Jena 4.10 + cleanup

.gitignore

@@ -62,4 +62,5 @@ docs/
 !gitkeep
 
 .cpcache
-.calva
+.calva
+.portal/

README.md

@@ -253,6 +253,22 @@ When executing against TDB it is recommended to use [transactions](https://jena.
 to prevent against data corruption.
 You can set the flags yourself on the `Dataset` or use the `with-transaction` macro, although support for this is somewhat lacking.
 
+## Running tests
+
+We use [kaoch test runner](https://github.com/lambdaisland/kaocha)
+
+See https://practical.li/clojure/testing/test-runners/kaocha-test-runner/#run-kaocha
+
+
+```shell
+
+clojure -X:test/run
+
+clojure -X:test/run :fail-fast? false
+
+```
+
+
 ## TODO
 - Authentication support for SPARQL Endpoints
 - Support [SPARQL S-Expressions](https://jena.apache.org/documentation/notes/sse.html) (?)

deps.edn

@@ -1,13 +1,32 @@
 {:paths ["src" "resources"]
  :deps
- {cider/cider-nrepl {:mvn/version "0.25.9"}
-  instaparse/instaparse {:mvn/version "1.4.1"}
-  org.apache.jena/jena-core {:mvn/version "4.3.1"}
-  org.apache.jena/jena-arq {:mvn/version "4.3.1"}
-  org.apache.jena/jena-tdb {:mvn/version "4.3.1"}}
- :aliases {:test {:extra-paths []
-                  :extra-deps
-                  {expectations/expectations {:mvn/version "2.1.3"}}}}
+ {instaparse/instaparse {:mvn/version "1.4.12"}
+  org.apache.jena/jena-core {:mvn/version "4.10.0"}
+  org.apache.jena/jena-arq {:mvn/version "4.10.0"}
+  org.apache.jena/jena-tdb {:mvn/version "4.10.0"}}
+ :aliases {:dev
+           {:extra-deps
+            {cider/cider-nrepl {:mvn/version "0.43.0"}}}
+           :test/run
+           {:extra-paths ["test"]
+            :extra-deps {lambdaisland/kaocha {:mvn/version "1.77.1236"}
+                         expectations/expectations {:mvn/version "2.1.10"}}
+            :main-opts   ["-m" "kaocha.runner"]
+            :exec-fn kaocha.runner/exec-fn
+            :exec-args {:fail-fast? true
+                        :randomize? false}}
+
+           ;; Kaocha test runner in watch mode
+           ;; clojure -X:test/watch
+           :test/watch
+           {:extra-paths ["test"]
+            :extra-deps {lambdaisland/kaocha {:mvn/version "1.77.1236"}
+                         expectations/expectations {:mvn/version "2.1.10"}}
+            :main-opts   ["-m" "kaocha.runner" "--watch" "--fail-fast" "--skip-meta" ":slow"]
+            :exec-fn kaocha.runner/exec-fn
+            :exec-args {:watch? true
+                        :randomize? false
+                        :fail-fast? true}}}
  :mvn/repos {"central" {:url "https://repo1.maven.org/maven2/"}
              "clojars" {:url "https://repo.clojars.org/"}
              "oss-snapshots-repo" {:url "https://oss.sonatype.org/content/groups/public"}}}

src/yesparql/core.clj

@@ -1,7 +1,7 @@
 (ns yesparql.core
-  (:require [yesparql.util :refer [slurp-from-classpath]]
-            [yesparql.generate :refer [generate-var]]
-            [yesparql.queryfile-parser :refer [parse-tagged-queries]]))
+  (:require [yesparql.generate :refer [generate-var]]
+            [yesparql.queryfile-parser :refer [parse-tagged-queries]]
+            [yesparql.util :refer [slurp-from-classpath]]))
 
