.

graph/src/error.rs

@@ -30,4 +30,7 @@ pub enum Error {
     
     #[error(transparent)]
     TonicStatus(#[from] gl_inference::tonic::Status),
+
+    #[error("Ontology client is not connected")]
+    NotConnected,
 }

graph/src/indexer.rs

@@ -1,16 +1,12 @@
 use rayon::iter::ParallelIterator;
 use std::collections::{HashMap, HashSet};
 use oxigraph::model::{Graph, NamedNode, TermRef, NamedOrBlankNodeRef, NamedNodeRef};
-use oxigraph::sparql::results::{QueryResultsFormat, QueryResultsParser, SliceQueryResultsParserOutput};
 use rayon::iter::IntoParallelRefIterator;
-use gl_inference::tonic::transport::Channel;
-use gl_inference::proto::ontology_client::OntologyClient;
-use gl_inference::proto::OntologyQueryRequest;
 use gl_search::{Field, OwnedValue, Schema};
 use crate::class::Class;
 use crate::{helpers, vocab, CurieHelper};
-use crate::helpers::{term_as_str, term_to_named_node};
 use crate::language::LanguageCondition;
+use crate::ontology::ResourceDescription;
 
 pub struct Indexer<'a> {
     language: LanguageCondition,
@@ -83,7 +79,7 @@ impl<'a> Indexer<'a> {
         ])
     }
 
-    pub fn graph(&self, graph: &Graph) -> crate::Result<Vec<HashMap<Field, OwnedValue>>> {
+    pub fn graph(&self, graph: &Graph) -> Vec<HashMap<Field, OwnedValue>> {
         let mut entities_and_types = HashSet::new();
         let triples = graph.triples_for_predicate(vocab::rdf::TYPE);
         for triple in triples {
@@ -119,85 +115,42 @@ impl<'a> Indexer<'a> {
                 })
             }).collect();
 
-        Ok(results)
+        results
     }
 
-    pub async fn ontology(&self, client: &mut OntologyClient<Channel>) -> crate::Result<Vec<HashMap<Field, OwnedValue>>> {
-        let filter = LanguageCondition::filter([
-            (String::from("label"), self.language.clone()),
-            (String::from("description"), self.language.clone()),
-        ]);
+    pub fn ontology(&self, entities: HashMap<NamedNode, (NamedNode, ResourceDescription)>) -> Vec<HashMap<Field, OwnedValue>> {
+        let label_field = Schema::field("label", self.language.primary_language());
+        let definition_field = Schema::field("definition", self.language.primary_language());
 
-        let mut request = OntologyQueryRequest::default();
-        request.sparql_query = Some(format!(r#"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
-
-SELECT ?class ?subject ?label ?description WHERE {{
-    VALUES ?class {{ rdf:Property rdfs:Class skos:Concept }}
-    ?subject a ?class ;
-    	rdfs:label ?label .
-
-    OPTIONAL {{ ?subject rdfs:comment ?comment }}
-    OPTIONAL {{ ?subject skos:definition ?definition }}
-    BIND(COALESCE(?definition, ?comment) AS ?description)
-    {filter}
-}}"#));
-
-        let response = client.query(request).await?;
-        let parser_output = QueryResultsParser::from_format(QueryResultsFormat::Json)
-            .for_slice(&response.get_ref().results)?;
-
-        let mut results = Vec::new();
-        if let SliceQueryResultsParserOutput::Solutions(solutions) = parser_output {
-            let primary_language = self.language.primary_language();
-            let label_field = Schema::field("label", primary_language);
-            let definition_field = Schema::field("definition", primary_language);
-            for solution in solutions.filter_map(Result::ok) {
+        entities.iter()
+            .map(|(subject, (class, description))| {
                 let mut document = HashMap::with_capacity(4);
 
-                let discriminant = solution
-                    .get("class")
-                    .and_then(term_to_named_node)
-                    .and_then(Class::try_from_named_node)
+                let discriminant = Class::try_from_named_node(class)
                     .map(|doc_type| doc_type as u64)
                     .map(OwnedValue::U64)
                     .unwrap_or(OwnedValue::Null);
                 document.insert(Schema::discriminant_field(), discriminant);
 
