From aaceda2c83f744645859008f4b37a54a840760a9 Mon Sep 17 00:00:00 2001
From: IgorRodchenkov <rodche@gmail.com>
Date: Thu, 4 Jul 2024 19:40:03 -0400
Subject: [PATCH] Fix for a NPE bug related to PathwayCommons/cpath2#321 case
 (when actual large blacklist of ubiquitous mol. was used)

---
 sbgn-converter/pom.xml                        |  5 ++++
 .../paxtools/io/sbgn/L3ToSBGNPDConverter.java |  8 ++++---
 .../paxtools/io/sbgn/SBGNConverterTest.java   | 24 +++++++++++++++++++
 3 files changed, 34 insertions(+), 3 deletions(-)

diff --git a/sbgn-converter/pom.xml b/sbgn-converter/pom.xml
index faa4ee0f9..aadcdddc9 100644
--- a/sbgn-converter/pom.xml
+++ b/sbgn-converter/pom.xml
@@ -30,5 +30,10 @@
         	<artifactId>chilay-sbgn</artifactId>
         	<version>3.1.0</version>
         </dependency>
+        <dependency>
+            <groupId>org.biopax.paxtools</groupId>
+            <artifactId>pattern</artifactId>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 </project>
\ No newline at end of file
diff --git a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/L3ToSBGNPDConverter.java b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/L3ToSBGNPDConverter.java
index 2d5e56444..028c2638d 100644
--- a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/L3ToSBGNPDConverter.java
+++ b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/L3ToSBGNPDConverter.java
@@ -314,7 +314,9 @@ public Sbgn createSBGN(Model model) {
 				//a Control without controlled process but with controller and is controlledOf
 				if(control.getControlled().isEmpty()) {
 					Glyph g = createControlStructure(control);
-					processControllers(control.getControlledOf(), g);
+					if(g != null) {
+						processControllers(control.getControlledOf(), g);
+					}
 				}//else - do nothing - as it's converted anyway when the controlled interactions are processed
 			}
 
@@ -1280,8 +1282,8 @@ private void addPorts(Glyph g) {
 	 * Creates an arc from the source to the target, and sets its class to the specified clazz.
 	 * Puts the new arc in the sullied arcMap.
 	 *
-	 * @param source source of the arc -- either Glyph or Port
-	 * @param target target of the arc -- either Glyph or Port
+	 * @param source - source of the arc -- either Glyph or Port
+	 * @param target - target of the arc -- either Glyph or Port
 	 * @param clazz class of the arc
 	 */
 	private void createArc(Object source, Object target, String clazz, Stoichiometry stoic)
diff --git a/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java b/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java
index 035e472f2..4a37ec31e 100644
--- a/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java
+++ b/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java
@@ -7,7 +7,9 @@
 import org.biopax.paxtools.model.BioPAXLevel;
 import org.biopax.paxtools.model.Model;
 import org.biopax.paxtools.model.level3.*;
+import org.biopax.paxtools.pattern.util.Blacklist;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.sbgn.GlyphClazz;
 import org.sbgn.SbgnUtil;
@@ -20,6 +22,8 @@
 import javax.xml.bind.Marshaller;
 import javax.xml.bind.Unmarshaller;
 import java.io.*;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -383,4 +387,24 @@ private Collection<Glyph> filterGlyphsByClazz(Collection<Glyph> collection, Stri
   private Collection<Arc> filterArcsByClazz(Collection<Arc> collection, String clazz) {
 		return collection.stream().filter(g -> g.getClazz().equals(clazz)).collect(Collectors.toUnmodifiableSet());
   }
+
+	@Disabled
+	@Test
+	public void convertPc14NearestNeighborhoodOfANK1_PTEN() throws Exception
+	{
+		Model level3 = handler.convertFromOWL(Files.newInputStream(Paths.get("/home/igor/Downloads/cpath2-issue-321-pc14-nhood-ank1-pten-data.owl")));
+		String out = "target/cpath2-321.sbgn";
+
+		UbiqueDetector bl = new ListUbiqueDetector(new Blacklist("/home/igor/Workspace/pc-stack/work/downloads/blacklist.txt").getListed());
+		L3ToSBGNPDConverter conv = new L3ToSBGNPDConverter(bl,null, false);
+		conv.writeSBGN(level3, out);
+
+		File outFile = new File(out);
+		SbgnUtil.isValid(outFile); //ignore CName warning
+		// Now read the SBGN model back
+		Sbgn result = (Sbgn) unmarshaller.unmarshal (outFile);
+		// Assert that the sbgn result contains glyphs
+		List<Glyph> glyphList = result.getMap().getGlyph();
+		assertFalse(glyphList.isEmpty());
+	}
 }