From ad3ce727926f1f5b7f1d6bddebe6b5390071f43d Mon Sep 17 00:00:00 2001
From: Kristoffer Kiil <kriskiil@users.noreply.github.com>
Date: Thu, 9 Jan 2025 13:52:11 +0100
Subject: [PATCH] Update aggregation.py

Resistance genes are put into a list, only unique elements are retained, and eventually the elements are concatenated to a string
---
 bifrost/bifrost_listener/aggregation.py | 32 +++++++++++++++++--------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/bifrost/bifrost_listener/aggregation.py b/bifrost/bifrost_listener/aggregation.py
index 0c0627dd..b4d839d2 100644
--- a/bifrost/bifrost_listener/aggregation.py
+++ b/bifrost/bifrost_listener/aggregation.py
@@ -87,20 +87,32 @@ def agg_pipeline(changed_ids=None):
                 "resistance_genes": {
                     "$reduce": {
                         "input": {
-                            "$map": {
-                                "input": {"$objectToArray": "$categories.resistance.report.phenotypes"},
-                                "as": "phenotype",
-                                "in": {
-                                    "$reduce": {
-                                        "input": {"$objectToArray": "$$phenotype.v.genes"},
-                                        "initialValue": "",
-                                        "in": {"$concat": ["$$value", {"$cond": [{"$eq": ["$$value", ""]}, "", ", "]}, "$$this.k"]}
+                            "$reduce": {
+                                "input": {
+                                    "$map": {
+                                        "input": {"$objectToArray": "$categories.resistance.report.phenotypes"},
+                                        "as": "phenotype",
+                                        "in": {
+                                            "$reduce": {
+                                                "input": {"$objectToArray": "$$phenotype.v.genes"},
+                                                "initialValue": [],
+                                                "in": {"$concatArrays": ["$$value", ["$$this.k"]]}
+                                            }
+                                        }
                                     }
-                                }
+                                },
+                                "initialValue": [],
+                                "in": {"$setUnion": ["$$value", "$$this"]}
                             }
                         },
                         "initialValue": "",
-                        "in": {"$concat": ["$$value", {"$cond": [{"$eq": ["$$value", ""]}, "", ", "]}, "$$this"]}
+                        "in": {
+                            "$cond": {
+                                "if": {"$eq": ["$$value",""]},
+                                "then": "$$this",
+                                "else": {"$concat":["$$value", ", ", "$$this"]}
+                            }
+                        }
                     }
                 },
                 "amr_profile": "$categories.resistance.summary",