out
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existing = node_id_by_key.get(key)
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if existing is not None:
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return existing
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if len(node_meta) >= node_limit:
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return None
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nid = len(node_meta)
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node_id_by_key[key] = nid
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node_meta.append(meta)
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return nid
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for b in bindings:
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s_term = b.get("s") or {}
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o_term = b.get("o") or {}
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p_term = b.get("p") or {}
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sid = get_or_add(s_term)
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oid = get_or_add(o_term)
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if sid is None or oid is None:
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continue
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pred = p_term.get("value")
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if not pred:
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continue
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out_edges.append({"source": sid, "target": oid, "predicate": str(pred)})
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out_nodes = [
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{"id": i, "termType": term_type, "iri": iri, "label": None}
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for i, (term_type, iri) in enumerate(node_meta)
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]
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return out_nodes, out_edges
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@@ -5,6 +5,7 @@ from contextlib import asynccontextmanager
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from fastapi import FastAPI, HTTPException, Query
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from fastapi.middleware.cors import CORSMiddleware
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from .graph_export import edge_retrieval_query, graph_from_sparql_bindings
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from .models import EdgesResponse, GraphResponse, NodesResponse, SparqlQueryRequest, StatsResponse
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from .rdf_store import RDFStore
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from .sparql_engine import AnzoGraphEngine, RdflibEngine, SparqlEngine, create_sparql_engine
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@@ -161,87 +162,13 @@ async def graph(
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) -> GraphResponse:
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sparql: SparqlEngine = app.state.sparql
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if settings.graph_backend == "rdflib":
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store: RDFStore = app.state.store
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return GraphResponse(
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nodes=store.node_slice(offset=0, limit=node_limit),
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edges=store.edge_slice(offset=0, limit=edge_limit),
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)
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# AnzoGraph mode: return a simple subgraph by pulling the first N triples.
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assert isinstance(sparql, AnzoGraphEngine)
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edges_bnode_filter = "" if settings.include_bnodes else "FILTER(!isBlank(?s) && !isBlank(?o))"
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edges_q = f"""
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SELECT ?s ?p ?o
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WHERE {{
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?s ?p ?o .
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FILTER(!isLiteral(?o))
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FILTER(?p NOT IN (
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<http://www.w3.org/2000/01/rdf-schema#label>,
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<http://www.w3.org/2004/02/skos/core#prefLabel>,
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<http://www.w3.org/2004/02/skos/core#altLabel>
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))
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{edges_bnode_filter}
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}}
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LIMIT {edge_limit}
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"""
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# Use SPARQL for graph export in BOTH modes so callers don't care which backend is in use.
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edges_q = edge_retrieval_query(edge_limit=edge_limit, include_bnodes=settings.include_bnodes)
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res = await sparql.query_json(edges_q)
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bindings = (((res.get("results") or {}).get("bindings")) or [])
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node_id_by_key: dict[tuple[str, str], int] = {}
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node_meta: list[tuple[str, str]] = [] # (termType, iri)
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out_edges: list[dict[str, object]] = []
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def _term_to_key_and_iri(term: dict[str, str]) -> tuple[tuple[str, str], tuple[str, str]] | None:
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t = term.get("type")
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v = term.get("value")
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if not t or v is None:
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return None
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if t == "literal":
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return None
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if t == "bnode" and not settings.include_bnodes:
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return None
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if t == "bnode":
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return (("bnode", v), ("bnode", f"_:{v}"))
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# Default to "uri".
