Upgrade to Jena 3

frmichel · Apr 24, 2020 · 7c1df27 · 7c1df27
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ## [1.2] 2020-04-22
 - Add config property output.file.max_triples (and parameter --outputMaxTriples) to generate files with a maximum number of triples
+- Upgrade to Jena 3
+- Update to Scala 2.12.11 + update misc. libraries
 
 
 ## [1.1-RC2] 2019-09-16: fix bug in Mongo query parsing

diff --git a/morph-base/src/main/scala/es/upm/fi/dia/oeg/morph/base/R2RMLMappingUtility.scala b/morph-base/src/main/scala/es/upm/fi/dia/oeg/morph/base/R2RMLMappingUtility.scala
@@ -2,8 +2,8 @@ package es.upm.fi.dia.oeg.morph.base
 
 import scala.collection.JavaConversions.asScalaBuffer
 
-import com.hp.hpl.jena.datatypes.xsd.XSDDatatype
-import com.hp.hpl.jena.rdf.model.Resource
+import org.apache.jena.datatypes.xsd.XSDDatatype
+import org.apache.jena.rdf.model.Resource
 
 /**
  * This utility class provides methods that navigate through JENA resources representing the mapping graph.

diff --git a/morph-base/src/main/scala/es/upm/fi/dia/oeg/morph/base/engine/MorphBaseDataTranslator.scala b/morph-base/src/main/scala/es/upm/fi/dia/oeg/morph/base/engine/MorphBaseDataTranslator.scala
@@ -1,32 +1,28 @@
 package es.upm.fi.dia.oeg.morph.base.engine
 
-import scala.collection.JavaConversions.asJavaIterator
+import scala.collection.JavaConverters.seqAsJavaListConverter
 
+import org.apache.jena.datatypes.xsd.XSDDatatype
+import org.apache.jena.rdf.model.AnonId
+import org.apache.jena.rdf.model.Literal
+import org.apache.jena.rdf.model.RDFNode
+import org.apache.jena.vocabulary.RDF
 import org.apache.log4j.Logger
 
-import com.hp.hpl.jena.datatypes.xsd.XSDDatatype
-import com.hp.hpl.jena.rdf.model.AnonId
-import com.hp.hpl.jena.rdf.model.Literal
-import com.hp.hpl.jena.rdf.model.RDFNode
-import com.hp.hpl.jena.vocabulary.RDF
-
 import es.upm.fi.dia.oeg.morph.base.Constants
 import es.upm.fi.dia.oeg.morph.base.GeneralUtility
-import es.upm.fi.dia.oeg.morph.base.exception.MorphException
-import es.upm.fi.dia.oeg.morph.base.query.AbstractQuery
-import es.upm.fi.dia.oeg.morph.r2rml.model.R2RMLMappingDocument
-import es.upm.fi.dia.oeg.morph.r2rml.model.R2RMLTriplesMap
 import es.upm.fi.dia.oeg.morph.base.RDFTerm
-import es.upm.fi.dia.oeg.morph.base.RDFTermLiteral
-import es.upm.fi.dia.oeg.morph.base.RDFTermIRI
-import arq.iri
+import es.upm.fi.dia.oeg.morph.base.RDFTermAlt
+import es.upm.fi.dia.oeg.morph.base.RDFTermBag
 import es.upm.fi.dia.oeg.morph.base.RDFTermBlankNode
+import es.upm.fi.dia.oeg.morph.base.RDFTermIRI
 import es.upm.fi.dia.oeg.morph.base.RDFTermList
-import es.upm.fi.dia.oeg.morph.base.RDFTermBag
-import es.upm.fi.dia.oeg.morph.base.RDFTermSeq
-import es.upm.fi.dia.oeg.morph.base.RDFTermAlt
+import es.upm.fi.dia.oeg.morph.base.RDFTermLiteral
 import es.upm.fi.dia.oeg.morph.base.RDFTermSeq
-import es.upm.fi.dia.oeg.morph.base.RDFTermAlt
+import es.upm.fi.dia.oeg.morph.base.exception.MorphException
+import es.upm.fi.dia.oeg.morph.base.query.AbstractQuery
+import es.upm.fi.dia.oeg.morph.r2rml.model.R2RMLMappingDocument
+import es.upm.fi.dia.oeg.morph.r2rml.model.R2RMLTriplesMap
 
