NextGraph
/
oxigraph
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Activity

Adds an enum for CanonicalizationAlgorithm

Browse Source 
Enables implementing other algorithms like RDFC-1.0
pull/819/head
Tpt 3 months ago committed by Thomas Tanon
parent f5b975e4d1
commit 0ac70e73dc
5 changed files with 120 additions and 83 deletions
Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL
Show Stats Download Patch File Download Diff File
  1. 7
      fuzz/fuzz_targets/trig.rs
  2. 162
      lib/oxrdf/src/dataset.rs
  3. 18
      lib/oxrdf/src/graph.rs
  4. 9
      testsuite/src/parser_evaluator.rs
  5. 7
      testsuite/src/sparql_evaluator.rs

7
fuzz/fuzz_targets/trig.rs
Unescape View File

@ -1,6 +1,7 @@
#![no_main]
use libfuzzer_sys::fuzz_target;
use oxrdf::graph::CanonicalizationAlgorithm;
use oxrdf::{Dataset, GraphName, Quad, Subject, Term, Triple};
use oxttl::{TriGParser, TriGSerializer};
@ -120,8 +121,8 @@ fuzz_target!(|data: &[u8]| {
} else if bnodes_count <= 4 {
let mut dataset_with_split = quads.iter().collect::<Dataset>();
let mut dataset_without_split = quads_without_split.iter().collect::<Dataset>();
dataset_with_split.canonicalize();
dataset_without_split.canonicalize();
dataset_with_split.canonicalize(CanonicalizationAlgorithm::Unstable);
dataset_without_split.canonicalize(CanonicalizationAlgorithm::Unstable);
assert_eq!(
dataset_with_split,
dataset_without_split,
@ -131,7 +132,7 @@ fuzz_target!(|data: &[u8]| {
);
if errors.is_empty() {
let mut dataset_unchecked = quads_unchecked.iter().collect::<Dataset>();
dataset_unchecked.canonicalize();
dataset_unchecked.canonicalize(CanonicalizationAlgorithm::Unstable);
assert_eq!(
dataset_with_split,
dataset_unchecked,