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return (("uri", v), ("uri", v))
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def _get_or_add(term: dict[str, str]) -> int | None:
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out = _term_to_key_and_iri(term)
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if out is None:
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return None
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key, meta = out
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existing = node_id_by_key.get(key)
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if existing is not None:
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return existing
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if len(node_meta) >= node_limit:
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return None
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nid = len(node_meta)
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node_id_by_key[key] = nid
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node_meta.append(meta)
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return nid
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for b in bindings:
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s_term = b.get("s") or {}
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o_term = b.get("o") or {}
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p_term = b.get("p") or {}
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sid = _get_or_add(s_term)
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oid = _get_or_add(o_term)
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if sid is None or oid is None:
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continue
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pred = p_term.get("value")
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if not pred:
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continue
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out_edges.append({"source": sid, "target": oid, "predicate": pred})
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out_nodes = [
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{"id": i, "termType": term_type, "iri": iri, "label": None}
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for i, (term_type, iri) in enumerate(node_meta)
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]
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return GraphResponse(nodes=out_nodes, edges=out_edges)
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nodes, edges = graph_from_sparql_bindings(
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bindings,
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node_limit=node_limit,
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include_bnodes=settings.include_bnodes,
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)
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return GraphResponse(nodes=nodes, edges=edges)
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1
backend/app/pipelines/__init__.py
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1
backend/app/pipelines/__init__.py
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@@ -0,0 +1 @@
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153
backend/app/pipelines/subclass_labels.py
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153
backend/app/pipelines/subclass_labels.py
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@@ -0,0 +1,153 @@
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from __future__ import annotations
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from typing import Any
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from ..sparql_engine import SparqlEngine
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RDFS_SUBCLASS_OF = "http://www.w3.org/2000/01/rdf-schema#subClassOf"
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RDFS_LABEL = "http://www.w3.org/2000/01/rdf-schema#label"
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def _bindings(res: dict[str, Any]) -> list[dict[str, Any]]:
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return (((res.get("results") or {}).get("bindings")) or [])
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def _term_key(term: dict[str, Any]) -> tuple[str, str] | None:
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t = term.get("type")
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v = term.get("value")
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if not t or v is None:
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return None
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if t == "literal":
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return None
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if t == "bnode":
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return ("bnode", str(v))
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return ("uri", str(v))
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def _key_to_entity_string(key: tuple[str, str]) -> str:
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t, v = key
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if t == "bnode":
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return f"_:{v}"
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return v
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def _label_score(binding: dict[str, Any]) -> int:
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"""
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Higher is better.
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Prefer English, then no-language, then anything else.
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"""
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lang = (binding.get("xml:lang") or "").lower()
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if lang == "en":
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return 3
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if lang == "":
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return 2
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return 1
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async def extract_subclass_entities_and_labels(
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sparql: SparqlEngine,
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*,
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include_bnodes: bool,
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label_batch_size: int = 500,
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) -> tuple[list[str], list[str | None]]:
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"""
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Pipeline:
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1) Query all rdfs:subClassOf triples.
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2) Build a unique set of entity terms from subjects+objects, convert to list.
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3) Fetch rdfs:label for those entities and return an aligned labels list.
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Returns:
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entities: list[str] (IRI or "_:bnodeId")
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labels: list[str|None], aligned with entities
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"""
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subclass_q = f"""
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SELECT ?s ?o
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WHERE {{
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?s <{RDFS_SUBCLASS_OF}> ?o .
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FILTER(!isLiteral(?o))
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{"FILTER(!isBlank(?s) && !isBlank(?o))" if not include_bnodes else ""}
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}}
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"""
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res = await sparql.query_json(subclass_q)
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entity_keys: set[tuple[str, str]] = set()
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for b in _bindings(res):
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sk = _term_key(b.get("s") or {})
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ok = _term_key(b.get("o") or {})
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if sk is not None and (include_bnodes or sk[0] != "bnode"):
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entity_keys.add(sk)
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if ok is not None and (include_bnodes or ok[0] != "bnode"):
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entity_keys.add(ok)
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# Deterministic ordering.
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entity_key_list = sorted(entity_keys, key=lambda k: (k[0], k[1]))
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entities = [_key_to_entity_string(k) for k in entity_key_list]
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# Build label map keyed by term key.
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best_label_by_key: dict[tuple[str, str], tuple[int, str]] = {}
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# URIs can be batch-queried via VALUES.
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uri_values = [v for (t, v) in entity_key_list if t == "uri"]
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for i in range(0, len(uri_values), label_batch_size):
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batch = uri_values[i : i + label_batch_size]
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values = " ".join(f"<{u}>" for u in batch)
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labels_q = f"""
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SELECT ?s ?label
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WHERE {{
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VALUES ?s {{ {values} }}
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?s <{RDFS_LABEL}> ?label .
