Merge pull request #7 from yetanalytics/collections

[PS-455] Implement RDF List and blank node collection syntax

Author: kelvinqian00

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 
+## 0.1.3
+- Support RDF List and blank node collection syntactic sugar.
+
 ## 0.1.2
 - Update Jena version to 4.8.0 to address [CVE-2023-22665](https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2023-22665).
 

README.md

@@ -8,12 +8,12 @@
 
 A companion library to [Flint](https://github.com/yetanalytics/flint) for the direct compilation of Flint data into [Apache Jena](https://jena.apache.org/)-based SPARQL queries and updates.
 
-Uses Flint version [v0.2.1](https://github.com/yetanalytics/flint/releases/tag/v0.2.1).
+Uses Flint version [v0.3.0](https://github.com/yetanalytics/flint/releases/tag/v0.3.0).
 
 ## Installation
 
 ```clojure
-{com.yetanalytics/flint-jena {:mvn/version "0.1.2"
+{com.yetanalytics/flint-jena {:mvn/version "0.1.3"
                               :exclusions [org.clojure/clojure]}}
 ```
 
@@ -72,4 +72,3 @@ Which then outputs the following to `target/bench/query.txt`:
 Copyright © 2022-2024 Yet Analytics, Inc.
 
 Distributed under the Apache License version 2.0.
-

deps.edn

@@ -5,7 +5,7 @@
         org.apache.jena/jena-arq  {:mvn/version "4.8.0"
                                    :exclusions  [org.slf4j/slf4j-api]}
         org.slf4j/slf4j-api       {:mvn/version "1.7.36"}
-        com.yetanalytics/flint    {:mvn/version "0.2.1"
+        com.yetanalytics/flint    {:mvn/version "0.3.0"
                                    :exclusions  [org.clojure/clojure
                                                  org.clojure/clojurescript]}}
  :aliases

dev-resources/test-fixtures/query/select/select-15.edn

@@ -0,0 +1,3 @@
+;; SELECT with lists
+{:select [?x]
+ :where  [[?s ?p (1 ?x 3 4)]]}

dev-resources/test-fixtures/query/select/select-16.edn

@@ -0,0 +1,7 @@
+;; SELECT with blank node vectors
+{:prefixes {:$    "<http://foo.org/>"
+            :foaf "<http://xmlns.com/foaf/0.1/>"}
+ :select   [?x ?name]
+ :where    [{[:p1 "v"] {:q1 #{"w"}}
+             :xxxxxxxx {:q2 #{[:p2 "v"]}}
+             [:foaf/name ?name :foaf/mbox "<mailto:bar@example.com>"] {}}]}

dev-resources/test-fixtures/query/select/select-17.edn

@@ -0,0 +1,4 @@
+;; SELECT with empty lists and blank node vectors
+{:select [?x ?y]
+ :where  [[() ?x []]
+          [[] ?y ()]]}

src/main/com/yetanalytics/flint_jena/triple.clj

@@ -1,6 +1,8 @@
 (ns com.yetanalytics.flint-jena.triple
   (:require [com.yetanalytics.flint-jena.ast :as ast])
   (:import [org.apache.jena.graph Node Triple]
+           [org.apache.jena.sparql.graph NodeConst]
+           [org.apache.jena.sparql.lang LabelToNodeMap]
            [org.apache.jena.sparql.path Path]
            [org.apache.jena.sparql.core
             BasicPattern
@@ -10,72 +12,7 @@
            [org.apache.jena.sparql.syntax
             ElementPathBlock
             ElementTriplesBlock
-            TripleCollector
-            TripleCollectorMark]))
-
-;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
-;; AST Methods
-;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
-
-;; These multimethod dispatches (specifically `:triple/vec` and `triple/nform`)
-;; return ElementPathBlocks since that is the most general syntax Element that
-;; can be used in all clauses (WHERE, CONSTRUCT, DELETE, INSERT, etc).
-
-(defmethod ast/ast-node->jena :triple/path [_ [_ path]]
-  path)
-
-(defprotocol Predicate
-  (-create-triple
-    [pred subj obj])
-  (-add-triple!
-    [pred subj obj triples]
-    [pred subj obj triples idx]))
-
-(extend-protocol Predicate
-  Node
-  (-create-triple
-    [p s o]
-    (Triple. s p o))
-  (-add-triple!
-    ([p s o ^TripleCollector coll]
-     (.addTriple coll ^Triple (-create-triple p s o)))
-    ([p s o ^TripleCollectorMark coll idx]
-     (.addTriple coll idx ^Triple (-create-triple p s o))))
-
-  Path
-  (-create-triple
-   [p s o]
-   (TriplePath. s p o))
-  (-add-triple!
-   ([p s o ^TripleCollector coll]
-    (.addTriplePath coll ^TriplePath (-create-triple p s o)))
-   ([p s o ^TripleCollectorMark coll idx]
-    (.addTriplePath coll idx ^TriplePath (-create-triple p s o)))))
-
-(defmethod ast/ast-node->jena :triple/vec [_ [_ [s p o]]]
-  (let [triple-block (ElementPathBlock.)]
-    (-add-triple! p s o triple-block)
-    triple-block))
-
-(defmethod ast/ast-node->jena :triple/nform [_ [_ nform]]
-  (let [triple-block (ElementPathBlock.)]
-    (dorun (map-indexed
-            (fn [idx [s p o]] (-add-triple! p s o triple-block idx))
-            nform))
-    triple-block))
-
-(defmethod ast/ast-node->jena :triple/spo [_ [_ spo]]
-  (mapcat (fn [[s po-coll]]
-            (map (fn [[p o]] [s p o]) po-coll))
-          spo))
-
-(defmethod ast/ast-node->jena :triple/po [_ [_ po]]
-  (mapcat (fn [[p o-coll]]
-            (map (fn [o] [p o]) o-coll))
-          po))
-
-(defmethod ast/ast-node->jena :triple/o [_ [_ o]]
-  o)
+            TripleCollector]))
 
