From a7c2c280f99638eecf39fddcf79b585c27482d99 Mon Sep 17 00:00:00 2001
From: vguerbet <valentin.guerbette@inria.fr>
Date: Thu, 20 Jun 2024 11:59:30 +0200
Subject: [PATCH] - Fixed issue with TTL and N3 format not loading

---
 kb/pom.xml                                    | 18 +++++++--
 kb/src/main/java/amie/data/KB.java            | 38 ++++++++++---------
 .../java/amie/data/StoreStatementToKB.java    |  6 +--
 mining/pom.xml                                |  2 +-
 mining/src/main/java/amie/mining/AMIE.java    |  2 -
 rules/pom.xml                                 |  6 +++
 6 files changed, 46 insertions(+), 26 deletions(-)

diff --git a/kb/pom.xml b/kb/pom.xml
index 7f12e57..381d0ce 100644
--- a/kb/pom.xml
+++ b/kb/pom.xml
@@ -26,8 +26,8 @@
                     <excludes>
                         <exclude>**/WikidataCleaner.java</exclude>
                     </excludes>
-                    <source>11</source>
-                    <target>11</target>
+                    <source>17</source>
+                    <target>17</target>
                 </configuration>
             </plugin>
         </plugins>
@@ -51,10 +51,22 @@
             <artifactId>javafx-base</artifactId>
             <version>11</version>
         </dependency>
+        <dependency>
+            <groupId>org.eclipse.rdf4j</groupId>
+            <artifactId>rdf4j-rio-turtle</artifactId>
+            <version>5.0.0-M3</version>
+            <type>pom</type>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.rdf4j</groupId>
+            <artifactId>rdf4j-rio-n3</artifactId>
+            <version>5.0.0-M3</version>
+            <type>pom</type>
+        </dependency>
         <dependency>
             <groupId>org.eclipse.rdf4j</groupId>
             <artifactId>rdf4j-storage</artifactId>
-            <version>4.3.2</version>
+            <version>5.0.0-M3</version>
             <type>pom</type>
         </dependency>
         <dependency>
diff --git a/kb/src/main/java/amie/data/KB.java b/kb/src/main/java/amie/data/KB.java
index 33c8786..873641e 100644
--- a/kb/src/main/java/amie/data/KB.java
+++ b/kb/src/main/java/amie/data/KB.java
@@ -3,7 +3,7 @@
 import static amie.data.U.decrease;
 import static amie.data.U.decreasingKeys;
 import static amie.data.U.increase;
-import static com.hp.hpl.jena.sparql.engine.optimizer.reorder.ReorderTransformationBase.log;
+//import static com.hp.hpl.jena.sparql.engine.optimizer.reorder.ReorderTransformationBase.log;
 
 import amie.data.starpattern.SignedPredicate;
 import amie.data.tuple.IntArrays;
@@ -33,6 +33,10 @@
 import org.eclipse.rdf4j.rio.RDFFormat;
 import org.eclipse.rdf4j.rio.RDFParser;
 import org.eclipse.rdf4j.rio.Rio;
+import org.eclipse.rdf4j.rio.helpers.AbstractRDFParser;
+import org.eclipse.rdf4j.rio.turtle.TurtleParser;
+import org.eclipse.rdf4j.rio.n3.N3Parser;
+
 