162
lib/oxrdf/src/dataset.rs
Unescape View File

@ -31,7 +31,6 @@
use crate::interning::*;
use crate::*;
use std::cmp::min;
use std::collections::hash_map::DefaultHasher;
use std::collections::{BTreeSet, HashMap, HashSet};
use std::fmt;
@ -510,6 +509,7 @@ impl Dataset {
///
/// Usage example ([Dataset isomorphism](https://www.w3.org/TR/rdf11-concepts/#dfn-dataset-isomorphism)):
/// ```
/// use oxrdf::dataset::CanonicalizationAlgorithm;
/// use oxrdf::*;
///
/// let iri = NamedNodeRef::new("http://example.com")?;
@ -527,32 +527,59 @@ impl Dataset {
/// graph2.insert(QuadRef::new(&bnode2, iri, iri, &g2));
///
/// assert_ne!(graph1, graph2);
/// graph1.canonicalize();
/// graph2.canonicalize();
/// graph1.canonicalize(CanonicalizationAlgorithm::Unstable);
/// graph2.canonicalize(CanonicalizationAlgorithm::Unstable);
/// assert_eq!(graph1, graph2);
/// # Result::<_,Box<dyn std::error::Error>>::Ok(())
/// ```
///
/// Warning 1: Blank node ids depends on the current shape of the graph. Adding a new quad might change the ids of a lot of blank nodes.
/// Hence, this canonization might not be suitable for diffs.
/// <div class="warning">Blank node ids depends on the current shape of the graph. Adding a new quad might change the ids of a lot of blank nodes.
/// Hence, this canonization might not be suitable for diffs.</div>
///
/// Warning 2: The canonicalization algorithm is not stable and canonical blank node ids might change between Oxigraph version.
///
/// Warning 3: This implementation worst-case complexity is in *O(b!)* with *b* the number of blank nodes in the input dataset.
pub fn canonicalize(&mut self) {
let bnodes = self.blank_nodes();
let quads_per_blank_node = self.quads_per_blank_nodes();
let (hash, partition) = self.hash_bnodes(
bnodes.into_iter().map(|bnode| (bnode, 0)).collect(),
&quads_per_blank_node,
);
let new_quads = self.distinguish(&hash, &partition, &quads_per_blank_node);
/// <div class="warning">This implementation worst-case complexity is in *O(b!)* with *b* the number of blank nodes in the input dataset.</div>
pub fn canonicalize(&mut self, algorithm: CanonicalizationAlgorithm) {
let bnode_mapping = self.canonicalize_interned_blank_nodes(algorithm);
let new_quads = self.map_blank_nodes(&bnode_mapping);
self.clear();
for quad in new_quads {
self.insert_encoded(quad);
}
}
/// Returns a map between the current dataset blank node and the canonicalized blank node
/// to create a canonical dataset.
///
/// See also [`canonicalize`](Self::canonicalize).
pub fn canonicalize_blank_nodes(
&self,
algorithm: CanonicalizationAlgorithm,
) -> HashMap<BlankNodeRef<'_>, BlankNode> {
self.canonicalize_interned_blank_nodes(algorithm)
.into_iter()
.map(|(from, to)| (from.decode_from(&self.interner), to))
.collect()
}
fn canonicalize_interned_blank_nodes(
&self,
algorithm: CanonicalizationAlgorithm,
) -> HashMap<InternedBlankNode, BlankNode> {
match algorithm {
CanonicalizationAlgorithm::Unstable => {
let bnodes = self.blank_nodes();
let quads_per_blank_node = self.quads_per_blank_nodes();
let (hash, partition) = self.hash_bnodes(
bnodes.into_iter().map(|bnode| (bnode, 0)).collect(),
&quads_per_blank_node,
);
self.distinguish(hash, &partition, &quads_per_blank_node)
.into_iter()
.map(|(from, to)| (from, BlankNode::new_from_unique_id(to.into())))
.collect()
}
}
}
fn blank_nodes(&self) -> HashSet<InternedBlankNode> {
let mut bnodes = HashSet::new();
for (g, s, _, o) in &self.gspo {
@ -781,16 +808,11 @@ impl Dataset {
}
fn distinguish(
&mut self,
hash: &HashMap<InternedBlankNode, u64>,
&self,
hash: HashMap<InternedBlankNode, u64>,
partition: &[(u64, Vec<InternedBlankNode>)],
quads_per_blank_node: &QuadsPerBlankNode,
) -> Vec<(
InternedSubject,
InternedNamedNode,
InternedTerm,
InternedGraphName,
)> {
) -> HashMap<InternedBlankNode, u64> {
let b_prime = partition.iter().map(|(_, b)| b).find(|b| b.len() > 1);
if let Some(b_prime) = b_prime {
b_prime
@ -800,19 +822,29 @@ impl Dataset {
hash_prime.insert(*b, Self::hash_tuple((hash_prime[b], 22)));
let (hash_prime_prime, partition_prime) =
self.hash_bnodes(hash_prime, quads_per_blank_node);
self.distinguish(&hash_prime_prime, &partition_prime, quads_per_blank_node)
self.distinguish(hash_prime_prime, &partition_prime, quads_per_blank_node)
})
.reduce(|a, b| {
let mut a_hashes = a.values().collect::<Vec<_>>();
a_hashes.sort();
let mut b_hashes = a.values().collect::<Vec<_>>();
b_hashes.sort();
if a_hashes <= b_hashes {
a
} else {
b
}
})