-                let subject_str = solution
-                    .get("subject")
-                    .and_then(term_to_named_node)
-                    .map(NamedNode::as_str);
-
-                let curie = subject_str
-                    .and_then(|subject| self.curie_helper.abbreviate(None, subject))
+                let curie = self.curie_helper.abbreviate(None, subject.as_str())
                     .map(OwnedValue::Str)
                     .unwrap_or(OwnedValue::Null);
                 document.insert(Schema::curie_field(), curie);
 
-                let subject = subject_str
-                    .map(OwnedValue::from)
-                    .unwrap_or(OwnedValue::Null);
+                let subject = OwnedValue::from(subject.as_str());
                 document.insert(Schema::iri_field(), subject);
 
-                let label = solution
-                    .get("label")
-                    .and_then(term_as_str)
+                let label = description.label.clone()
                     .map(OwnedValue::from)
                     .unwrap_or(OwnedValue::Null);
                 document.insert(label_field, label);
 
-                let definition = solution
-                    .get("description")
-                    .and_then(term_as_str)
+                let definition = description.description.clone()
                     .map(OwnedValue::from)
                     .unwrap_or(OwnedValue::Null);
                 document.insert(definition_field, definition);
 
-                results.push(document);
-            }
-        }
-        Ok(results)
+                document
+            }).collect()
     }
 }

graph/src/language.rs

@@ -53,47 +53,35 @@ impl LanguageCondition {
         }
     }
 
-    pub fn filter(conditions: impl IntoIterator<Item = (String, Self)>) -> String {
-        let exact_expression = |variable: String, language| Expression::FunctionCall(
+    pub fn filter(&self, variable: impl Into<String>) -> String {
+        let variable = variable.into();
+
+        let exact = |language: &LanguageTag<String>| Expression::FunctionCall(
             Function::LangMatches, vec![
                 Expression::FunctionCall(Function::Lang, vec![
-                    Expression::Variable(Variable::new_unchecked(variable))
+                    Expression::Variable(Variable::new_unchecked(&variable))
                 ]),
-                Expression::Literal(Literal::new_simple_literal(language))
+                Expression::Literal(Literal::new_simple_literal(language.to_string()))
             ],
         );
-
-        let untagged_expression = |variable| Expression::Not(
+        
+        let untagged = Expression::Not(
             Box::new(Expression::FunctionCall(Function::HasLang, vec![
-                Expression::Variable(Variable::new_unchecked(variable))
+                Expression::Variable(Variable::new_unchecked(&variable))
             ]))
         );
 
-        let condition_to_expression = |variable, condition| match condition {
-            LanguageCondition::ExactMatchOnly(language) =>
-                Some(exact_expression(variable, language.to_string())),
-            LanguageCondition::ExactMatchOrUntagged(language) => {
-                Some(Expression::Or(
-                    Box::new(exact_expression(variable.clone(), language.to_string())),
-                    Box::new(untagged_expression(variable)),
-                ))
-            }
-            LanguageCondition::UntaggedOnly => Some(untagged_expression(variable)),
-            LanguageCondition::AnyOrNone => None,
-        };
-
-        let mut iter = conditions.into_iter();
-        let first_expression = iter.next()
-            .and_then(|(variable, condition)| condition_to_expression(variable, condition));
-        if let Some(expression) = first_expression {
-            let expr = iter.filter_map(|(variable, condition)| condition_to_expression(variable, condition))
-                .fold(expression, |acc, next_exp| Expression::Or(Box::new(acc), Box::new(next_exp)));
-            GraphPattern::Filter {
-                expr,
-                inner: Box::new(GraphPattern::Bgp { patterns: vec![] }),
-            }.to_string()
-        } else {
-            String::default()
-        }
+        match self {
+            Self::ExactMatchOnly(language) => Some(exact(language)),
+            Self::ExactMatchOrUntagged(language) => Some(Expression::Or(
+                Box::new(exact(language)),
+                Box::new(untagged),
+            )),
+            Self::UntaggedOnly => Some(untagged),
+            Self::AnyOrNone => None,
+        }.map(|expr| GraphPattern::Filter {
+            expr,
+            inner: Box::new(GraphPattern::Bgp { patterns: vec![] }),
+        }.to_string()).unwrap_or_default()
     }
 }

