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Upgrade rdf4j to 3.0.0 #150

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merged 4 commits into from Aug 29, 2019
Merged

Upgrade rdf4j to 3.0.0 #150

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d6ef852
Upgrade rdf4j to 3.0.0 and fix incompatibilities
kiramclean Aug 29, 2019
c9871cc
Revise dependencies to include new artifact
RickMoynihan Aug 29, 2019
13430d4
support getting statements from rdf4j Models
kiramclean Aug 29, 2019
4277e53
Change CI to use openjdk8 as oracle no longer allow oraclejdk8
RickMoynihan Aug 29, 2019
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2 changes: 1 addition & 1 deletion .travis.yml
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Expand Up @@ -2,7 +2,7 @@ language: clojure
sudo: required
lein: 2.7.1
jdk:
- oraclejdk8
- openjdk8
before_install:
- sudo ./travis/setup-lein-travis.sh

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51 changes: 26 additions & 25 deletions project.clj
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@@ -1,4 +1,4 @@
(defproject grafter/grafter "2.0.3-SNAPSHOT"
(defproject grafter/grafter "2.0.4-SNAPSHOT"
:description "Tools for the hard graft of linked data processing"
:url "http://grafter.org/"
:license {:name "Eclipse Public License - v1.0"
Expand All @@ -10,36 +10,37 @@

:dependencies [[org.clojure/clojure "1.10.0"]

;;[org.eclipse.rdf4j/rdf4j-runtime "2.5.0" :exclusions [ch.qos.logback/logback-classic]]
;;[org.eclipse.rdf4j/rdf4j-runtime "3.0.0" :exclusions [ch.qos.logback/logback-classic]]

;; Include a smaller set of dependencies than we used
;; to by default, if you want everything from RDF4j
;; you can include:

;; [org.eclipse.rdf4j/rdf4j-runtime "2.5.0" :exclusions [ch.qos.logback/logback-classic]]
[org.eclipse.rdf4j/rdf4j-rio-api "2.5.0"]
[org.eclipse.rdf4j/rdf4j-rio-binary "2.5.0"]
[org.eclipse.rdf4j/rdf4j-rio-jsonld "2.5.0"]
[org.eclipse.rdf4j/rdf4j-rio-n3 "2.5.0"]
[org.eclipse.rdf4j/rdf4j-rio-nquads "2.5.0"]
[org.eclipse.rdf4j/rdf4j-rio-rdfjson "2.5.0"]
[org.eclipse.rdf4j/rdf4j-rio-rdfxml "2.5.0"]
[org.eclipse.rdf4j/rdf4j-rio-trig "2.5.0"]
[org.eclipse.rdf4j/rdf4j-rio-trix "2.5.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-api "2.5.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-binary "2.5.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-binary "2.5.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-sparqljson "2.5.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-sparqlxml "2.5.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-text "2.5.0"]

[org.eclipse.rdf4j/rdf4j-repository-api "2.5.0"]
[org.eclipse.rdf4j/rdf4j-repository-http "2.5.0"]
[org.eclipse.rdf4j/rdf4j-repository-sail "2.5.0"]
[org.eclipse.rdf4j/rdf4j-repository-dataset "2.5.0"]
[org.eclipse.rdf4j/rdf4j-sail-memory "2.5.0"]
[org.eclipse.rdf4j/rdf4j-sail-nativerdf "2.5.0"]
[org.eclipse.rdf4j/rdf4j-repository-manager "2.5.0"]
[org.eclipse.rdf4j/rdf4j-rio-api "3.0.0"]
[org.eclipse.rdf4j/rdf4j-rio-binary "3.0.0"]
[org.eclipse.rdf4j/rdf4j-rio-jsonld "3.0.0"]
[org.eclipse.rdf4j/rdf4j-rio-n3 "3.0.0"]
[org.eclipse.rdf4j/rdf4j-rio-nquads "3.0.0"]
[org.eclipse.rdf4j/rdf4j-rio-rdfjson "3.0.0"]
[org.eclipse.rdf4j/rdf4j-rio-rdfxml "3.0.0"]
[org.eclipse.rdf4j/rdf4j-rio-trig "3.0.0"]
[org.eclipse.rdf4j/rdf4j-rio-trix "3.0.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-api "3.0.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-binary "3.0.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-binary "3.0.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-sparqljson "3.0.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-sparqlxml "3.0.0"]
[org.eclipse.rdf4j/rdf4j-queryresultio-text "3.0.0"]

[org.eclipse.rdf4j/rdf4j-repository-api "3.0.0"]
[org.eclipse.rdf4j/rdf4j-repository-http "3.0.0"]
[org.eclipse.rdf4j/rdf4j-repository-sail "3.0.0"]
[org.eclipse.rdf4j/rdf4j-repository-dataset "3.0.0"]
[org.eclipse.rdf4j/rdf4j-sail-memory "3.0.0"]
[org.eclipse.rdf4j/rdf4j-sail-inferencer "3.0.0"]
[org.eclipse.rdf4j/rdf4j-sail-nativerdf "3.0.0"]
[org.eclipse.rdf4j/rdf4j-repository-manager "3.0.0"]