 ;; Most of the non-SPARQL code is directly from [Yesql](https://github.com/krisajenkins/yesql/blob/devel/src/yesql/core.clj) by Kris Jenkins
 

src/yesparql/generate.clj

@@ -1,13 +1,9 @@
 (ns yesparql.generate
-  (:require
-   [clojure.set :as set]
-   [clojure.string :refer [join lower-case]]
-   [yesparql.util :refer [create-root-var]]
-   [yesparql.sparql :as sparql]
-   [yesparql.types :refer [map->Query]])
-  (:import [yesparql.types Query]
-           [org.apache.jena.shared PrefixMapping PrefixMapping$Factory]
-           [org.apache.jena.query ParameterizedSparqlString Syntax]))
+  (:require [clojure.string :refer [join]]
+            [yesparql.sparql :as sparql]
+            [yesparql.util :refer [create-root-var]])
+  (:import [org.apache.jena.query Syntax]
+           [org.apache.jena.shared PrefixMapping]))
 
 (defn query-type
   [^String name]

src/yesparql/instaparse_util.clj

@@ -1,12 +1,13 @@
 (ns yesparql.instaparse-util
-  (:require [instaparse.core :as instaparse])
+  (:require [instaparse.core :as instaparse]
+            [instaparse.failure :as failure])
   (:import [java.io StringWriter]))
 
 (defn process-instaparse-result
   [parse-results context]
   (if-let [failure (instaparse/get-failure parse-results)]
     (binding [*out* (StringWriter.)]
-      (instaparse.failure/pprint-failure failure)
+      (failure/pprint-failure failure)
       (throw (ex-info (str *out*)
                       failure)))
     (if (second parse-results)

src/yesparql/queryfile_parser.clj

@@ -2,9 +2,10 @@
   (:require [clojure.java.io :as io]
             [clojure.string :refer [join trim]]
             [instaparse.core :as instaparse]
+            [instaparse.transform :as transform]
+            [yesparql.instaparse-util :refer [process-instaparse-result]]
             [yesparql.types :refer [map->Query]]
-            [yesparql.util :refer [str-non-nil]]
-            [yesparql.instaparse-util :refer [process-instaparse-result]]))
+            [yesparql.util :refer [str-non-nil]]))
 
 (def parser
   (let [url (io/resource "yesparql/queryfile.bnf")]
@@ -31,7 +32,7 @@
   "Parses a string with Yesparql's defqueries syntax into a sequence of maps."
   [text]
   (process-instaparse-result
-   (instaparse/transform
+   (transform/transform
     parser-transforms
     (instaparse/parses parser
                        (str text "\n") ;;; TODO This is a workaround for files with no end-of-line marker.

src/yesparql/sparql.clj

@@ -1,30 +1,40 @@
 (ns yesparql.sparql
-  (:import
-   [java.lang IllegalArgumentException]
-   [java.net URL URI]
-   [org.apache.jena.graph Node]
-   [org.apache.jena.update
-    Update UpdateAction
-    UpdateFactory UpdateProcessor
-    UpdateRequest UpdateExecutionFactory]
-   [org.apache.jena.rdf.model Model
-    StmtIterator Statement Resource Property
-    RDFNode Resource Literal]
-   [org.apache.jena.shared PrefixMapping]
-   [org.apache.jena.query Dataset]
-   [org.apache.jena.sparql.resultset RDFOutput]
-   [org.apache.jena.rdf.model ModelFactory]
-   [org.apache.jena.datatypes BaseDatatype]
-   [org.apache.jena.graph Node Node_Literal]
-   [org.apache.jena.sparql.core Var ResultBinding]
-   [org.apache.jena.query
-    Query QuerySolution QueryExecution Syntax
-    QueryExecutionFactory QueryFactory QuerySolutionMap
-    ParameterizedSparqlString ResultSetFactory
-    ResultSetRewindable ResultSet ResultSetFormatter]))
-
-(defn ^java.io.ByteArrayOutputStream output-stream []
-  (java.io.ByteArrayOutputStream.))
+  (:import [java.lang IllegalArgumentException]
+           [java.net URI URL]
+           [java.io ByteArrayOutputStream]
+           [org.apache.jena.datatypes BaseDatatype]
+           [org.apache.jena.graph Node]
+           [org.apache.jena.graph Node Node_Literal]
+           [org.apache.jena.query Dataset]
+           [org.apache.jena.query
+            ParameterizedSparqlString
+            Query
+            QueryExecution
+            QueryExecutionFactory
+            QueryFactory
+            ResultSet
+            ResultSetFactory
+            ResultSetFormatter
+            ResultSetRewindable
+            Syntax]
+           [org.apache.jena.rdf.model
+            Literal
+            Model
+            RDFNode
+            Statement]
+           [org.apache.jena.rdf.model ModelFactory]
+           [org.apache.jena.shared PrefixMapping]
+           [org.apache.jena.sparql.core ResultBinding Var]
+           [org.apache.jena.sparql.resultset RDFOutput]
+           [org.apache.jena.update
+            UpdateExecutionFactory
+            UpdateFactory
+            UpdateProcessor
+            UpdateRequest]))
+
+(defn output-stream
+  ^ByteArrayOutputStream []
+  (ByteArrayOutputStream.))
 
