From 87642d2620d93a8814adca3d1fe66481946e5b14 Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Thu, 31 Oct 2024 14:36:55 -0400
Subject: [PATCH] fix(ingestion): create contig indices once after final header
 line found

---
 src/api/services/ingestion.go | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/src/api/services/ingestion.go b/src/api/services/ingestion.go
index ca2dc62..4eb1569 100644
--- a/src/api/services/ingestion.go
+++ b/src/api/services/ingestion.go
@@ -408,27 +408,27 @@ func (i *IngestionService) ProcessVcf(
 					}
 				}
 
-				discoveredHeaders = true
+				// If we got to the VCF final header line, we've found all the contigs possible
+				// --> create required indices with mappings to ensure ES types are consistent
+				fmt.Printf("Got %d contigs: %v\n", len(contigs), contigs)
+				for _, c := range contigs {
+					var client = i.ElasticsearchClient
+
+					mappings, _ := json.Marshal(indexes.VARIANT_INDEX_MAPPING)
+					var createBody = fmt.Sprintf(`{"mappings": %s}`, mappings)
+
+					client.Indices.Create(
+						variantIndexName(c),
+						client.Indices.Create.WithBody(strings.NewReader(createBody)),
+					)
+				}
 
 				fmt.Println("Found the headers: ", headers)
-				continue
+				discoveredHeaders = true
 			}
 			continue
 		}
 
-		// Create required indices with mappings to ensure ES types are cosnsitent
-		for _, c := range contigs {
-			var client = i.ElasticsearchClient
-
-			mappings, _ := json.Marshal(indexes.VARIANT_INDEX_MAPPING)
-			var createBody = fmt.Sprintf(`{"mappings": %s}`, mappings)
-
-			client.Indices.Create(
-				variantIndexName(c),
-				client.Indices.Create.WithBody(strings.NewReader(createBody)),
-			)
-		}
-
 		// take a spot in the queue
 		lineProcessingQueue <- true
 		_fileWG.Add(1)