Merge branch 'experimental' into feature/dependency-updates

Author: LorenzBuehmann

pom.xml

@@ -177,6 +177,16 @@
         <artifactId>jena-arq</artifactId>
         <version>${jena.version}</version>
       </dependency>
+      <dependency>
+        <groupId>org.apache.jena</groupId>
+        <artifactId>jena-tdb</artifactId>
+        <version>${jena.version}</version>
+      </dependency>
+      <dependency>
+        <groupId>org.apache.jena</groupId>
+        <artifactId>jena-cmds</artifactId>
+        <version>${jena.version}</version>
+      </dependency>
 
       <!-- OWL API -->
       <dependency>
@@ -202,14 +212,14 @@
 
       <!-- Graph API -->
       <dependency>
-        <groupId>com.assembla.scala-incubator</groupId>
+        <groupId>org.scala-graph</groupId>
         <artifactId>graph-core_${scala.binary.version}</artifactId>
-        <version>1.10.0</version>
+        <version>1.12.3</version>
       </dependency>
       <dependency>
-        <groupId>com.assembla.scala-incubator</groupId>
+        <groupId>org.scala-graph</groupId>
         <artifactId>graph-dot_${scala.binary.version}</artifactId>
-        <version>1.9.0</version>
+        <version>1.11.5</version>
       </dependency>
       <dependency>
         <groupId>org.jgrapht</groupId>

sansa-inference-common/pom.xml

@@ -31,21 +31,19 @@
     <dependency>
       <groupId>org.apache.jena</groupId>
       <artifactId>jena-tdb</artifactId>
-      <version>3.5.0</version>
     </dependency>
     <dependency>
       <groupId>org.apache.jena</groupId>
       <artifactId>jena-cmds</artifactId>
-      <version>3.5.0</version>
     </dependency>
 
     <!-- Graph API -->
     <dependency>
-      <groupId>com.assembla.scala-incubator</groupId>
+      <groupId>org.scala-graph</groupId>
       <artifactId>graph-core_${scala.binary.version}</artifactId>
     </dependency>
     <dependency>
-      <groupId>com.assembla.scala-incubator</groupId>
+      <groupId>org.scala-graph</groupId>
       <artifactId>graph-dot_${scala.binary.version}</artifactId>
     </dependency>
     <dependency>
@@ -69,7 +67,7 @@
           <artifactId>google-collections</artifactId>
         </exclusion>
       </exclusions>
-      <scope>provided</scope>
+      <scope>compile</scope>
     </dependency>
 
     <!-- Guava -->
@@ -89,6 +87,11 @@
       <version>3.5.0</version>
     </dependency>
 
+    <!-- Scopt CLI API-->
+    <dependency>
+      <groupId>com.github.scopt</groupId>
+      <artifactId>scopt_${scala.binary.version}</artifactId>
+    </dependency>
 
     <!-- Test -->
     <dependency>

sansa-inference-common/src/main/resources/log4j.properties

@@ -1,5 +1,5 @@
 # Root logger option
-log4j.rootLogger=INFO, stdout
+log4j.rootLogger=DEBUG, stdout
 
 # Direct log messages to a log file
 log4j.appender.file=org.apache.log4j.RollingFileAppender
@@ -20,3 +20,5 @@ log4j.logger.akka.remote.Remoting=ERROR
 
 log4j.logger.org.apache.hadoop=ERROR
 log4j.logger.org.apache.calcite=ERROR
+
+log4j.logger.scalax.collection.connectivity.GraphComponents=OFF

sansa-inference-common/src/main/scala/net/sansa_stack/inference/rules/RuleDependencyGraphAnalyzer.scala

@@ -137,8 +137,8 @@ object RuleDependencyGraphAnalyzer extends Logging{
   def main(args: Array[String]) {
     // we re-use the JENA API for parsing rules
     val filenames = List(
-//      "rules/rdfs-simple.rules"
-      "rules/owl_horst.rules"
+      "rules/rdfs-simple.rules"
+//      "rules/owl_horst.rules"
 //    "rules/owl_rl.rules"
     )
 
@@ -154,7 +154,7 @@ object RuleDependencyGraphAnalyzer extends Logging{
 
       // print each rule as graph
       rules.foreach { r =>
-        val g = RuleUtils.asGraph(r).export(new File(graphDir, r.getName + ".graphml").toString)
+        RuleUtils.asGraph(r).export(new File(graphDir, r.getName + ".graphml").toString)
       }
 
       // generate graph

sansa-inference-common/src/main/scala/net/sansa_stack/inference/rules/RuleDependencyGraphGenerator.scala

@@ -5,6 +5,7 @@ import java.util.stream.Collectors
 import scala.collection
 import scala.collection.JavaConverters._
 import scala.language.{existentials, implicitConversions}
+
 import scalax.collection.GraphPredef._
 import scalax.collection.GraphTraversal.Parameters
 import scalax.collection._
@@ -13,7 +14,6 @@ import scalax.collection.edge._
 import scalax.collection.mutable.DefaultGraphImpl
 import scalax.collection.GraphPredef._
 import scalax.collection.GraphEdge._
-
 import org.apache.jena.graph.{Node, NodeFactory}
 import org.apache.jena.reasoner.TriplePattern
 import org.apache.jena.reasoner.rulesys.Rule
@@ -259,12 +259,12 @@ object RuleDependencyGraphGenerator extends Logging {
         pairsOfRules :+= (cycle.last, cycle(0))
 
