From 17bd9beaf7f358a44e5bf36a5855fe6727d506dc Mon Sep 17 00:00:00 2001
From: Federico Igne <federico.igne@cs.ox.ac.uk>
Date: Tue, 10 May 2022 18:17:06 +0100
Subject: [pagoda] Move project to Scala

This commit includes a few changes:
- The repository still uses Maven to manage dependency but it is now a
  Scala project.
- The code has been ported from OWLAPI 3.4.10 to 5.1.20
- A proof of concept program using both RSAComb and PAGOdA has been
  added.
---
 pom.xml | 402 ++++++++++++++++++++++++++++++++++++++++++++--------------------
 1 file changed, 279 insertions(+), 123 deletions(-)

(limited to 'pom.xml')

diff --git a/pom.xml b/pom.xml
index 466383a..63a853d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,16 +1,35 @@
-<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<groupId>uk.ac.ox.cs.pagoda</groupId>
-	<artifactId>pagoda</artifactId>
-	<version>2.1.2</version>
+<?xml version="1.0" encoding="UTF-8"?>
+
+<project
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="http://maven.apache.org/POM/4.0.0"
+    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"
+>
+    <modelVersion>4.0.0</modelVersion>
+
+    <name>ACQuA</name>
+    <description>Answering Conjunctive Queries using Approximation</description>
+
+    <groupId>uk.ac.ox.cs.acqua</groupId>
+    <artifactId>acqua</artifactId>
+    <version>0.1.0</version>
+
 	<packaging>jar</packaging>
-	<name>PAGOdA</name>
-    <properties>
-        <skipTests>true</skipTests>
-    </properties>
+
+  <properties>
+    <maven.compiler.source>1.8</maven.compiler.source>
+    <maven.compiler.target>1.8</maven.compiler.target>
+    <!-- <encoding>UTF-8</encoding> -->
+    <scala.version>2.13.6</scala.version>
+    <scala.compat.version>2.13</scala.compat.version>
+    <spec2.version>4.2.0</spec2.version>
+    <skipTests>true</skipTests>
+  </properties>
+
     <repositories>
-        <!--other repositories if any-->
+        <!-- Old RDFox 1.0.0 dependency
+             To be eventually removed!
+          -->
         <repository>
             <id>project.local</id>
             <name>pagoda</name>
@@ -18,118 +37,17 @@
         </repository>
     </repositories>
 
-    <build>
-		<sourceDirectory>src</sourceDirectory>
-		<testSourceDirectory>test</testSourceDirectory>
-		<resources>
-			<resource>
-				<directory>src/resources</directory>
-				<excludes>
-					<exclude>pagoda.properties</exclude>
-				</excludes>
-			</resource>
-
-		</resources>
-		<testResources>
-			<testResource>
-				<directory>test/resources</directory>
-			</testResource>
-		</testResources>
-		<plugins>
-			<plugin>
-				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.1</version>
-				<configuration>
-					<source>1.8</source>
-					<target>1.8</target>
-				</configuration>
-			</plugin>
-			<plugin>
-				<artifactId>maven-project-info-reports-plugin</artifactId>
-				<version>2.7</version>
-			</plugin>
-			<plugin>
-				<artifactId>maven-assembly-plugin</artifactId>
-				<configuration>
-					<archive>
-						<manifest>
-							<mainClass>uk.ac.ox.cs.pagoda.Pagoda</mainClass>
-						</manifest>
-					</archive>
-					<descriptorRefs>
-						<descriptorRef>jar-with-dependencies</descriptorRef>
-					</descriptorRefs>
-				</configuration>
-				<executions>
-					<execution>
-						<id>make-assembly</id> <!-- this is used for inheritance merges -->
-						<phase>package</phase> <!-- bind to the packaging phase -->
-						<goals>
-							<goal>single</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-		</plugins>