.reduce(min)
.unwrap_or_default()
} else {
self.label(hash)
hash
}
}
#[allow(clippy::needless_collect)]
fn label(
fn map_blank_nodes(
&mut self,
hashes: &HashMap<InternedBlankNode, u64>,
bnode_mapping: &HashMap<InternedBlankNode, BlankNode>,
) -> Vec<(
InternedSubject,
InternedNamedNode,
@ -820,19 +852,22 @@ impl Dataset {
InternedGraphName,
)> {
let old_quads: Vec<_> = self.spog.iter().cloned().collect();
let mut quads: Vec<_> = old_quads
old_quads
.into_iter()
.map(|(s, p, o, g)| {
(
match s {
InternedSubject::NamedNode(_) => s,
InternedSubject::BlankNode(bnode) => {
InternedSubject::BlankNode(self.map_bnode(bnode, hashes))
InternedSubject::BlankNode(InternedBlankNode::encoded_into(
bnode_mapping[&bnode].as_ref(),
&mut self.interner,
))
}
#[cfg(feature = "rdf-star")]
InternedSubject::Triple(triple) => {
InternedSubject::Triple(Box::new(InternedTriple::encoded_into(
self.label_triple(&triple, hashes).as_ref(),
self.map_triple_blank_nodes(&triple, bnode_mapping).as_ref(),
&mut self.interner,
)))
}
@ -841,12 +876,15 @@ impl Dataset {
match o {
InternedTerm::NamedNode(_) | InternedTerm::Literal(_) => o,
InternedTerm::BlankNode(bnode) => {
InternedTerm::BlankNode(self.map_bnode(bnode, hashes))
InternedTerm::BlankNode(InternedBlankNode::encoded_into(
bnode_mapping[&bnode].as_ref(),
&mut self.interner,
))
}
#[cfg(feature = "rdf-star")]
InternedTerm::Triple(triple) => {
InternedTerm::Triple(Box::new(InternedTriple::encoded_into(
self.label_triple(&triple, hashes).as_ref(),
self.map_triple_blank_nodes(&triple, bnode_mapping).as_ref(),
&mut self.interner,
)))
}
@ -854,58 +892,41 @@ impl Dataset {
match g {
InternedGraphName::NamedNode(_) | InternedGraphName::DefaultGraph => g,
InternedGraphName::BlankNode(bnode) => {
InternedGraphName::BlankNode(self.map_bnode(bnode, hashes))
InternedGraphName::BlankNode(InternedBlankNode::encoded_into(
bnode_mapping[&bnode].as_ref(),
&mut self.interner,
))
}
},
)
})
.collect();
quads.sort_unstable();
quads
.collect()
}
#[cfg(feature = "rdf-star")]
fn label_triple(
fn map_triple_blank_nodes(
&mut self,
triple: &InternedTriple,
hashes: &HashMap<InternedBlankNode, u64>,
bnode_mapping: &HashMap<InternedBlankNode, BlankNode>,
) -> Triple {
Triple {
subject: if let InternedSubject::BlankNode(bnode) = &triple.subject {
Self::gen_bnode(*bnode, hashes).into()
bnode_mapping[bnode].clone().into()
} else if let InternedSubject::Triple(t) = &triple.subject {
self.label_triple(t, hashes).into()
self.map_triple_blank_nodes(t, bnode_mapping).into()
} else {
triple.subject.decode_from(&self.interner).into_owned()
},
predicate: triple.predicate.decode_from(&self.interner).into_owned(),
object: if let InternedTerm::BlankNode(bnode) = &triple.object {
Self::gen_bnode(*bnode, hashes).into()
bnode_mapping[bnode].clone().into()
} else if let InternedTerm::Triple(t) = &triple.object {
self.label_triple(t, hashes).into()
self.map_triple_blank_nodes(t, bnode_mapping).into()
} else {
triple.object.decode_from(&self.interner).into_owned()
},
}
}
fn map_bnode(
&mut self,
old_bnode: InternedBlankNode,
hashes: &HashMap<InternedBlankNode, u64>,
) -> InternedBlankNode {
InternedBlankNode::encoded_into(
Self::gen_bnode(old_bnode, hashes).as_ref(),
&mut self.interner,
)
}
fn gen_bnode(
old_bnode: InternedBlankNode,
hashes: &HashMap<InternedBlankNode, u64>,
) -> BlankNode {
BlankNode::new_from_unique_id(hashes[&old_bnode].into())
}
}
impl PartialEq for Dataset {
@ -1569,6 +1590,19 @@ type QuadsPerBlankNode = HashMap<
)>,
>;
/// An algorithm used to canonicalize graph and datasets.
///
/// See [`Graph::canonicalize`] and [`Dataset::canonicalize`].
#[derive(Default, Debug, Clone, Copy, Eq, PartialEq, Hash)]
#[non_exhaustive]
pub enum CanonicalizationAlgorithm {
/// The algorithm preferred by OxRDF.
///
/// <div class="warning">The canonicalization algorithm is not stable and canonical blank node ids might change between Oxigraph version.</div>
#[default]
Unstable,
}
#[cfg(test)]
mod tests {
use super::*;
@ -1588,7 +1622,7 @@ mod tests {
BlankNode::default().as_ref(),
GraphNameRef::DefaultGraph,
));
dataset.canonicalize();
dataset.canonicalize(CanonicalizationAlgorithm::Unstable);
let mut dataset2 = Dataset::new();
dataset2.insert(QuadRef::new(
BlankNode::default().as_ref(),
@ -1602,7 +1636,7 @@ mod tests {
BlankNode::default().as_ref(),
GraphNameRef::DefaultGraph,
));
dataset2.canonicalize();
dataset2.canonicalize(CanonicalizationAlgorithm::Unstable);
assert_eq!(dataset, dataset2);
}
}

