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Fix serialization of blank nodes #39

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Merged
jamesaoverton merged 1 commit into from
May 26, 2026
Merged

Fix serialization of blank nodes #39

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81 changes: 32 additions & 49 deletions src/ldtab/thick_rdf.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -164,67 +164,50 @@
(and (string? input)
(str/starts-with? input "<ldtab:blanknode")))

(defn blanknode-triple-map
[blanknode-triples]
(cs/generate-string
(into {}
(map (fn [{:keys [predicate object datatype]}]
[predicate [{"object" (parse-json object),
"datatype" datatype}]])
blanknode-triples))))

(defn merge-existential-blanknodes
"Merge thin triples belonging to the same existential blank nodes into a 'raw' LDTab triple."
[triples]
(let [blanknodes (filter #(is-ldtab-blanknode (:subject %)) triples)
blanknode-2-triples (group-by :subject blanknodes)
complex-blanknodes (into {} (filter (fn [[k v]] (> (count v) 1)) blanknode-2-triples))
triples (remove #(contains? complex-blanknodes (:subject %)) triples)
raw-blank-nodes (map (fn [[k v]] {:assertion (:assertion (first v)),
:retraction (:retraction (first v)),
:graph (:graph (first v)),
:subject k,
:predicate "unknown",
:object (blanknode-triple-map v),
:datatype "_JSONMAP",
:annotation (:annotation (first v))})
complex-blanknodes)
final (concat triples raw-blank-nodes)]
final))
(defn resolve-subject ^Resource
[subject-string prefix-2-base ^Model model skolem-bnode]
(let [subject-json (parse-json subject-string)]
(cond
skolem-bnode skolem-bnode
(string? subject-json) (translate-iri subject-json prefix-2-base model)
:else (translate-json-map subject-json prefix-2-base model))))

(defn thick-row->triples
[^Model model prefix-2-base skolem-bnode row]
(let [tt {"object" (parse-json-object row)
"datatype" (:datatype row)}
subject (resolve-subject (:subject row) prefix-2-base model skolem-bnode)
predicate (translate-property (:predicate row) prefix-2-base model)
object (translate-predicate-map tt prefix-2-base model)
annotation (parse-json (:annotation row))]
(when annotation
(translate-annotation subject predicate object annotation prefix-2-base model))
(.add model subject predicate object)))

(defn thick-2-rdf-model ^Model
[thick-triple prefixes]
(let [;{:keys [assertion retraction graph s p o datatype annotation]} thick-triple
model (set-prefix-map (ModelFactory/createDefaultModel) prefixes)
(let [model (set-prefix-map (ModelFactory/createDefaultModel) prefixes)
prefix-2-base (get-prefix-map prefixes)
tt {"object" (parse-json-object thick-triple)
"datatype" (:datatype thick-triple)}
;subject (translate-iri (:subject thick-triple) prefix-2-base model)
;provisional handling of GCIs (with JSON objects in the position of subject column)
subject-json (parse-json (:subject thick-triple))
subject (if (string? subject-json)
(translate-iri 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))]
(when annotation
(translate-annotation subject predicate object annotation prefix-2-base model))
(if (is-ldtab-blanknode subject-json)
model ;remove generated ldtab:blank nodes
(.add model subject predicate object))))
skolem-bnode (when (is-ldtab-blanknode (:subject thick-triple))
(.createResource model))]
(thick-row->triples model prefix-2-base skolem-bnode thick-triple)
model))

(defn triples-2-rdf-model-stream
[thick-triples prefixes output]
(let [thick-triples (merge-existential-blanknodes thick-triples)
out-stream (io/output-stream output)
(let [out-stream (io/output-stream output)
model (set-prefix-map (ModelFactory/createDefaultModel) prefixes)
prefix-2-base (get-prefix-map prefixes)
prefix-map (.lock model)
writer-stream (StreamRDFWriter/getWriterStream out-stream RDFFormat/TURTLE_BLOCKS)]
(.start writer-stream)
(StreamRDFOps/sendPrefixesToStream prefix-map writer-stream)
(doseq [triple thick-triples]
(StreamRDFOps/sendTriplesToStream (.getGraph (thick-2-rdf-model triple prefixes)) writer-stream))
(doseq [[subject rows] (group-by :subject thick-triples)]
(let [m (set-prefix-map (ModelFactory/createDefaultModel) prefixes)
skolem-bnode (when (is-ldtab-blanknode subject) (.createResource m))]
(doseq [row rows]
(thick-row->triples m prefix-2-base skolem-bnode row))
(StreamRDFOps/sendTriplesToStream (.getGraph m) writer-stream)))
(.finish writer-stream)))

(defn load-db
Expand Down
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