 (defn reset-if-rewindable!
   "Resets a `RewindableResulSet`
@@ -137,8 +147,8 @@
 
 (defn keyword-str [kw] (if (keyword? kw) (name kw) kw))
 
-(defn ^Literal clj->literal
-  [{:keys [value type lang]}]
+(defn clj->literal
+  ^Literal [{:keys [value type lang]}]
   (cond
     type (.createTypedLiteral
           default-model value (BaseDatatype. ^String (str type)))
@@ -147,11 +157,11 @@
     :else (.createTypedLiteral
            default-model value)))
 
-(defn ^ParameterizedSparqlString parameterized-query
-  [^String statement]
+(defn parameterized-query
+  ^ParameterizedSparqlString [^String statement]
   (ParameterizedSparqlString. statement))
 
-(defn ^ParameterizedSparqlString query-with-bindings
+(defn query-with-bindings
   "The `query` can be provided with a map of `bindings`.
    Each binding is a String->URL, String->URI, String->Node or String->RDFNode.
    Any other type (e.g. String, Float) will be set as Literal.
@@ -161,7 +171,7 @@
    which will be coerced to the appropriate `Literal` automatically.
 
    Does not warn when setting a binding that does not exist."
-  [^ParameterizedSparqlString pq ^PrefixMapping prefixes bindings]
+  ^ParameterizedSparqlString [^ParameterizedSparqlString pq ^PrefixMapping prefixes bindings]
   (doall
    (map
     (fn [[var resource]]
@@ -418,10 +428,10 @@
    ^UpdateRequest update
    ^Dataset connection))
 
-(defn ^UpdateRequest as-update
-  ([^String ustr]
+(defn as-update
+  (^UpdateRequest [^String ustr]
    (as-update Syntax/defaultUpdateSyntax ustr))
-  ([^Syntax syntax ^String qstr]
+  (^UpdateRequest [^Syntax syntax ^String qstr]
    (UpdateFactory/create qstr syntax)))
 
 (defn update!

src/yesparql/tdb.clj

@@ -1,16 +1,15 @@
 (ns yesparql.tdb
-  (:import
-   [org.apache.jena.query Dataset DatasetFactory]
-   [org.apache.jena.tdb TDBFactory TDBLoader StoreConnection TDB]))
+  (:import [org.apache.jena.query Dataset DatasetFactory]
+           [org.apache.jena.tdb TDBFactory]))
 
-(defn ^Dataset create-file-based
+(defn create-file-based
   "Creates a new TDB-backed `Dataset` in the `directory` (absolute path)"
-  [^String directory]
+  ^Dataset [^String directory]
   (TDBFactory/createDataset directory))
 
-(defn ^Dataset create-in-memory
+(defn create-in-memory
   "Create an in-memory, modifiable TDB `Dataset`"
-  []
+  ^Dataset []
   (TDBFactory/createDataset))
 
 (defn ^Dataset create-bare

src/yesparql/util.clj

@@ -1,7 +1,6 @@
 (ns yesparql.util
   (:require [clojure.java.io :as io]
-            [clojure.string :as string]
-            [clojure.pprint :refer [pprint]])
+            [clojure.string :as string])
   (:import [java.io FileNotFoundException]))
 
 (defn underscores-to-dashes