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}}
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"""
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lres = await sparql.query_json(labels_q)
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for b in _bindings(lres):
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sk = _term_key(b.get("s") or {})
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if sk is None or sk[0] != "uri":
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continue
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label_term = b.get("label") or {}
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if label_term.get("type") != "literal":
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continue
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label_value = label_term.get("value")
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if label_value is None:
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continue
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score = _label_score(label_term)
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prev = best_label_by_key.get(sk)
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if prev is None or score > prev[0]:
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best_label_by_key[sk] = (score, str(label_value))
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# Blank nodes can't reliably be addressed by ID across queries, but if enabled we can still
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# fetch all bnode labels and filter locally.
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if include_bnodes:
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bnode_keys = {k for k in entity_key_list if k[0] == "bnode"}
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if bnode_keys:
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bnode_labels_q = f"""
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SELECT ?s ?label
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WHERE {{
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?s <{RDFS_LABEL}> ?label .
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FILTER(isBlank(?s))
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}}
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"""
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blres = await sparql.query_json(bnode_labels_q)
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for b in _bindings(blres):
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sk = _term_key(b.get("s") or {})
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if sk is None or sk not in bnode_keys:
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continue
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label_term = b.get("label") or {}
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if label_term.get("type") != "literal":
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continue
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label_value = label_term.get("value")
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if label_value is None:
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continue
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score = _label_score(label_term)
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prev = best_label_by_key.get(sk)
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if prev is None or score > prev[0]:
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best_label_by_key[sk] = (score, str(label_value))
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labels: list[str | None] = []
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for k in entity_key_list:
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item = best_label_by_key.get(k)
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labels.append(item[1] if item else None)
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return entities, labels
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@@ -132,3 +132,19 @@ class RDFStore:
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}
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)
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return out
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def edges_within_nodes(self, *, max_node_id_exclusive: int, limit: int) -> list[dict[str, Any]]:
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out: list[dict[str, Any]] = []
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for row in self._edges:
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if row.source >= max_node_id_exclusive or row.target >= max_node_id_exclusive:
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continue
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out.append(
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{
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"source": row.source,
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"target": row.target,
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"predicate": row.predicate,
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}
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)
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if len(out) >= limit:
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break
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return out
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@@ -33,6 +33,7 @@ class Settings(BaseSettings):
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sparql_timeout_s: float = Field(default=300.0, alias="SPARQL_TIMEOUT_S")
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sparql_ready_retries: int = Field(default=30, alias="SPARQL_READY_RETRIES")
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sparql_ready_delay_s: float = Field(default=4.0, alias="SPARQL_READY_DELAY_S")
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sparql_ready_timeout_s: float = Field(default=10.0, alias="SPARQL_READY_TIMEOUT_S")
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# Comma-separated, or "*" (default).
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cors_origins: str = Field(default="*", alias="CORS_ORIGINS")
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@@ -56,6 +56,7 @@ class AnzoGraphEngine:
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self.timeout_s = settings.sparql_timeout_s
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self.ready_retries = settings.sparql_ready_retries
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self.ready_delay_s = settings.sparql_ready_delay_s
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self.ready_timeout_s = settings.sparql_ready_timeout_s
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self.user = settings.sparql_user
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self.password = settings.sparql_pass
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@@ -135,15 +136,34 @@ class AnzoGraphEngine:
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resp.raise_for_status()
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async def _wait_ready(self) -> None:
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if self._client is None:
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raise RuntimeError("AnzoGraphEngine not started")
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# Match the repo's Julia readiness gate: real SPARQL POST + valid JSON parse.
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headers = {
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"Content-Type": "application/x-www-form-urlencoded",
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"Accept": "application/sparql-results+json",
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}
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if self._auth_header:
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headers["Authorization"] = self._auth_header
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last_err: Exception | None = None
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for _ in range(self.ready_retries):
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try:
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# Keep it cheap and JSON-parseable.
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await self.query_json("ASK WHERE { ?s ?p ?o }")
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resp = await self._client.post(
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self.endpoint,
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headers=headers,
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data={"query": "ASK WHERE { ?s ?p ?o }"},
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timeout=self.ready_timeout_s,
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)
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resp.raise_for_status()
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# Ensure it's JSON, not HTML/text during boot.
