From 6b8a194a13fad5196aa57c7a46d8c58c00c6ea9d Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <guillaumepoiriermorency@gmail.com>
Date: Sun, 17 Sep 2023 11:34:33 -0700
Subject: [PATCH] Use Jena 2.12.1 implementation of the rulesys reasoner

The implementation supplied by Jena 2.7 is very inefficient because it
has a O(n^2) complexity for inferring axioms.

This is achieved by shading Jena under ubic.basecode.ontology.jena.impl
package namespace. It also implicates that baseCode does not depend on
Jena anymore.

Jena 2.13.0 has breaking implementation changes and cannot be integrated
this way.
---
 pom.xml | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 94 insertions(+)

diff --git a/pom.xml b/pom.xml
index e83c2a14..39cd22ae 100644
--- a/pom.xml
+++ b/pom.xml
@@ -347,6 +347,100 @@
 					</gitFlowConfig>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-dependency-plugin</artifactId>
+				<version>3.3.0</version>
+				<executions>
+					<execution>
+						<id>unpack-jena-rete-engine</id>
+						<phase>generate-sources</phase>
+						<goals>
+							<goal>unpack</goal>
+						</goals>
+						<configuration>
+							<artifactItems>
+								<artifactItem>
+									<groupId>org.apache.jena</groupId>
+									<artifactId>jena-core</artifactId>
+									<version>2.12.1</version>
+									<classifier>sources</classifier>
+									<outputDirectory>${project.build.directory}/generated-sources/jena-core</outputDirectory>
+									<includes>com/hp/hpl/jena/reasoner/rulesys/impl/*.java,com/hp/hpl/jena/graph/NodeFactory.java</includes>
+								</artifactItem>
+							</artifactItems>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>build-helper-maven-plugin</artifactId>
+				<version>3.3.0</version>
+				<executions>
+					<execution>
+						<phase>generate-sources</phase>
+						<goals>
+							<goal>add-source</goal>
+						</goals>
+						<configuration>
+							<!-- dependencies:unpack does not add a source root -->
+							<sources>${project.build.directory}/generated-sources/jena-core</sources>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-shade-plugin</artifactId>
+				<version>3.5.0</version>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>shade</goal>
+						</goals>
+						<configuration>
+							<artifactSet>
+								<includes>
+									<include>org.apache.jena:*</include>
+								</includes>
+							</artifactSet>
+							<filters>
+								<filter>
+									<artifact>org.apache.jena:*</artifact>
+									<includes>
+										<include>com/hp/hpl/jena/**/*</include>
+										<include>org/apache/jena/**/*</include>
+										<include>org/openjena/**/*</include>
+										<include>etc/**/*</include>
+										<include>vocabularies/**/*</include>
+									</includes>
+									<excludes>
+										<!-- this one we compiled ourselves -->
+										<exclude>com/hp/hpl/jena/reasoner/rulesys/impl/**/*</exclude>
+									</excludes>
+								</filter>
+							</filters>
+							<!-- relocate Jena under a private package name to prevent conflicts -->
+							<relocations>
+								<relocation>
+									<pattern>com.hp.hpl.jena</pattern>
+									<shadedPattern>ubic.basecode.ontology.jena.impl</shadedPattern>
+								</relocation>
+								<relocation>
+									<pattern>org.apache.jena</pattern>
+									<shadedPattern>ubic.basecode.ontology.jena.impl</shadedPattern>
+								</relocation>
+								<relocation>
+									<pattern>org.openjena</pattern>
+									<shadedPattern>ubic.basecode.ontology.jena.impl</shadedPattern>
+								</relocation>
+							</relocations>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>