-	</build>
-	<reporting>
-		<plugins>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-javadoc-plugin</artifactId>
-				<version>2.9.1</version>
-				<configuration>
-					<show>public</show>
-				</configuration>
-			</plugin>
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>findbugs-maven-plugin</artifactId>
-				<version>3.0.0</version>
-				<configuration>
-					<xmlOutput>true</xmlOutput>
-					<!-- Optional directory to put findbugs xdoc xml report -->
-					<xmlOutputDirectory>target/site</xmlOutputDirectory>
-				</configuration>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-checkstyle-plugin</artifactId>
-				<version>2.5</version>
-				<configuration>
-					<configLocation>config/sun_checks.xml</configLocation><!-- default -->
-					<!-- <configLocation>config/maven_checks.xml</configLocation> -->
-					<!-- <configLocation>config/turbine_checks.xml</configLocation> -->
-					<!-- <configLocation>config/avalon_checks.xml</configLocation> -->
-				</configuration>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-jxr-plugin</artifactId>
-				<version>2.1</version>
-			</plugin>
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>dashboard-maven-plugin</artifactId>
-				<version>1.0.0-beta-1</version>
-			</plugin>
-			<!--<plugin>-->
-				<!--<groupId>org.apache.maven.plugins</groupId>-->
-				<!--<artifactId>maven-surefire-plugin</artifactId>-->
-				<!--<version>2.13</version>-->
-				<!--<configuration>-->
-					<!--<forkMode>always</forkMode>-->
-					<!--<systemPropertyVariables>-->
-						<!--<reporter.debug>false</reporter.debug>-->
-					<!--</systemPropertyVariables>-->
-					<!--<suiteXmlFiles>-->
-						<!--<suiteXmlFile>testResources/LightTests.xml</suiteXmlFile>-->
-					<!--</suiteXmlFiles>-->
-				<!--</configuration>-->
-			<!--</plugin>-->
-		</plugins>
-	</reporting>
 	<dependencies>
+		<dependency>
+			<groupId>org.scala-lang</groupId>
+			<artifactId>scala-library</artifactId>
+            <version>${scala.version}</version>
+		</dependency>
+        <dependency>
+            <groupId>com.lihaoyi</groupId>
+            <artifactId>os-lib_2.13</artifactId>
+            <version>0.8.1</version>
+        </dependency>
 		<dependency>
 			<groupId>commons-cli</groupId>
 			<artifactId>commons-cli</artifactId>
@@ -143,7 +61,8 @@
 		<dependency>
 			<groupId>net.sourceforge.owlapi</groupId>
 			<artifactId>owlapi-distribution</artifactId>
-			<version>3.4.10</version>
+			<version>5.1.20</version>
+			<!-- <version>3.4.10</version> -->
 		</dependency>
 		<dependency>
 			<groupId>org.openrdf.sesame</groupId>
@@ -207,5 +126,242 @@
 			<!--<artifactId>plexus-utils</artifactId>-->
 			<!--<version>1.1</version>-->
 		<!--</dependency>-->
+    <dependency>
+      <groupId>org.scalatest</groupId>
+      <artifactId>scalatest_${scala.compat.version}</artifactId>
+      <version>3.2.10</version>
+      <scope>test</scope>
+    </dependency>
+		<dependency>
+			<groupId>uk.ox.ac.uk.rsacomb</groupId>
+			<artifactId>rsacomb</artifactId>
+			<version>1.0.0</version>
+            <scope>system</scope>
+            <systemPath>${project.basedir}/lib/RSAComb-1.0.0.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>tech.oxfordsemantic.jrdfox</groupId>
+			<artifactId>jrdfox</artifactId>
+			<version>5.4</version>
+            <scope>system</scope>
+            <systemPath>${project.basedir}/lib/JRDFox.jar</systemPath>
+		</dependency>
+
+
+
+
 	</dependencies>
+