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resp.json()
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return
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except Exception as e:
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last_err = e
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await asyncio.sleep(self.ready_delay_s)
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raise RuntimeError(f"AnzoGraph not ready at {self.endpoint}") from last_err
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371
docs/anzograph-readiness-julia.md
Normal file
371
docs/anzograph-readiness-julia.md
Normal file
@@ -0,0 +1,371 @@
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# Waiting for AnzoGraph readiness from Julia (how this repo does it)
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This repo runs a Julia pipeline (`julia/main.jl`) against an AnzoGraph SPARQL endpoint. The key problem is that **“container started” ≠ “SPARQL endpoint is ready to accept queries”**.
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So, before the Julia code does anything that depends on SPARQL (like `LOAD <...>` or large `SELECT`s), it explicitly **waits until AnzoGraph is actually responding to a real SPARQL POST request with valid JSON results**.
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This document explains the exact mechanism used here, why it works, and gives copy/paste-ready patterns you can transfer to another project.
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|
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---
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## 1) Where the waiting happens (pipeline control flow)
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In `julia/main.jl`, the entrypoint calls:
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```julia
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# Step 1: Wait for AnzoGraph
|
||||
wait_for_anzograph()
|
||||
|
||||
# Step 2: Load TTL file
|
||||
result = sparql_update("LOAD <$SPARQL_DATA_FILE>")
|
||||
```
|
||||
|
||||
So the “await” is not a Julia `Task`/`async` wait; it is a **blocking retry loop** that only returns when it can successfully execute a small SPARQL query.
|
||||
|
||||
Reference: `julia/main.jl` defines `wait_for_anzograph()` and calls it from `main()`.
|
||||
|
||||
---
|
||||
|
||||
## 2) Why this is needed even with Docker Compose `depends_on`
|
||||
|
||||
This repo’s `docker-compose.yml` includes an AnzoGraph `healthcheck`:
|
||||
|
||||
```yaml
|
||||
anzograph:
|
||||
healthcheck:
|
||||
test: ["CMD-SHELL", "curl -f http://localhost:8080/sparql || exit 1"]
|
||||
interval: 10s
|
||||
timeout: 5s
|
||||
retries: 30
|
||||
start_period: 60s
|
||||
```
|
||||
|
||||
However, `julia-layout` currently depends on `anzograph` with:
|
||||
|
||||
```yaml
|
||||
depends_on:
|
||||
anzograph:
|
||||
condition: service_started
|
||||
```
|
||||
|
||||
Meaning:
|
||||
- Compose will ensure the **container process has started**.
|
||||
- Compose does **not** guarantee the AnzoGraph HTTP/SPARQL endpoint is ready (unless you use `service_healthy`, and even then a “healthy GET” is not always equivalent to “SPARQL POST works with auth + JSON”).
|
||||
|
||||
So the Julia code includes its own readiness gate to prevent failures like:
|
||||
- TCP connection refused (port not open yet)
|
||||
- HTTP endpoint reachable but not fully initialized
|
||||
- Non-JSON/HTML error responses while the service is still booting
|
||||
|
||||
---
|
||||
|
||||
## 3) What “ready” means in this repo
|
||||
|
||||
In this repo, “AnzoGraph is ready” means:
|
||||
|
||||
1. An HTTP `POST` to `${SPARQL_HOST}/sparql` succeeds, with headers:
|
||||
- `Content-Type: application/x-www-form-urlencoded`
|
||||
- `Accept: application/sparql-results+json`
|
||||
- `Authorization: Basic ...`
|
||||
2. The body parses as SPARQL JSON results (`application/sparql-results+json`)
|
||||
|
||||
It does **not** strictly mean:
|
||||
- Your dataset is already loaded
|
||||
- The loaded data is fully indexed (that can matter in some systems after `LOAD`)
|
||||
|
||||
This repo uses readiness as a **“SPARQL endpoint is alive and speaking the protocol”** check.