         // map to list of edges
-        val edges: Buffer[graph.EdgeT] = pairsOfRules.map(e => {
+        val edges: Buffer[graph.EdgeT] = pairsOfRules.flatMap(e => {
           val node1 = graph get e._1
           val node2 = graph get e._2
 
           node1.outgoing.filter(_.target == node2)
-        }).flatten
+        })
         debug("Edges: " + edges.mkString(", "))
 
         // map to edge labels, i.e. the predicates

sansa-inference-common/src/main/scala/net/sansa_stack/inference/rules/minimizer/RuleDependencyGraphMinimizer.scala

@@ -1,10 +1,12 @@
 package net.sansa_stack.inference.rules.minimizer
 import scala.collection.mutable.{ArrayBuffer, Buffer}
+
 import scalax.collection.Graph
 import scalax.collection.edge.LDiEdge
 import scala.collection.JavaConverters._
-import scalax.collection.GraphTraversal.Parameters
+import scala.collection.mutable
 
+import scalax.collection.GraphTraversal.Parameters
 import org.apache.jena.graph.{Node, NodeFactory}
 import org.apache.jena.reasoner.TriplePattern
 import org.apache.jena.reasoner.rulesys.Rule
@@ -16,7 +18,6 @@ import net.sansa_stack.inference.rules.RuleDependencyGraphGenerator.{asString, d
 import net.sansa_stack.inference.utils.{GraphUtils, RuleUtils}
 import net.sansa_stack.inference.utils.graph.LabeledEdge
 import net.sansa_stack.inference.utils.RuleUtils._
-
 import scalax.collection.GraphTraversal.Parameters
 import scalax.collection._
 import scalax.collection.edge.Implicits._
@@ -294,11 +295,13 @@ abstract class RuleDependencyGraphMinimizer extends MinimizationRuleExecutor {
 //          debug(cycles.asScala.mkString(","))
 
           // cycles that contain the current node
-          val cyclesWithNode: Buffer[Buffer[Rule]] = allCycles.asScala.filter(cycle => cycle.contains(node.value)).map(cycle => cycle.asScala)
+          val cyclesWithNode: mutable.Buffer[mutable.Buffer[Rule]] = allCycles.asScala
+            .filter(cycle => cycle.contains(node.value))
+            .map(cycle => cycle.asScala)
           debug("Cycles: " + cyclesWithNode.map(c => c.map(r => r.getName)).mkString(","))
 
           // cycles that use the same property
-          val cyclesWithNodeSameProp: Map[Node, scala.List[Buffer[graph.EdgeT]]] = cyclesWithNode.map(cycle => {
+          val cyclesWithNodeSameProp: Map[Node, scala.List[mutable.Buffer[graph.EdgeT]]] = cyclesWithNode.map(cycle => {
 
             debug("Cycle: " + cycle.map(r => r.getName).mkString(", "))
 
@@ -307,12 +310,12 @@ abstract class RuleDependencyGraphMinimizer extends MinimizationRuleExecutor {
             pairsOfRules :+= (cycle.last, cycle(0))
 
             // map to list of edges
-            val edges: Buffer[graph.EdgeT] = pairsOfRules.map(e => {
+            val edges: mutable.Buffer[graph.EdgeT] = pairsOfRules.flatMap(e => {
               val node1 = graph get e._1
               val node2 = graph get e._2
 
               node1.outgoing.filter(_.target == node2)
-            }).flatten
+            })
             debug("Edges: " + edges.mkString(", "))
 
             // map to edge labels, i.e. the predicates
@@ -325,9 +328,14 @@ abstract class RuleDependencyGraphMinimizer extends MinimizationRuleExecutor {
             if (samePred) Some(predicates(0), edges) else None
           }).filter(_.isDefined).map(_.get).groupBy(e => e._1).mapValues(e => e.map(x => x._2).toList)
 
-          var removedCycles: collection.mutable.Set[Buffer[graph.EdgeT]] = collection.mutable.Set()
+          var removedCycles: collection.mutable.Set[mutable.Buffer[graph.EdgeT]] = collection.mutable.Set()
 
-          val tmp: Map[Node, Map[Int, List[Buffer[graph.EdgeT]]]] = cyclesWithNodeSameProp.mapValues(value => value.map(cycle => (cycle.size, cycle)).groupBy(_._1).mapValues(e => e.map(x => x._2).toList))
+          val tmp: Map[Node, Map[Int, List[mutable.Buffer[graph.EdgeT]]]] =
+            cyclesWithNodeSameProp
+              .mapValues(value =>
+                value.map(cycle => (cycle.size, cycle))
+                  .groupBy(_._1)
+                  .mapValues(e => e.map(x => x._2)))
 
           tmp.foreach(predicate2Cycles => {
             debug("predicate: " + predicate2Cycles._1)