[grafter/url "0.2.5"]
[grafter/vocabularies "0.2.6"]
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11 changes: 7 additions & 4 deletions src/grafter_2/rdf4j/io.clj
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Expand Up @@ -13,7 +13,7 @@
[java.net MalformedURLException URL]
java.time.temporal.ChronoField
[javax.xml.datatype DatatypeConstants DatatypeFactory XMLGregorianCalendar]
[org.eclipse.rdf4j.model BNode Literal Statement URI]
[org.eclipse.rdf4j.model BNode Literal Statement URI Model]
[org.eclipse.rdf4j.model.impl BNodeImpl ContextStatementImpl LiteralImpl SimpleValueFactory StatementImpl URIImpl]
[org.eclipse.rdf4j.rio RDFFormat RDFHandler Rio]))

Expand Down Expand Up @@ -663,7 +663,12 @@

java.io.Reader
(pr/to-statements [this opts]
(to-statements* this opts)))
(to-statements* this opts))

Model
(to-statements [this _opts]
;; Works because a Model is a java.util.Set
(map backend-quad->grafter-quad this)))

(extend-protocol IURIable
org.eclipse.rdf4j.model.URI
Expand All @@ -690,8 +695,6 @@
org.eclipse.rdf4j.model.URI
(->-rdf4j-uri [this] this)
GrafterURL
(->-rdf4j-uri [this] (URIImpl. (str this)))
org.eclipse.rdf4j.model.Graph
(->-rdf4j-uri [this] (URIImpl. (str this))))

(defn statements
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31 changes: 1 addition & 30 deletions src/grafter_2/rdf4j/repository.clj
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Expand Up @@ -6,7 +6,7 @@
[grafter-2.rdf4j.formats :as format]
[grafter-2.rdf4j.io :as rio]
[me.raynes.fs :as fs])
(:import [org.eclipse.rdf4j.model Graph Resource Statement URI]
(:import [org.eclipse.rdf4j.model Resource Statement URI]
[org.eclipse.rdf4j.query BindingSet BooleanQuery GraphQuery Query QueryLanguage TupleQuery Update]
[org.eclipse.rdf4j.repository Repository RepositoryConnection]
[org.eclipse.rdf4j.sail.inferencer.fc CustomGraphQueryInferencer DirectTypeHierarchyInferencer ForwardChainingRDFSInferencer])
Expand Down Expand Up @@ -339,35 +339,6 @@
(pr/to-statements [this options]
(throw-deprecated-exception!)))

(extend-type Graph
pr/ITripleReadable
(pr/to-statements [this options]
(map rio/backend-quad->grafter-quad (iterator-seq (.match this nil nil nil (resource-array)))))

pr/ITripleWriteable

(pr/add-statement
([this graph statement]
(.add this
(rio/->backend-type (pr/subject statement))
(rio/->backend-type (pr/predicate statement))
(rio/->backend-type (pr/object statement))
(resource-array (rio/->rdf4j-uri graph)))))

(pr/add
([this triples]
(pr/add this nil triples))

([this graph triples]
(doseq [triple triples]
(pr/add-statement this graph triple)))

([this graph format triple-stream]
(pr/add this graph triple-stream))

([this graph base-uri format triple-stream]
(pr/add this graph triple-stream))))

(defn ^:no-doc sesame-results->seq
"Convert a sesame results object into a lazy sequence of results."
([prepared-query] (sesame-results->seq prepared-query identity))
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12 changes: 0 additions & 12 deletions test/grafter_2/rdf4j/repository_test.clj
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Expand Up @@ -7,24 +7,12 @@
[grafter-2.rdf4j.templater :refer [graph]]
[grafter.url :refer [->GrafterURL]])
(:import [java.net URI URL]
org.eclipse.rdf4j.model.impl.GraphImpl
org.eclipse.rdf4j.repository.sparql.SPARQLRepository))

(def quad-fixture-file-path (io/resource "grafter/rdf/rdf-types.trig"))

(def triple-fixture-file-path (io/resource "grafter/rdf/rdf-types.ttl"))

(deftest reading-writing-to-Graph
(let [graph (GraphImpl.)
g (URI. "http://foo")
s (URI. "http://s")
p (URI. "http://p")
o (URI. "http://o")]
(core/add-statement graph "http://foo" (core/->Quad s p o nil))

(is (= (core/->Quad s p o g)
(first (rio/statements graph))))))

(deftest with-transaction-test
(with-open [test-db (repo/->connection (sail-repo))]
(testing "Transactions return last result of form if there's no error."
Expand Down