|
||||
|
||||
---
|
||||
|
||||
## 4) The actual Julia implementation (as in `julia/main.jl`)
|
||||
|
||||
### 4.1 Configuration (endpoint + auth)
|
||||
|
||||
The Julia script builds endpoint and auth from environment variables:
|
||||
|
||||
```julia
|
||||
const SPARQL_HOST = get(ENV, "SPARQL_HOST", "http://localhost:8080")
|
||||
const SPARQL_ENDPOINT = "$SPARQL_HOST/sparql"
|
||||
const SPARQL_USER = get(ENV, "SPARQL_USER", "admin")
|
||||
const SPARQL_PASS = get(ENV, "SPARQL_PASS", "Passw0rd1")
|
||||
const AUTH_HEADER = "Basic " * base64encode("$SPARQL_USER:$SPARQL_PASS")
|
||||
```
|
||||
|
||||
In Docker Compose for this repo, the Julia container overrides `SPARQL_HOST` to use the service DNS name:
|
||||
|
||||
```yaml
|
||||
environment:
|
||||
- SPARQL_HOST=http://anzograph:8080
|
||||
```
|
||||
|
||||
### 4.2 The smoke query used for readiness
|
||||
|
||||
This is the query used in the wait loop:
|
||||
|
||||
```julia
|
||||
const SMOKE_TEST_QUERY = "SELECT ?s ?p ?o WHERE { ?s ?p ?o } LIMIT 3"
|
||||
```
|
||||
|
||||
Notes:
|
||||
- It’s intentionally small (`LIMIT 3`) to keep the readiness check cheap.
|
||||
- It returns *some* bindings when data exists, but **even an empty dataset can still return a valid empty result set**. The code treats “valid response” as ready.
|
||||
|
||||
If you want a readiness check that does not depend on any data being present, an `ASK` query is also common:
|
||||
|
||||
```sparql
|
||||
ASK WHERE { ?s ?p ?o }
|
||||
```
|
||||
|
||||
### 4.3 SPARQL query function (request + minimal retry)
|
||||
|
||||
`sparql_query(query; retries=...)` is a generic helper that makes SPARQL POST requests:
|
||||
|
||||
```julia
|
||||
function sparql_query(query::String; retries::Int=5)::SparqlResult
|
||||
for attempt in 1:retries
|
||||
try
|
||||
response = HTTP.post(
|
||||
SPARQL_ENDPOINT,
|
||||
[
|
||||
"Content-Type" => "application/x-www-form-urlencoded",
|
||||
"Accept" => "application/sparql-results+json",
|
||||
"Authorization" => AUTH_HEADER
|
||||
];
|
||||
body = "query=" * HTTP.URIs.escapeuri(query)
|
||||
)
|
||||
|
||||
if response.status == 200
|
||||
json = JSON.parse(String(response.body))
|
||||
return SparqlResult(json["results"]["bindings"])
|
||||
elseif response.status >= 500 && attempt < retries
|
||||
sleep(10)
|
||||
continue
|
||||
else
|
||||
error("SPARQL query failed with status $(response.status)")
|
||||
end
|
||||
catch e
|
||||
if attempt < retries
|
||||
sleep(10)
|
||||
continue
|
||||
end
|
||||
rethrow(e)
|
||||
end
|
||||
end
|
||||
error("SPARQL query failed after $retries attempts")
|
||||
end
|
||||
```
|
||||
|
||||
Important behaviors to preserve when transferring:
|
||||
- It uses **POST** (not GET) to the SPARQL endpoint.
|
||||
- It requires a **200** response and successfully parses SPARQL JSON results.
|
||||
- It retries on:
|
||||
- `>= 500` server errors
|
||||
- network / protocol / parsing errors (caught exceptions)
|
||||
|
||||
### 4.4 The readiness gate: `wait_for_anzograph`
|
||||
|
||||
This is the “await until ready” logic:
|
||||
|
||||
```julia
|
||||
function wait_for_anzograph(max_retries::Int=30)::Bool
|
||||
println("Waiting for AnzoGraph at $SPARQL_ENDPOINT...")