+	<build>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-compiler-plugin</artifactId>
+					<version>3.8.1</version>
+					<configuration>
+                      <source>1.8</source>
+                      <target>1.8</target>
+                    </configuration>
+				</plugin>
+				<plugin>
+					<groupId>net.alchim31.maven</groupId>
+					<artifactId>scala-maven-plugin</artifactId>
+					<version>4.5.6</version>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<configuration>
+                  <source>1.8</source>
+                  <target>1.8</target>
+                </configuration>
+				<executions>
+					<execution>
+						<phase>compile</phase>
+						<goals>
+							<goal>compile</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>net.alchim31.maven</groupId>
+				<artifactId>scala-maven-plugin</artifactId>
+				<executions>
+					<execution>
+						<!-- <id>scala-compile-first</id> -->
+						<phase>compile</phase>
+						<goals>
+							<goal>add-source</goal>
+							<goal>compile</goal>
+						</goals>
+					</execution>
+					<execution>
+						<id>scala-test-compile</id>
+						<phase>process-test-resources</phase>
+						<goals>
+							<goal>testCompile</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<configuration>
+					<archive>
+						<manifest>
+							<mainClass>uk.ac.ox.cs.acqua.Acqua</mainClass>
+						</manifest>
+					</archive>
+					<descriptorRefs>
+						<descriptorRef>jar-with-dependencies</descriptorRef>
+					</descriptorRefs>
+				</configuration>
+				<executions>
+					<execution>
+						<id>make-assembly</id> <!-- this is used for inheritance merges -->
+						<phase>package</phase> <!-- bind to the packaging phase -->
+						<goals>
+							<goal>single</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+	</build>
+
+  <!--  <build>-->
+  <!--      <sourceDirectory>src/main/scala</sourceDirectory>-->
+  <!--      <testSourceDirectory>src/test/scala</testSourceDirectory>-->
+		<!--<resources>-->
+			<!--<resource>-->
+				<!--<directory>src/main/java/resources</directory>-->
+				<!--<excludes>-->
+					<!--<exclude>pagoda.properties</exclude>-->
+				<!--</excludes>-->
+			<!--</resource>-->
+
+		<!--</resources>-->
+		<!--<testResources>-->
+			<!--<testResource>-->
+  <!--              <directory>src/test/java/resources</directory>-->
+			<!--</testResource>-->
+		<!--</testResources>-->
+		<!--<plugins>-->
+			<!--<plugin>-->
+				<!--<artifactId>maven-compiler-plugin</artifactId>-->
+				<!--<version>3.1</version>-->
+				<!--<configuration>-->
+					<!--<source>1.8</source>-->
+					<!--<target>1.8</target>-->
+				<!--</configuration>-->
+			<!--</plugin>-->
+
+
+			<!--<plugin>-->
+				<!--<artifactId>maven-project-info-reports-plugin</artifactId>-->
+				<!--<version>2.7</version>-->
+			<!--</plugin>-->
+
+  <!--        <plugin>-->
+  <!--          <groupId>org.apache.maven.plugins</groupId>-->
+  <!--          <artifactId>maven-surefire-plugin</artifactId>-->
+  <!--          <version>2.21.0</version>-->
+  <!--          <configuration>-->
+  <!--            <!-1- Tests will be run with scalatest-maven-plugin instead -1->-->
+  <!--            <skipTests>true</skipTests>-->
+  <!--          </configuration>-->
+  <!--        </plugin>-->
+  <!--        <plugin>-->
+  <!--          <groupId>org.scalatest</groupId>-->
+  <!--          <artifactId>scalatest-maven-plugin</artifactId>-->
+  <!--          <version>2.0.0</version>-->
+  <!--          <configuration>-->
