From c56f1e2d6c069d69d561d04d037aa9bf01b06348 Mon Sep 17 00:00:00 2001
From: IgorRodchenkov <rodche@gmail.com>
Date: Mon, 9 Oct 2023 19:17:30 -0400
Subject: [PATCH] Upgraded Jena dependency; improved the enum typeOf methods
 (allows any capitalization and both '-' and '_' in the values).

---
 json-converter/pom.xml                        | 48 +------------------
 .../io/jsonld/JsonldBiopaxConverterTest.java  |  3 +-
 .../paxtools/pattern/miner/SIFEnum.java       | 10 ++--
 .../paxtools/query/algorithm/Direction.java   | 18 ++++++-
 .../paxtools/query/algorithm/LimitType.java   | 19 +++++++-
 5 files changed, 44 insertions(+), 54 deletions(-)

diff --git a/json-converter/pom.xml b/json-converter/pom.xml
index 882767328..58a99ff3b 100644
--- a/json-converter/pom.xml
+++ b/json-converter/pom.xml
@@ -15,58 +15,12 @@
 		<tag>HEAD</tag>
 	</scm>
 
-	<build>
-		<plugins>
-			<plugin>
-				<artifactId>maven-assembly-plugin</artifactId>
-				<configuration>
-					<descriptorRefs>
-						<descriptorRef>jar-with-dependencies</descriptorRef>
-					</descriptorRefs>
-				</configuration>
-				<executions>
-					<execution>
-						<id>make-assembly</id>
-						<phase>package</phase>
-						<goals>
-							<goal>single</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-		</plugins>
-	</build>
-
 	<dependencies>
 		<dependency>
 			<groupId>org.apache.jena</groupId>
 			<artifactId>apache-jena-libs</artifactId>
+			<version>4.9.0</version>
 			<type>pom</type>
-			<version>3.2.0</version>
-			<exclusions>
-				<exclusion>
-					<groupId>log4j</groupId>
-					<artifactId>log4j</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.slf4j</groupId>
-					<artifactId>slf4j-log4j12</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-		<dependency>
-			<groupId>com.hp.hpl.jena</groupId>
-			<artifactId>jena</artifactId>
-			<exclusions>
-				<exclusion>
-					<groupId>log4j</groupId>
-					<artifactId>log4j</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.slf4j</groupId>
-					<artifactId>slf4j-log4j12</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.biopax.paxtools</groupId>
diff --git a/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java b/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java
index c8cfcb2fc..d6496fd7d 100644
--- a/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java
+++ b/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java
@@ -19,8 +19,7 @@ public final void test() throws IOException {
 		JsonldConverter intf = new JsonldBiopaxConverter();
 
 		// convert owl test file in resource directory to jsonld format
-		InputStream in = getClass().getResourceAsStream(
-				"/PC2v5test-Signaling-By-BMP-Pathway-REACT_12034.2.owl");
+		InputStream in = getClass().getResourceAsStream("/PC2v5test-Signaling-By-BMP-Pathway-REACT_12034.2.owl");
 		intf.convertToJsonld(in, new FileOutputStream(jsonldTestFileName));
 
 		// convert jsonld test file back to rdf format
diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFEnum.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFEnum.java
index dc0ba74b2..9e1407e76 100644
--- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFEnum.java
+++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFEnum.java
@@ -1,5 +1,7 @@
 package org.biopax.paxtools.pattern.miner;
 
+import org.apache.commons.lang3.StringUtils;
+
 import java.util.Arrays;
 import java.util.List;
 
@@ -107,10 +109,12 @@ public List<Class<? extends SIFMiner>> getMiners()
 
 	public static SIFEnum typeOf(String tag)
 	{
-		tag = tag.toUpperCase().replaceAll("-", "_");
+		if(StringUtils.isBlank(tag))
+			return null;
+
 		SIFEnum type = null;
-		try
-		{
+		try {
+			tag = tag.toUpperCase().replaceAll("-", "_");
 			type = valueOf(tag);
 		}
 		catch (IllegalArgumentException e){}
diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Direction.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Direction.java
index 051092263..e01269547 100644
--- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Direction.java
+++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Direction.java
@@ -1,5 +1,7 @@
 package org.biopax.paxtools.query.algorithm;
 
+import org.apache.commons.lang3.StringUtils;
+
 /**
  * Direction is used for specifying upstream, downstream or both. Neighborhood and CommonStream
  * queries use this enum as parameter.
@@ -28,7 +30,7 @@ public enum Direction
 	 * Constructor with description.
 	 * @param description Description
 	 */
-	private Direction(String description)
+	Direction(String description)
 	{
 		this.description = description;
 	}
@@ -41,4 +43,18 @@ public String getDescription()
 	{
 		return description;
 	}
+
+	public static Direction typeOf(String tag)
+	{
+		if(StringUtils.isBlank(tag))
+			return null;
+
+		Direction type = null;
+		try {
+			type = valueOf(tag.toUpperCase());
+		}
+		catch (IllegalArgumentException e){}
+
+		return type;
+	}
 }
diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/LimitType.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/LimitType.java
index 8d62bd461..cde938949 100644
--- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/LimitType.java
+++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/LimitType.java
@@ -1,5 +1,7 @@
 package org.biopax.paxtools.query.algorithm;
 
+import org.apache.commons.lang3.StringUtils;
+
 /**
  * Specifies whether the length limit is a normal limit or shortest_plus_k limit. PathsFromToQuery
  * use this as a parameter.
@@ -9,5 +11,20 @@
 public enum LimitType
 {
 	NORMAL,
-	SHORTEST_PLUS_K
+	SHORTEST_PLUS_K;
+
+	public static LimitType typeOf(String tag)
+	{
+		if(StringUtils.isBlank(tag))
+			return null;
+
+		LimitType type = null;
+		try {
+			tag = tag.toUpperCase().replaceAll("-", "_");
+			type = valueOf(tag);
+		}
+		catch (IllegalArgumentException e){}
+
+		return type;
+	}
 }