 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 ;; Triple Conversion
@@ -146,3 +83,196 @@
                  :let   [quad (Quad. graph-node triple)]]
              (.add pattern quad)))
     pattern))
+
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+;; Protocols
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+
+(defprotocol SubjectObject
+  "Protocol for triple subjects and objects. This covers RDF Lists,
+    blank node collections, and regular nodes."
+  (-head-node [subject-or-object]
+    "Return the Node that external Triples should point to..")
+  (-nested-triples [subject-or-object]
+    "Return any Triples that are nested in the subject or object."))
+
+(extend-protocol SubjectObject
+  Node
+  (-head-node [node] node)
+  (-nested-triples [_] []))
+
+(defrecord RDFList [first-node triples]
+  SubjectObject
+  (-head-node [_] first-node)
+  (-nested-triples [_] (triple-element->seq triples)))
+
+(defrecord BlankNodeColl [subject-node triples]
+  SubjectObject
+  (-head-node [_] subject-node)
+  (-nested-triples [_] (triple-element->seq triples)))
+
+(defprotocol Predicate
+  "Protocol for triple predicates. This covers paths and regular nodes."
+  (-create-triple [predicate subject object]
+    "Create a triple from `subject`, `predicate`, and `object`."))
+
+(extend-protocol Predicate
+  Node
+  (-create-triple [pred subj obj]
+    (Triple. subj pred obj))
+
+  Path
+  (-create-triple [pred subj obj]
+    (TriplePath. subj pred obj)))
+
+(defprotocol ASTTriple
+  "Protocol for triples (we can't call this \"Triple\" since that would clash
+    with Jena's Triple class)."
+  (-add-triple! [triple triple-acc]
+    "Add `triple` to `triple-acc` (which should be an instance of
+     TripleCollector)."))
+
+(extend-protocol ASTTriple
+  Triple
+  (-add-triple! [triple ^TripleCollector triple-acc]
+    (.addTriple triple-acc triple))
+  
+  TriplePath
+  (-add-triple! [triple-path ^TripleCollector triple-acc]
+    (.addTriplePath triple-acc triple-path)))
+
+(defn- create-triple [subj pred obj]
+  (-create-triple pred subj obj))
+
+(defn- add-triple! [triple-acc triple]
+  (-add-triple! triple triple-acc))
+
+(defn- add-triple-coll! [triple-acc triples]
+  (dorun (map (fn [triple] (add-triple! triple-acc triple))
+              triples)))
+
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+;; Blank Node + Triple Helpers
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+
+(def rdf-first NodeConst/nodeFirst)
+(def rdf-rest NodeConst/nodeRest)
+(def rdf-nil NodeConst/nodeNil)
+
+(defn- new-bnode! ^Node [^LabelToNodeMap bnode-m]
+  (.allocNode bnode-m))
+
+(defn- s->triples [s]
+  (or (not-empty (-nested-triples s))
+      (throw (ex-info "Subject without predicates or objects is not an RDF list or blank node collecton!"
+                      {:kind    ::illegal-subject
+                       :subject s}))))
+
+(defn- spo->triples [s p o]
+  (let [s-node    (-head-node s)
+        o-node    (-head-node o)
+        s-triples (-nested-triples s)
+        o-triples (-nested-triples o)
+        triple    (create-triple s-node p o-node)]
+    (concat s-triples [triple] o-triples)))
+
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+;; AST Methods
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+
+;; These multimethod dispatches (specifically `:triple.vec/spo` and
+;; `triple.nform/spo`) return ElementPathBlocks since that is the most general
+;; syntax Element that can be used in all clauses (WHERE, CONSTRUCT, DELETE,
+;; INSERT, etc).
+
+(defmethod ast/ast-node->jena :triple/path [_ [_ path]]
+  path)
+
+(defn- make-rdf-list [bnode-m list]
+  (let [triple-block (ElementPathBlock.)
+        init-node    (new-bnode! bnode-m)]
+    (loop [curr-bnode init-node
+           next-bnode (new-bnode! bnode-m)
+           list       list]