+  <!--            <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>-->
+  <!--            <junitxml>.</junitxml>-->
+  <!--            <filereports>TestSuiteReport.txt</filereports>-->
+  <!--            <!-1- Comma separated list of JUnit test class names to execute -1->-->
+  <!--            <jUnitClasses>samples.AppTest</jUnitClasses>-->
+  <!--          </configuration>-->
+  <!--          <executions>-->
+  <!--            <execution>-->
+  <!--              <id>test</id>-->
+  <!--              <goals>-->
+  <!--                <goal>test</goal>-->
+  <!--              </goals>-->
+  <!--            </execution>-->
+  <!--          </executions>-->
+  <!--        </plugin>-->
+		<!--</plugins>-->
+	<!--</build>-->
+
+	<!--<reporting>-->
+		<!--<plugins>-->
+			<!--<plugin>-->
+				<!--<groupId>org.apache.maven.plugins</groupId>-->
+				<!--<artifactId>maven-javadoc-plugin</artifactId>-->
+				<!--<version>2.9.1</version>-->
+				<!--<configuration>-->
+					<!--<show>public</show>-->
+				<!--</configuration>-->
+			<!--</plugin>-->
+			<!--<plugin>-->
+				<!--<groupId>org.codehaus.mojo</groupId>-->
+				<!--<artifactId>findbugs-maven-plugin</artifactId>-->
+				<!--<version>3.0.0</version>-->
+				<!--<configuration>-->
+					<!--<xmlOutput>true</xmlOutput>-->
+					<!--<!-1- Optional directory to put findbugs xdoc xml report -1->-->
+					<!--<xmlOutputDirectory>target/site</xmlOutputDirectory>-->
+				<!--</configuration>-->
+			<!--</plugin>-->
+			<!--<plugin>-->
+				<!--<groupId>org.apache.maven.plugins</groupId>-->
+				<!--<artifactId>maven-checkstyle-plugin</artifactId>-->
+				<!--<version>2.5</version>-->
+				<!--<configuration>-->
+					<!--<configLocation>config/sun_checks.xml</configLocation><!-1- default -1->-->
+					<!--<!-1- <configLocation>config/maven_checks.xml</configLocation> -1->-->
+					<!--<!-1- <configLocation>config/turbine_checks.xml</configLocation> -1->-->
+					<!--<!-1- <configLocation>config/avalon_checks.xml</configLocation> -1->-->
+				<!--</configuration>-->
+			<!--</plugin>-->
+			<!--<plugin>-->
+				<!--<groupId>org.apache.maven.plugins</groupId>-->
+				<!--<artifactId>maven-jxr-plugin</artifactId>-->
+				<!--<version>2.1</version>-->
+			<!--</plugin>-->
+			<!--<plugin>-->
+				<!--<groupId>org.codehaus.mojo</groupId>-->
+				<!--<artifactId>dashboard-maven-plugin</artifactId>-->
+				<!--<version>1.0.0-beta-1</version>-->
+			<!--</plugin>-->
+			<!--<!-1-<plugin>-1->-->
+				<!--<!-1-<groupId>org.apache.maven.plugins</groupId>-1->-->
+				<!--<!-1-<artifactId>maven-surefire-plugin</artifactId>-1->-->
+				<!--<!-1-<version>2.13</version>-1->-->
+				<!--<!-1-<configuration>-1->-->
+					<!--<!-1-<forkMode>always</forkMode>-1->-->
+					<!--<!-1-<systemPropertyVariables>-1->-->
+						<!--<!-1-<reporter.debug>false</reporter.debug>-1->-->
+					<!--<!-1-</systemPropertyVariables>-1->-->
+					<!--<!-1-<suiteXmlFiles>-1->-->
+						<!--<!-1-<suiteXmlFile>testResources/LightTests.xml</suiteXmlFile>-1->-->
+					<!--<!-1-</suiteXmlFiles>-1->-->
+				<!--<!-1-</configuration>-1->-->
+			<!--<!-1-</plugin>-1->-->
+		<!--</plugins>-->
+	<!--</reporting>-->
+
+	<!--<dependencies>-->
+  <!--  <dependency>-->
+  <!--    <groupId>org.scala-lang</groupId>-->
+  <!--    <artifactId>scala-library</artifactId>-->
+  <!--    <version>${scala.version}</version>-->
+  <!--  </dependency>-->
+	<!--</dependencies>-->
 </project>
-- 
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