 /**
  * @author Freddy Priyatna
@@ -112,9 +108,11 @@ abstract class MorphBaseDataTranslator(val factory: IMorphFactory) {
             term match {
                 case a: RDFTermLiteral => this.createLiteralNode(a)
                 case a: RDFTermIRI => factory.getMaterializer.model.createResource(a.getIRI)
+
                 case a: RDFTermBlankNode => factory.getMaterializer.model.createResource(new AnonId(a.value.asInstanceOf[String]))
+
                 case a: RDFTermList => {
-                    val members = a.getMembers.map(this.createRDFNode)
+                    val members = a.getMembers.map(this.createRDFNode).asJava
                     val node = factory.getMaterializer.model.createList(members.iterator)
                     factory.getMaterializer.model.add(node, RDF.`type`, RDF.List)
                     node

diff --git a/morph-base/src/main/scala/es/upm/fi/dia/oeg/morph/base/engine/MorphBaseRunner.scala b/morph-base/src/main/scala/es/upm/fi/dia/oeg/morph/base/engine/MorphBaseRunner.scala
@@ -1,17 +1,16 @@
 package es.upm.fi.dia.oeg.morph.base.engine
 
 import java.io.BufferedWriter
+import java.io.File
 import java.io.FileWriter
 import java.io.IOException
 import java.io.PrintWriter
 
+import org.apache.jena.query.Query
+import org.apache.jena.query.QueryFactory
 import org.apache.log4j.Logger
 
-import com.hp.hpl.jena.query.Query
-import com.hp.hpl.jena.query.QueryFactory
-
 import es.upm.fi.dia.oeg.morph.base.querytranslator.SparqlUtility
-import java.io.File
 
 /**
  * @author Freddy Priyatna

diff --git a/morph-base/src/main/scala/es/upm/fi/dia/oeg/morph/base/engine/MorphBaseRunnerFactory.scala b/morph-base/src/main/scala/es/upm/fi/dia/oeg/morph/base/engine/MorphBaseRunnerFactory.scala
@@ -1,9 +1,8 @@
 package es.upm.fi.dia.oeg.morph.base.engine
 
+import org.apache.jena.sparql.core.describe.DescribeHandlerRegistry
 import org.apache.log4j.Logger
 
-import com.hp.hpl.jena.sparql.core.describe.DescribeHandlerRegistry
-
 import es.upm.fi.dia.oeg.morph.base.GenericConnection
 import es.upm.fi.dia.oeg.morph.base.MorphProperties
 import es.upm.fi.dia.oeg.morph.base.materializer.ExtendedDescribeBNodeCloserFactory
@@ -74,7 +73,7 @@ abstract class MorphBaseRunnerFactory extends IMorphFactory {
     private def createMaterializer: MorphBaseMaterializer = {
 
         // Initialize the SPARQL DESCRIBE handler
-        DescribeHandlerRegistry.get.add(new ExtendedDescribeBNodeCloserFactory)
+        //DescribeHandlerRegistry.get.add(new ExtendedDescribeBNodeCloserFactory)
 
         val jenaMode = this.getProperties.jenaMode;
         val materializer = MorphBaseMaterializer(this, jenaMode)
@@ -100,19 +99,6 @@ object MorphBaseRunnerFactory {
 
     var mappingDocument: R2RMLMappingDocument = null
 
-    //var sparkContext: SparkContext = null
-
-    /* private def createSparkContext(masterUrl: String): SparkContext = {
-        val conf = new SparkConf().setAppName("Morph-xR2RML").setMaster(masterUrl)
-        //conf.setJars(List("file://C:/Users/fmichel/Documents/Development/eclipse-ws-xr2rml/morph-xr2rml/morph-xr2rml-dist/target/morph-xr2rml-dist-1.0-SNAPSHOT-jar-with-dependencies.jar"))
-        //conf.set("spark.driver.memory", "4g")
-        //conf.set("spark.eventLog.enabled", "true")
-        //conf.set("spark.local.dir", "/C:/Users/fmichel/.spark")
-        val sc = new SparkContext(conf)
-        sc.getConf.getAll.foreach(println)
-        sc
-    } */
-
     /**
      * Initialize the factory: create global objects that can be shared by parallel executions
      * of a runner, i.e. properties and mapping document.
@@ -122,9 +108,6 @@ object MorphBaseRunnerFactory {
     def initFactory(props: MorphProperties) = {
         MorphBaseRunnerFactory.properties = props
         MorphBaseRunnerFactory.mappingDocument = R2RMLMappingDocument(properties)
-
-        //if (properties.apacheSpark)
-        //    MorphBaseRunnerFactory.sparkContext = MorphBaseRunnerFactory.createSparkContext(properties.apacheSparkMaster)
     }
 
     /**