From 2ad365322efe158bda79f7ad3781b23d31b1fd39 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Tue, 22 Oct 2024 16:29:32 +0200
Subject: [PATCH] refactor(collapse-edges): Refactor how edges are collapsed to
 remove clutter

---
 R/utils_getSubnetworkFromIndra.R | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/R/utils_getSubnetworkFromIndra.R b/R/utils_getSubnetworkFromIndra.R
index 36c8985..ad8198b 100644
--- a/R/utils_getSubnetworkFromIndra.R
+++ b/R/utils_getSubnetworkFromIndra.R
@@ -48,8 +48,7 @@
     edge$evidence_list <- paste(
         "https://db.indra.bio/statements/from_agents?subject=",
         edge$source_id, "@HGNC&object=",
-        edge$target_id, "@HGNC&type=",
-        edge$data$stmt_type, "&format=html",
+        edge$target_id, "&format=html",
         sep = ""
     )
     edge$source_uniprot_id <- input[input$HgncId == edge$source_id, ]$Protein
@@ -69,18 +68,26 @@
     edgeToMetadataMapping <- hashmap()
 
     for (edge in res) {
-        key <- paste(edge$source_id, edge$target_id, edge$data$stmt_type,
-            sep = "_"
-        )
+        key <- paste(edge$source_id, edge$target_id, sep = "_")
         if (key %in% keys(edgeToMetadataMapping)) {
             edgeToMetadataMapping[[key]]$data$evidence_count <-
                 edgeToMetadataMapping[[key]]$data$evidence_count +
                 edge$data$evidence_count
+            edgeToMetadataMapping[[key]]$data$stmt_type <- c(
+                edgeToMetadataMapping[[key]]$data$stmt_type,
+                edge$data$stmt_type)
         } else {
             edge <- .addAdditionalMetadataToIndraEdge(edge, input)
             edgeToMetadataMapping[[key]] <- edge
         }
     }
+    
+    for (key in keys(edgeToMetadataMapping)) {
+        edgeToMetadataMapping[[key]]$data$stmt_type <-
+            unique(edgeToMetadataMapping[[key]]$data$stmt_type)
+        edgeToMetadataMapping[[key]]$data$stmt_type <-
+            paste(edgeToMetadataMapping[[key]]$data$stmt_type, collapse = ", ")
+    }
 
     return(edgeToMetadataMapping)
 }