From f3dbe9cdf3507baad9d7b7c3fc60d912de82c572 Mon Sep 17 00:00:00 2001
From: dustine32 <dustine32@gmail.com>
Date: Tue, 12 Mar 2024 14:22:57 -0700
Subject: [PATCH] Allow Reactome to share intermediate small mols for #308

---
 .../gocam/exchange/BioPaxtoGO.java            |  6 +++---
 .../gocam/exchange/BioPaxtoGOTest.java        | 21 +++++--------------
 2 files changed, 8 insertions(+), 19 deletions(-)

diff --git a/exchange/src/main/java/org/geneontology/gocam/exchange/BioPaxtoGO.java b/exchange/src/main/java/org/geneontology/gocam/exchange/BioPaxtoGO.java
index 81247a7..e8d575e 100644
--- a/exchange/src/main/java/org/geneontology/gocam/exchange/BioPaxtoGO.java
+++ b/exchange/src/main/java/org/geneontology/gocam/exchange/BioPaxtoGO.java
@@ -1331,7 +1331,7 @@ else if (entity instanceof Interaction){
 							input_id = UUID.randomUUID().toString();
 						}
 						String input_location = null;
-						if (small_mol_do_not_join_ids.contains(input_id) || input.getCellularLocation() == null || entityStrategy.equals(EntityStrategy.REACTO)) {
+						if (small_mol_do_not_join_ids.contains(input_id) || input.getCellularLocation() == null) {
 							// Gotta make these locations specific to rxn ID for do_not_join classes
 							input_location = entity_id;
 						} else {
@@ -1341,7 +1341,7 @@ else if (entity instanceof Interaction){
 							}
 							input_location = String.join("_", in_location_terms);
 						}
-						if(entityStrategy.equals(EntityStrategy.YeastCyc) && !small_mol_do_not_join_ids.contains(input_id)){
+						if(!small_mol_do_not_join_ids.contains(input_id)){
 							// Try to reuse previous rxn's output instance
 							for(PathwayStep previous_step : previous_steps) {
 								BiochemicalReaction reaction = getBiochemicalReaction(previous_step);
@@ -1379,7 +1379,7 @@ else if (entity instanceof Interaction){
 							output_id = UUID.randomUUID().toString();
 						}
 						String output_location = null;
-						if (small_mol_do_not_join_ids.contains(output_id) || output.getCellularLocation() == null || entityStrategy.equals(EntityStrategy.REACTO)) {
+						if (small_mol_do_not_join_ids.contains(output_id) || output.getCellularLocation() == null) {
 							// Gotta make these locations specific to rxn ID for do_not_join classes
 							output_location = entity_id;
 						} else {
diff --git a/exchange/src/test/java/org/geneontology/gocam/exchange/BioPaxtoGOTest.java b/exchange/src/test/java/org/geneontology/gocam/exchange/BioPaxtoGOTest.java
index fc49f45..04cbba5 100644
--- a/exchange/src/test/java/org/geneontology/gocam/exchange/BioPaxtoGOTest.java
+++ b/exchange/src/test/java/org/geneontology/gocam/exchange/BioPaxtoGOTest.java
@@ -1013,31 +1013,20 @@ public final void testInferRegulatesViaOutputEnables() {
 		System.out.println("Done testing regulates via output enables");
 	}
 	
-	//gomodel:R-HSA-4641262/R-HSA-201677 / RO:0002413 / gomodel:R-HSA-4641262/R-HSA-201691
-	// #inferProvidesInput	
-	/**
-	 * Test method for {@link org.geneontology.gocam.exchange.GoCAM#inferProvidesInput}.
-	 * Use pathway R-HSA-4641262 , reaction1 = R-HSA-201677 reaction2 = R-HSA-201691
-	 * Relation should be RO:0002413 directly positive regulates
-	 * Phosphorylation of LRP5/6 cytoplasmic domain by membrane-associated GSK3beta
-	 * Phosphorylation of LRP5/6 cytoplasmic domain by CSNKI
-	 * 	https://reactome.org/content/detail/R-HSA-4641262 
-	 * Compare to http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-4641262
-	 * 
-	 * Also an active site detection test
-	 */
 	@Test
-	public final void testInferProvidesInput() {
+	public final void testSharedIntermediateInputs() {
 		System.out.println("Testing provides input");
 		TupleQueryResult result = null;
 		try {
+			// Check for shared input/output entity instance between rxns
 			result = blaze.runSparqlQuery(
 				"prefix obo: <http://purl.obolibrary.org/obo/> "
 				+ "select ?pathway " + 
 				"where { " + 
 				"VALUES ?reaction1 { <http://model.geneontology.org/R-HSA-201677> } . "+ 
 				"VALUES ?reaction2 { <http://model.geneontology.org/R-HSA-201691> } . "+
-				" ?reaction1 obo:RO_0002413 ?reaction2 . "
+				" ?reaction1 obo:RO_0002234 ?small_mol . " +
+				" ?reaction2 obo:RO_0002233 ?small_mol . "
 				+ "?reaction1 obo:BFO_0000050 ?pathway "+				
 				"}");
 			int n = 0; String pathway = null;
@@ -1059,7 +1048,7 @@ public final void testInferProvidesInput() {
 				e.printStackTrace();
 			}
 		}
-		System.out.println("Done testing regulates via output enables");
+		System.out.println("Done testing sharing of intermediate small molecules");
 	}
 	
 	@Test