18
lib/oxrdf/src/graph.rs
Unescape View File

@ -25,6 +25,7 @@
//!
//! See also [`Dataset`] if you want to get support of multiple RDF graphs at the same time.
pub use crate::dataset::CanonicalizationAlgorithm;
use crate::dataset::*;
use crate::*;
use std::fmt;
@ -188,6 +189,7 @@ impl Graph {
///
/// Usage example ([Graph isomorphism](https://www.w3.org/TR/rdf11-concepts/#dfn-graph-isomorphism)):
/// ```
/// use oxrdf::graph::CanonicalizationAlgorithm;
/// use oxrdf::*;
///
/// let iri = NamedNodeRef::new("http://example.com")?;
@ -203,20 +205,18 @@ impl Graph {
/// graph2.insert(TripleRef::new(&bnode2, iri, iri));
///
/// assert_ne!(graph1, graph2);
/// graph1.canonicalize();
/// graph2.canonicalize();
/// graph1.canonicalize(CanonicalizationAlgorithm::Unstable);
/// graph2.canonicalize(CanonicalizationAlgorithm::Unstable);
/// assert_eq!(graph1, graph2);
/// # Result::<_,Box<dyn std::error::Error>>::Ok(())
/// ```
///
/// Warning 1: Blank node ids depends on the current shape of the graph. Adding a new triple might change the ids of a lot of blank nodes.
/// Hence, this canonization might not be suitable for diffs.
/// <div class="warning">Blank node ids depends on the current shape of the graph. Adding a new quad might change the ids of a lot of blank nodes.
/// Hence, this canonization might not be suitable for diffs.</div>
///
/// Warning 2: The canonicalization algorithm is not stable and canonical blank node Ids might change between Oxigraph version.
///
/// Warning 3: This implementation worst-case complexity is in *O(b!)* with *b* the number of blank nodes in the input graph.
pub fn canonicalize(&mut self) {
self.dataset.canonicalize()
/// <div class="warning">This implementation worst-case complexity is in *O(b!)* with *b* the number of blank nodes in the input dataset.</div>
pub fn canonicalize(&mut self, algorithm: CanonicalizationAlgorithm) {
self.dataset.canonicalize(algorithm)
}
}

9
testsuite/src/parser_evaluator.rs
Unescape View File

@ -4,6 +4,7 @@ use crate::manifest::Test;
use crate::report::{dataset_diff, format_diff};
use anyhow::{bail, ensure, Context, Result};
use oxigraph::io::RdfFormat;
use oxigraph::model::graph::CanonicalizationAlgorithm;
use oxigraph::model::{BlankNode, Dataset, Quad};
use oxttl::n3::{N3Quad, N3Term};
@ -138,11 +139,11 @@ fn evaluate_eval_test(test: &Test, format: RdfFormat, ignore_errors: bool) -> Re
let action = test.action.as_deref().context("No action found")?;
let mut actual_dataset = load_dataset(action, format, ignore_errors)
.with_context(|| format!("Parse error on file {action}"))?;
actual_dataset.canonicalize();
actual_dataset.canonicalize(CanonicalizationAlgorithm::Unstable);
let results = test.result.as_ref().context("No tests result found")?;
let mut expected_dataset = load_dataset(results, guess_rdf_format(results)?, false)
.with_context(|| format!("Parse error on file {results}"))?;
expected_dataset.canonicalize();
expected_dataset.canonicalize(CanonicalizationAlgorithm::Unstable);
ensure!(
expected_dataset == actual_dataset,
"The two files are not isomorphic. Diff:\n{}",
@ -156,12 +157,12 @@ fn evaluate_n3_eval_test(test: &Test, ignore_errors: bool) -> Result<()> {
let mut actual_dataset = n3_to_dataset(
load_n3(action, ignore_errors).with_context(|| format!("Parse error on file {action}"))?,
);
actual_dataset.canonicalize();
actual_dataset.canonicalize(CanonicalizationAlgorithm::Unstable);
let results = test.result.as_ref().context("No tests result found")?;
let mut expected_dataset = n3_to_dataset(
load_n3(results, false).with_context(|| format!("Parse error on file {results}"))?,
);
expected_dataset.canonicalize();
expected_dataset.canonicalize(CanonicalizationAlgorithm::Unstable);
ensure!(
expected_dataset == actual_dataset,
"The two files are not isomorphic. Diff:\n{}",

7
testsuite/src/sparql_evaluator.rs
Unescape View File

@ -5,6 +5,7 @@ use crate::report::{dataset_diff, format_diff};
use crate::vocab::*;
use anyhow::{bail, ensure, Context, Error, Result};
use oxigraph::io::RdfParser;
use oxigraph::model::dataset::CanonicalizationAlgorithm;
use oxigraph::model::vocab::*;
use oxigraph::model::*;
use oxigraph::sparql::results::QueryResultsFormat;
@ -235,9 +236,9 @@ fn evaluate_update_evaluation_test(test: &Test) -> Result<()> {
store.update(update).context("Failure to execute update")?;
let mut store_dataset: Dataset = store.iter().collect::<Result<_, _>>()?;
store_dataset.canonicalize();
store_dataset.canonicalize(CanonicalizationAlgorithm::Unstable);
let mut result_store_dataset: Dataset = result_store.iter().collect::<Result<_, _>>()?;
result_store_dataset.canonicalize();
result_store_dataset.canonicalize(CanonicalizationAlgorithm::Unstable);
ensure!(
store_dataset == result_store_dataset,
"Not isomorphic result dataset.\nDiff:\n{}\nParsed update:\n{}\n",
@ -533,7 +534,7 @@ impl StaticQueryResults {
})
}
} else {
graph.canonicalize();
graph.canonicalize(CanonicalizationAlgorithm::Unstable);
Ok(Self::Graph(graph))
}
}

Write Preview
Loading…
Cancel
Save