graph/src/ontology.rs

@@ -1,12 +1,13 @@
 use std::collections::{HashMap, HashSet};
 use std::fmt::Debug;
+use std::str::FromStr;
 use oxigraph::io::{RdfFormat, RdfParser, RdfSerializer};
-use oxigraph::model::{Graph, NamedNode, Triple, TripleRef};
+use oxigraph::model::{Graph, NamedNode, NamedNodeRef, Triple};
 use oxigraph::sparql::results::{QueryResultsFormat, QueryResultsParser, SliceQueryResultsParserOutput};
-use tracing::debug;
+use spargebra::algebra::GraphPattern;
+use spargebra::term::{GroundTerm, Variable};
 use gl_inference::proto::ontology_client::OntologyClient;
 use gl_inference::proto::OntologyQueryRequest;
-use gl_inference::tonic::codegen::StdError;
 use gl_inference::tonic::transport::{Channel, Endpoint};
 use crate::helpers::{term_as_str, term_to_named_node};
 use crate::language::LanguageCondition;
@@ -24,31 +25,51 @@ pub enum ReadOnlyEntity {
     Class(NamedNode),
 }
 
+pub struct OntologyBuilder {
+    endpoint: Endpoint,
+    language: LanguageCondition,
+}
+
+impl OntologyBuilder {
+    pub fn from_string(endpoint: &str, language: LanguageCondition) -> crate::Result<Self> {
+        let endpoint = Endpoint::from_str(endpoint)?
+            .connect_timeout(std::time::Duration::from_secs(10))
+            .tcp_keepalive(Some(std::time::Duration::from_secs(30)))
+            .http2_keep_alive_interval(std::time::Duration::from_secs(15))
+            .keep_alive_timeout(std::time::Duration::from_secs(20))
+            .keep_alive_while_idle(true);
+
+        Ok(Self {
+            endpoint,
+            language,
+        })
+    }
+
+    pub async fn connect(self) -> crate::Result<ConnectedOntology> {
+        let client = OntologyClient::connect(self.endpoint)
+            .await?
+            .max_decoding_message_size(1024 * 1024 * 1024);
+
+        Ok(ConnectedOntology {
+            client,
+            language: self.language,
+        })
+    }
+}
+
 #[derive(Clone)]
-pub struct Ontology {
+pub struct ConnectedOntology {
     client: OntologyClient<Channel>,
     language: LanguageCondition,
 }
 
-impl Debug for Ontology {
+impl Debug for ConnectedOntology {
     fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
         f.write_str("ontology")
     }
 }
 
-impl Ontology {
-    pub async fn new<D>(endpoint: D, language: LanguageCondition) -> crate::Result<Self>
-    where
-        D: TryInto<Endpoint>,
-        D::Error: Into<StdError>,
-    {
-        let client = OntologyClient::connect(endpoint).await?;
-        Ok(Self {
-            client,
-            language,
-        })
-    }
-
+impl ConnectedOntology {
     pub async fn run_inference(&mut self, graph: &Graph) -> crate::Result<Graph> {
         let mut output_buffer = Vec::new();
         let mut serializer = RdfSerializer::from_format(RdfFormat::Turtle)
@@ -118,23 +139,24 @@ SELECT ?subject ?class WHERE {{
     }
 
     pub async fn datatypes(&mut self) -> crate::Result<HashMap<NamedNode, ResourceDescription>> {
-        let filter = LanguageCondition::filter([
-            (String::from("label"), self.language.clone()),
-            (String::from("description"), self.language.clone()),
-        ]);
+        let label_filter = self.language.filter("label");
+        let comment_filter = self.language.filter("comment");
 
         let mut request = OntologyQueryRequest::default();
         request.sparql_query = Some(format!(r#"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 
-SELECT ?subject ?label ?description WHERE {{
-    ?subject a rdfs:Datatype
-    OPTIONAL {{ ?subject rdfs:label ?label }}
-    OPTIONAL {{ ?subject rdfs:comment ?comment }}
-    OPTIONAL {{ ?subject skos:definition ?definition }}
-    BIND(COALESCE(?definition, ?comment) AS ?description)
-    {filter}
+SELECT ?subject ?label ?comment WHERE {{
+    OPTIONAL {{
+        ?subject a rdfs:Datatype
+    }} OPTIONAL {{
+        ?subject rdfs:label ?label
+        {label_filter}
+    }} OPTIONAL {{
+        ?subject rdfs:comment ?comment
+        {comment_filter}
+    }}
 }}"#));
 
         let response = self.client.query(request).await?;
@@ -167,12 +189,10 @@ SELECT ?subject ?label ?description WHERE {{
         Ok(results)
     }
 