|
||||
|
||||
for attempt in 1:max_retries
|
||||
try
|
||||
smoke_result = sparql_query(SMOKE_TEST_QUERY; retries=1)
|
||||
println(" AnzoGraph is ready (attempt $attempt, smoke rows=$(length(smoke_result.bindings)))")
|
||||
return true
|
||||
catch e
|
||||
println(" Attempt $attempt/$max_retries: $(typeof(e))")
|
||||
sleep(4)
|
||||
end
|
||||
end
|
||||
|
||||
error("AnzoGraph not available after $max_retries attempts")
|
||||
end
|
||||
```
|
||||
|
||||
Why it calls `sparql_query(...; retries=1)`:
|
||||
- It makes each outer “readiness attempt” a **single** request.
|
||||
- The outer loop controls cadence (`sleep(4)`) and total wait time.
|
||||
- This avoids “nested retry loops” (inner sleeps + outer sleeps) that can make waits much longer than intended.
|
||||
|
||||
Time bound in the current implementation:
|
||||
- `max_retries = 30`
|
||||
- `sleep(4)` between attempts
|
||||
- Roughly ~120 seconds of waiting (plus request time).
|
||||
|
||||
---
|
||||
|
||||
## 5) What failures cause it to keep waiting
|
||||
|
||||
`wait_for_anzograph()` catches any exception thrown by `sparql_query()` and retries. In practice, that includes:
|
||||
|
||||
- **Connection errors** (DNS not ready, connection refused, etc.)
|
||||
- **Timeouts** (if HTTP request takes too long and the library throws)
|
||||
- **Non-200 HTTP statuses** that cause `error(...)`
|
||||
- **Non-JSON / unexpected JSON** responses causing `JSON.parse(...)` to throw
|
||||
|
||||
That last point is a big reason a “real SPARQL request + parse” is stronger than just “ping the port”.
|
||||
|
||||
---
|
||||
|
||||
## 6) Transferable, self-contained version (recommended pattern)
|
||||
|
||||
If you want to reuse this in another project, it’s usually easier to:
|
||||
- avoid globals,
|
||||
- make endpoint/auth explicit,
|
||||
- use a **time-based timeout** instead of `max_retries` (more robust),
|
||||
- add request timeouts so the wait loop can’t hang forever on a single request.
|
||||
|
||||
Below is a drop-in module you can copy into your project.
|
||||
|
||||
```julia
|
||||
module AnzoGraphReady
|
||||
|
||||
using HTTP
|
||||
using JSON
|
||||
using Base64
|
||||
using Dates
|
||||
|
||||
struct SparqlResult
|
||||
bindings::Vector{Dict{String, Any}}
|
||||
end
|
||||
|
||||
function basic_auth_header(user::AbstractString, pass::AbstractString)::String
|
||||
return "Basic " * base64encode("$(user):$(pass)")
|
||||
end
|
||||
|
||||
function sparql_query(
|
||||
endpoint::AbstractString,
|
||||
auth_header::AbstractString,
|
||||
query::AbstractString;
|
||||
retries::Int = 1,
|
||||
retry_sleep_s::Real = 2,
|
||||
request_timeout_s::Real = 15,
|
||||
)::SparqlResult
|
||||
for attempt in 1:retries
|
||||
try
|
||||
response = HTTP.post(
|
||||
String(endpoint),
|
||||
[
|
||||
"Content-Type" => "application/x-www-form-urlencoded",
|
||||
"Accept" => "application/sparql-results+json",
|
||||
"Authorization" => auth_header,
|
||||
];
|
||||
body = "query=" * HTTP.URIs.escapeuri(String(query)),
|
||||
readtimeout = request_timeout_s,
|
||||
)
|
||||
|
||||
if response.status != 200
|
||||
error("SPARQL query failed with status $(response.status)")
|
||||
end
|
||||
|
||||
parsed = JSON.parse(String(response.body))
|
||||
bindings = get(get(parsed, "results", Dict()), "bindings", Any[])
|
||||
return SparqlResult(Vector{Dict{String, Any}}(bindings))
|
||||
catch e
|
||||
if attempt < retries
|
||||
sleep(retry_sleep_s)
|
||||
continue
|
||||
end
|
||||
rethrow(e)
|
||||
end
|
||||
end
|
||||
error("sparql_query: unreachable")
|
||||
end
|
||||
|
||||
"""
|
||||
Wait until AnzoGraph responds to a real SPARQL POST with parseable JSON.