+      (if-some [list-entry (first list)]
+        (let [node         (-head-node list-entry)
+              triples      (-nested-triples list-entry)
+              first-triple (create-triple curr-bnode rdf-first node)
+              rest-triple  (if (some? (second list))
+                             (create-triple curr-bnode rdf-rest next-bnode)
+                             (create-triple curr-bnode rdf-rest rdf-nil))]
+          (add-triple! triple-block first-triple)
+          (add-triple-coll! triple-block triples)
+          (add-triple! triple-block rest-triple)
+          (recur next-bnode (new-bnode! bnode-m) (rest list)))
+        (->RDFList init-node triple-block)))))
+
+(defmethod ast/ast-node->jena :triple/list
+  [{:keys [active-bnode-map] :as opts} [_ list]]
+  (if (empty? list)
+    rdf-nil
+    (make-rdf-list (get opts @active-bnode-map) list)))
+
+(defn- make-bnode-coll [bnode-m po-pairs]
+  (let [triple-block (ElementPathBlock.)
+        subj-node    (new-bnode! bnode-m)]
+    (dorun
+     (for [[p o] po-pairs
+           :let [o-node    (-head-node o)
+                 o-triples (-nested-triples o)
+                 triple    (create-triple subj-node p o-node)]]
+       (do
+         (add-triple! triple-block triple)
+         (add-triple-coll! triple-block o-triples))))
+    (->BlankNodeColl subj-node triple-block)))
+
+(defmethod ast/ast-node->jena :triple/bnodes
+  [{:keys [active-bnode-map] :as opts} [_ po-pairs]]
+  (make-bnode-coll (get opts @active-bnode-map) po-pairs))
+
+;; Vectors
+
+(defmethod ast/ast-node->jena :triple.vec/spo [_ [_ [s p o]]]
+  (let [triple-block (ElementPathBlock.)
+        triples      (spo->triples s p o)]
+    (add-triple-coll! triple-block triples)
+    triple-block))
+
+(defmethod ast/ast-node->jena :triple.vec/s [_ [_ [s]]]
+  (let [triple-block (ElementPathBlock.)
+        triples      (s->triples s)]
+    (add-triple-coll! triple-block triples)
+    triple-block))
+
+;; Normal Forms
+
+(defmethod ast/ast-node->jena :triple.nform/spo [_ [_ spo]]
+  (let [triple-block (ElementPathBlock.)
+        triples      (mapcat
+                      (fn [[s po-coll]]
+                        (if (empty? po-coll)
+                          (s->triples s)
+                          (mapcat (fn [[p o]] (spo->triples s p o)) po-coll)))
+                      spo)]
+    (add-triple-coll! triple-block triples)
+    triple-block))
+
+(defmethod ast/ast-node->jena :triple.nform/po [_ [_ po]]
+  (mapcat (fn [[p o-coll]] (map (fn [o] [p o]) o-coll))
+          po))
+
+(defmethod ast/ast-node->jena :triple.nform/po-empty [_ _]
+  [])
+
+(defmethod ast/ast-node->jena :triple.nform/o [_ [_ o]]
+  o)
+
+;; Quads
+
+(defmethod ast/ast-node->jena :triple.quad/spo
+  [_opts [_ triple-elements]]
+  (triple-elements->basic-pattern triple-elements))
+
+(defmethod ast/ast-node->jena :triple.quad/gspo
+  [_opts [_ [graph-node triple-bgp]]]
+  (basic-pattern->quad-pattern triple-bgp graph-node))

src/main/com/yetanalytics/flint_jena/update.clj

@@ -123,14 +123,6 @@
 ;; Graph Update
 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 
-(defmethod ast/ast-node->jena :triple/quad-triples
-  [_opts [_ triple-elements]]
-  (t/triple-elements->basic-pattern triple-elements))
-
-(defmethod ast/ast-node->jena :triple/quads
-  [_opts [_ [graph-node triple-bgp]]]
-  (t/basic-pattern->quad-pattern triple-bgp graph-node))
-
 ;; Construct quad accumulators (i.e. QuadBlocks -> QuadAcc)
 ;; These are defined in this namespace since QuadAcc/QuadDataAcc are found
 ;; in the sparql.modify.request package, i.e. they're specific to updates.

src/main/com/yetanalytics/flint_jena/where.clj

@@ -186,3 +186,7 @@
 (defmethod ast/ast-node->jena :where/special
   [_ [_ element]]
   element)
+
+(defmethod ast/ast-node->jena :where/triple
+  [_ [_ element]]
+  element)