Merge pull request #25 from ontodev/rdf-lists

Change format for RDF lists

src/ldtab/rdf_list_handling.clj

@@ -0,0 +1,66 @@
+(ns ldtab.rdf-list-handling
+  (:require [cheshire.core :as cs])
+  (:gen-class))
+
+(declare encode-rdf-list)
+
+(defn collect-list-elements [json acc]
+  (let [element (first (get json "rdf:first"))
+        remainder (:object (first (get json "rdf:rest")))]
+    (if (= remainder "rdf:nil")
+      (conj acc element)
+      (recur remainder (conj acc element)))))
+
+(defn is-top-level-rdf-list? [json]
+  (if (and (map? json)
+           (contains? json :subject)
+           (contains? json :predicate)
+           (contains? json :object))
+    (let [object (:object json)
+          datatype (:datatype json)]
+      (and (map? object)
+           (contains? object "rdf:first")
+           (contains? object "rdf:rest")
+           (= datatype "_JSONMAP")))
+    false))
+
+(defn is-rdf-list? [json]
+  (if (map? json)
+    (let [object (:object json)
+          datatype (:datatype json)]
+      (and (map? object)
+           (contains? object "rdf:first")
+           (contains? object "rdf:rest")
+           (= datatype "_JSONMAP")))
+    false))
+
+;json is required to be an rdf list
+(defn encode-rdf-list-object [json]
+  (let [elements (collect-list-elements json [])
+        encoded-elements (map #(encode-rdf-list %) elements)]
+    {:object (into [] encoded-elements)
+     :datatype "_JSONLIST"}))
+
+(defn map-on-hash-map-vals
+  "Given a hashmap m and a function f, 
+  apply f to all values of m.
+  Example:
+  Given m = {:a 1, :b 2}  and f = (fn [x] (inc x)),
+  then (map-on-hash-map-vals f m) = {:a 2, :b 3}"
+  [f m]
+  (zipmap (keys m) (map f (vals m))))
+
+(defn encode-top-level-rdf-list [json]
+  (let [object (:object json)
+        list-object (:object (encode-rdf-list-object object))]
+    (assoc json :object list-object :datatype "_JSONLIST")))
+
+(defn encode-rdf-list
+  "Given a JSON value, return a lexicographically ordered representation."
+  [m]
+  (cond
+    (is-top-level-rdf-list? m) (encode-top-level-rdf-list m)
+    (is-rdf-list? m) (encode-rdf-list-object (:object m))
+    (map? m) (map-on-hash-map-vals encode-rdf-list m)
+    (coll? m) (into [] (map encode-rdf-list m))
+    :else m))

src/ldtab/thick_rdf.clj

@@ -63,7 +63,7 @@
   (let [uri (curie-2-uri datatype prefix-2-base)]
     (.createTypedLiteral model literal uri)))
 
-(defn translate-json ^Resource
+(defn translate-json-map ^Resource
   [json prefix-2-base ^Model model]
   (let [bnode (.createResource model)]
     (doseq [k (keys json)]
@@ -74,11 +74,27 @@
               (translate-predicate-map x prefix-2-base model))))
     bnode))
 
+(defn translate-rdf-list ^Resource
+  [json prefix-2-base ^Model model]
+  (let [bnode (.createResource model)
+        rdf-first (.createProperty model (curie-2-uri "rdf:first" prefix-2-base))
+        rdf-rest (.createProperty model (curie-2-uri "rdf:rest" prefix-2-base))
+        rdf-nil (.createResource model (curie-2-uri "rdf:nil" prefix-2-base))
+        rdf-type (.createProperty model (curie-2-uri "rdf:type" prefix-2-base))
+        rdf-first-value (first json)
+        rdf-rest-value (rest json)]
+    (.add model bnode rdf-first (translate-predicate-map rdf-first-value prefix-2-base model))
+    (if (and rdf-rest-value (not (empty? rdf-rest-value)))
+      (.add model bnode rdf-rest (translate-rdf-list rdf-rest-value prefix-2-base model))
+      (.add model bnode rdf-rest rdf-nil))
+    bnode))
+
 (defn translate-predicate-map ^Resource
   [predicateMap prefix-2-base ^Model model]
   (case (get predicateMap "datatype")
     "_IRI" (translate-iri (get predicateMap "object") prefix-2-base model)
-    "_JSON" (translate-json (get predicateMap "object") prefix-2-base model)
+    "_JSONMAP" (translate-json-map (get predicateMap "object") prefix-2-base model)
+    "_JSONLIST" (translate-rdf-list (get predicateMap "object") prefix-2-base model)
     (translate-literal (get predicateMap "object") (get predicateMap "datatype") prefix-2-base model)))
 