 /**
  * Class KB
@@ -221,25 +225,25 @@ protected void load(File f, String message)
 					+ String.format("%d s", (System.currentTimeMillis()
 					- time) / 1000));
 		}
-		if (f.getPath().endsWith(".ttl") || f.getPath().endsWith(".nt")) {
+		if (f.getPath().endsWith(RDFFormat.TURTLE.getDefaultFileExtension()) ||
+				f.getPath().endsWith(RDFFormat.N3.getDefaultFileExtension())) {
+			InputStream in = null;
 			try {
-				InputStream in = Files.newInputStream(Paths.get(f.getPath()));
-
-				if (f.getPath().endsWith(".ttl")){
-					StoreStatementToKB abstractRDFHandler = new StoreStatementToKB(this);
-					RDFParser rdfParser = Rio.createParser(RDFFormat.TURTLE);
-					rdfParser.setRDFHandler(abstractRDFHandler);
-					rdfParser.parse(in);
-				}
-				else{
-					StoreStatementToKB abstractRDFHandler = new StoreStatementToKB(this);
-					RDFParser rdfParser = Rio.createParser(RDFFormat.N3);
-					rdfParser.setRDFHandler(abstractRDFHandler);
-					rdfParser.parse(in);
-				}
+				in = Files.newInputStream(Paths.get(f.getPath()));
+				StoreStatementToKB abstractRDFHandler = new StoreStatementToKB(this);
+			AbstractRDFParser rdfParser ;
+			if (f.getPath().endsWith(RDFFormat.TURTLE.getDefaultFileExtension())){
+				rdfParser = new TurtleParser();
+			}	else{
+				rdfParser = new N3Parser();
+			}
+			rdfParser.setRDFHandler(abstractRDFHandler);
+			rdfParser.parse(in);
 			} catch (Exception e) {
-				log.error("ParseInputFiles.parseTTLOrNTFileInLine parse TTL or NT error, filePath:{}", f.getPath(),e );
 				throw e ;
+			} finally {
+                if (in != null)
+                	in.close() ;
 			}
 		} else {
 			for (String line : new FileLines(f, "UTF-8", message)) {
diff --git a/kb/src/main/java/amie/data/StoreStatementToKB.java b/kb/src/main/java/amie/data/StoreStatementToKB.java
index d99caba..64a4d29 100644
--- a/kb/src/main/java/amie/data/StoreStatementToKB.java
+++ b/kb/src/main/java/amie/data/StoreStatementToKB.java
@@ -10,18 +10,18 @@
 public class StoreStatementToKB extends AbstractRDFHandler {
 
     private static int counter = 0;
-    private AbstractKB kb;
+    private KB kb;
     private static Map<String,String> prefixes=new HashMap<>();
 
 
-    StoreStatementToKB(AbstractKB kb){
+    StoreStatementToKB(KB kb){
         this.kb = kb;
     }
     public void handleStatement(Statement st) {
         String subject = getFormattedValue(String.valueOf(st.getSubject()));
         String object = getFormattedValue(String.valueOf(st.getObject()));
         String predict = getFormattedValue(String.valueOf(st.getPredicate()));
-        ((KB) kb).add(subject, predict, object);
+        kb.add(subject, predict, object);
     }
 
     public String getFormattedValue(String value) {
diff --git a/mining/pom.xml b/mining/pom.xml
index c523106..11dc943 100644
--- a/mining/pom.xml
+++ b/mining/pom.xml
@@ -66,7 +66,7 @@
                             <descriptorRefs>
                                 <descriptorRef>jar-with-dependencies</descriptorRef>
                             </descriptorRefs>
-                            <finalName>amie3.5</finalName>
+                            <finalName>amie3.5.1</finalName>
                             <appendAssemblyId>false</appendAssemblyId>
                             <outputDirectory>../bin</outputDirectory>
                         </configuration>
diff --git a/mining/src/main/java/amie/mining/AMIE.java b/mining/src/main/java/amie/mining/AMIE.java
index 1fc0c4d..8be2bfa 100644
--- a/mining/src/main/java/amie/mining/AMIE.java
+++ b/mining/src/main/java/amie/mining/AMIE.java
@@ -36,8 +36,6 @@
 
 import amie.data.javatools.datatypes.MultiMap;
 import org.apache.commons.lang.StringUtils;
-import org.apache.zookeeper.Op;
-
 /**
  * Main class that implements the AMIE algorithm for rule mining on ontologies.
  * The ontology must be provided as a list of TSV files where each line has the
diff --git a/rules/pom.xml b/rules/pom.xml
index 4e9f562..df20aeb 100644
--- a/rules/pom.xml
+++ b/rules/pom.xml
@@ -26,5 +26,11 @@
     	<artifactId>kb</artifactId>
     	<version>1.0</version>
     </dependency>
+      <dependency>
+          <groupId>org.apache.commons</groupId>
+          <artifactId>commons-math3</artifactId>
+          <version>3.6.1</version>
+          <scope>compile</scope>
+      </dependency>
   </dependencies>
 </project>