|
||||
|
||||
This is the direct analog of this repo's `wait_for_anzograph()`, but with:
|
||||
- a time-based timeout (`timeout`)
|
||||
- a request timeout per attempt (`request_timeout_s`)
|
||||
- simple exponential backoff
|
||||
"""
|
||||
function wait_for_anzograph(
|
||||
endpoint::AbstractString,
|
||||
auth_header::AbstractString;
|
||||
timeout::Period = Minute(3),
|
||||
initial_delay_s::Real = 0.5,
|
||||
max_delay_s::Real = 5.0,
|
||||
request_timeout_s::Real = 10.0,
|
||||
query::AbstractString = "ASK WHERE { ?s ?p ?o }",
|
||||
)::Nothing
|
||||
deadline = now() + timeout
|
||||
delay_s = initial_delay_s
|
||||
|
||||
while now() < deadline
|
||||
try
|
||||
# A single attempt: if it succeeds, we declare "ready".
|
||||
sparql_query(
|
||||
endpoint,
|
||||
auth_header,
|
||||
query;
|
||||
retries = 1,
|
||||
request_timeout_s = request_timeout_s,
|
||||
)
|
||||
return
|
||||
catch
|
||||
sleep(delay_s)
|
||||
delay_s = min(max_delay_s, delay_s * 1.5)
|
||||
end
|
||||
end
|
||||
|
||||
error("AnzoGraph not available before timeout=$(timeout)")
|
||||
end
|
||||
|
||||
end # module
|
||||
```
|
||||
|
||||
Typical usage (matching this repo’s environment variables):
|
||||
|
||||
```julia
|
||||
using .AnzoGraphReady
|
||||
|
||||
sparql_host = get(ENV, "SPARQL_HOST", "http://localhost:8080")
|
||||
endpoint = "$(sparql_host)/sparql"
|
||||
user = get(ENV, "SPARQL_USER", "admin")
|
||||
pass = get(ENV, "SPARQL_PASS", "Passw0rd1")
|
||||
|
||||
auth = AnzoGraphReady.basic_auth_header(user, pass)
|
||||
AnzoGraphReady.wait_for_anzograph(endpoint, auth; timeout=Minute(5))
|
||||
|
||||
# Now it is safe to LOAD / query.
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## 7) Optional: waiting for “data is ready” after `LOAD`
|
||||
|
||||
Some systems accept `LOAD` but need time before results show up reliably (indexing / transaction visibility).
|
||||
If you run into that in your other project, add a second gate after `LOAD`, for example:
|
||||
|
||||
1) load, then
|
||||
2) poll a query that must be true after load (e.g., “triple count > 0”, or a known IRI exists).
|
||||
|
||||
Example “post-load gate”:
|
||||
|
||||
```julia
|
||||
post_load_query = """
|
||||
SELECT (COUNT(*) AS ?n)
|
||||
WHERE { ?s ?p ?o }
|
||||
"""
|
||||
|
||||
res = AnzoGraphReady.sparql_query(endpoint, auth, post_load_query; retries=1)
|
||||
# Parse `?n` out of bindings and require it to be > 0; retry until it is.
|
||||
```
|
||||
|
||||
(This repo does not currently enforce “non-empty”; it only enforces “SPARQL is working”.)
|
||||
|
||||
---
|
||||
|
||||
## 8) Practical checklist when transferring to another project
|
||||
|
||||
- Make readiness checks hit the **real SPARQL POST** path you will use in production.
|
||||
- Require a **valid JSON parse**, not just “port open”.
|
||||
- Add **per-request timeouts**, so a single hung request cannot hang the whole pipeline.
|
||||
- Prefer **time-based overall timeout** for predictable behavior in CI.
|
||||
- Keep the query **cheap** (`ASK` or `LIMIT 1/3`).
|
||||
- If you use Docker Compose healthchecks, consider also using `depends_on: condition: service_healthy`, but still keep the in-app wait as a safety net (it’s closer to the real contract your code needs).
|
||||
|
||||
Reference in New Issue
Block a user