-    pub async fn resource_description(&mut self, subject: NamedNode) -> crate::Result<ResourceDescription> {
-        let filter = LanguageCondition::filter([
-            (String::from("label"), self.language.clone()),
-            (String::from("description"), self.language.clone()),
-        ]);
-        debug!("Filter: {filter}");
+    pub async fn resource_description_from_subject(&mut self, subject: NamedNode) -> crate::Result<ResourceDescription> {
+        let label_filter = self.language.filter("label");
+        let comment_filter = self.language.filter("comment");
+        let definition_filter = self.language.filter("definition");
 
         let mut request = OntologyQueryRequest::default();
         request.sparql_query = Some(format!(r#"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
@@ -180,13 +200,21 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 
 SELECT ?label ?description WHERE {{
-    OPTIONAL {{ {subject} rdfs:label ?label }}
-    OPTIONAL {{ {subject} rdfs:comment ?comment }}
-    OPTIONAL {{ {subject} skos:definition ?definition }}
+    OPTIONAL {{
+        {subject} rdfs:label ?label
+        {label_filter}
+    }} OPTIONAL {{
+        {subject} rdfs:comment ?comment
+        {comment_filter}
+    }} OPTIONAL {{
+        {subject} skos:definition ?definition
+        {definition_filter}
+    }}
     BIND(COALESCE(?definition, ?comment) AS ?description)
-    {filter}
 }}"#));
 
+        let foo = request.sparql_query.clone().unwrap();
+
         let response = self.client.query(request).await?;
         let parser_output = QueryResultsParser::from_format(QueryResultsFormat::Json)
             .for_slice(&response.get_ref().results)?;
@@ -213,4 +241,79 @@ SELECT ?label ?description WHERE {{
             )
         } else { unreachable!() }
     }
+
+    fn named_nodes_to_values_expression<'a>(variable: &str, nodes: impl IntoIterator<Item = NamedNodeRef<'a>>) -> String {
+        let bindings = nodes.into_iter()
+            .map(|node| GroundTerm::NamedNode(node.into_owned()))
+            .map(Some)
+            .map(|item| vec![item])
+            .collect();
+
+        GraphPattern::Values {
+            variables: vec![Variable::new_unchecked(variable)],
+            bindings,
+        }.to_string()
+    }
+
+    pub async fn resource_descriptions_from_classes<'a>(&mut self, classes: impl IntoIterator<Item = NamedNodeRef<'a>>) -> crate::Result<HashMap<NamedNode, (NamedNode, ResourceDescription)>> {
+        let values = Self::named_nodes_to_values_expression("class", classes);
+        let label_filter = self.language.filter("label");
+        let comment_filter = self.language.filter("comment");
+        let definition_filter = self.language.filter("definition");
+
+        let mut request = OntologyQueryRequest::default();
+        request.sparql_query = Some(format!(r#"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+
+SELECT ?class ?subject ?label ?description WHERE {{
+    {values}
+    ?subject a ?class .
+    OPTIONAL {{
+    	?subject rdfs:label ?label .
+    	{label_filter}
+    }} OPTIONAL {{
+        ?subject rdfs:comment ?comment .
+        {comment_filter}
+    }} OPTIONAL {{
+        ?subject skos:definition ?definition .
+        {definition_filter}
+    }}
+    BIND(COALESCE(?definition, ?comment) AS ?description)
+}}"#));
+
+        let response = self.client.query(request).await?;
+        let parser_output = QueryResultsParser::from_format(QueryResultsFormat::Json)
+            .for_slice(&response.get_ref().results)?;
+
+        let mut results = HashMap::new();
+        if let SliceQueryResultsParserOutput::Solutions(solutions) = parser_output {
+            for solution in solutions.filter_map(Result::ok) {
+                let class = solution
+                    .get("class")
+                    .and_then(term_to_named_node);
+
+                let subject = solution
+                    .get("subject")
+                    .and_then(term_to_named_node)
+                    .map(|node| node.clone());
+
+                if let Some(subject) = subject &&
+                    let Some(class) = class {
+                    let label = solution
+                        .get("label")
+                        .and_then(term_as_str)
+                        .map(String::from);
+
+                    let description = solution
+                        .get("description")
+                        .and_then(term_as_str)
+                        .map(String::from);
+
+                    results.insert(subject, (class.clone(), ResourceDescription { label, description }));
+                }
+            }
+        }
+        Ok(results)
+    }
 }