 (defn translate-annotation ^Resource
@@ -126,7 +142,9 @@
   (let [success (try
                   (cs/parse-string json)
                   (catch Exception e nil))
-        success (map? success)]
+        success (or (map? success)
+                    (coll? success)
+                    (seq? success))]
     (if success
       (cs/parse-string json)
       json)))
@@ -148,7 +166,7 @@
         subject-json (parse-json (:subject thick-triple))
         subject (if (string? subject-json)
                   (translate-iri subject-json prefix-2-base model)
-                  (translate-json subject-json prefix-2-base model))
+                  (translate-json-map subject-json prefix-2-base model))
         predicate (translate-property (:predicate thick-triple) prefix-2-base model)
         object (translate-predicate-map tt prefix-2-base model)
         annotation (parse-json (:annotation thick-triple))]

src/ldtab/thin2thick.clj

@@ -2,6 +2,7 @@
   (:require [clojure.set :as set]
             [clojure.string :as str]
             [ldtab.annotation-handling :as ann]
+            [ldtab.rdf-list-handling :as rdf-list]
             [ldtab.gci-handling :as gci]
             [cheshire.core :as cs])
   (:import [org.apache.jena.graph NodeFactory Triple Node])
@@ -119,7 +120,7 @@
 (defn get-datatype
   ([^Node node]
    (cond
-     (.isBlank node) "_JSON"
+     (.isBlank node) "_JSONMAP"
      (.isURI node) "_IRI"
     ;NB: Jena can't identify plain literals
      (.isLiteral node) (let [datatype (.getLiteralDatatypeURI node)
@@ -130,7 +131,7 @@
      :else "ERROR"))
   ([^Node node iri2prefix]
    (cond
-     (.isBlank node) "_JSON"
+     (.isBlank node) "_JSONMAP"
      (.isURI node) "_IRI"
      ;NB: Jena can't identify plain literals
      (.isLiteral node) (let [datatype (curify-with (.getLiteralDatatypeURI node) iri2prefix)
@@ -206,11 +207,30 @@
   "Given a JSON value, return a lexicographically ordered representation."
   [m]
   (cond
-    (map? m) (into (sorted-map) (map-on-hash-map-vals sort-json m)) ;sort by key
-    (coll? m) (vec (map cs/parse-string ;sort by string comparison
-                        (sort (map #(cs/generate-string (sort-json %))
-                                   m))))
-    :else m))
+    ; sort RDF lists
+    (and (map? m)
+         (contains? m :datatype)
+         (= (:datatype m) "_JSONLIST"))
+    (let [sorted-list {:datatype "_JSONLIST", :object (map sort-json (:object m))}]
+      (if (contains? m :subject) ; top-level RDF list
+        (into (sorted-map) (merge sorted-list
+                                  {:subject (sort-json (:subject m))
+                                   :predicate (:predicate m)
+                                   :graph (:graph m)
+                                   :assertion (:assertion m)
+                                   :retraction (:retraction m)
+                                   :annotation (:annotation m)}))
+        (into (sorted-map) sorted-list))); nested RDF list
+
+    (map? m)
+    (into (sorted-map) (map-on-hash-map-vals sort-json m)) ; sort by key
+
+    (coll? m)
+    (vec (map cs/parse-string ; sort by string comparison
+              (sort (map #(cs/generate-string (sort-json %)) m))))
+
+    :else
+    m))
 
 (defn map-subject-2-thin-triples
   "Given a set of thin triples,
@@ -263,7 +283,8 @@
                                    (= (:predicate %) "rdf:Statement"))
                              (ann/encode-raw-annotation-map (:object %))
                              %) gcis)
-         sorted (map sort-json annotations)
+         rdf-lists (map rdf-list/encode-rdf-list annotations)
+         sorted (map sort-json rdf-lists)
          hashed (map hash-existential-subject-blanknode sorted)
          normalised (map #(cs/parse-string (cs/generate-string %)) hashed)];TODO: stringify keys - this is a (probably an inefficient?) workaround 
      normalised))
@@ -277,7 +298,8 @@
                                    (= (:predicate %) "rdf:Statement"))
                              (ann/encode-raw-annotation-map (:object %))
                              %) gcis)
-         sorted (map sort-json annotations)
+         rdf-lists (map rdf-list/encode-rdf-list annotations)
+         sorted (map sort-json rdf-lists)
          hashed (map hash-existential-subject-blanknode sorted)
          normalised (map #(cs/parse-string (cs/generate-string %)) hashed)];TODO: stringify keys - this is a (probably an inefficient?) workaround 
      normalised)))