From aca23b1f76c4bea6a2c5aa28edfea62f23fd54c2 Mon Sep 17 00:00:00 2001
From: Samuel Brand <48288458+SamuelBrand1@users.noreply.github.com>
Date: Fri, 16 Aug 2024 14:39:58 +0100
Subject: [PATCH] Fix the truthdata output to be missing or Int (#429)

---
 pipeline/src/simulate/TruthSimulationConfig.jl   | 2 +-
 pipeline/test/pipeline/test_pipelinefunctions.jl | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipeline/src/simulate/TruthSimulationConfig.jl b/pipeline/src/simulate/TruthSimulationConfig.jl
index be336d3f1..09dc2203e 100644
--- a/pipeline/src/simulate/TruthSimulationConfig.jl
+++ b/pipeline/src/simulate/TruthSimulationConfig.jl
@@ -67,7 +67,7 @@ function simulate(config::TruthSimulationConfig)
         (std = 1.0, cluster_factor = config.cluster_factor,
             ϵ_t = config.logit_daily_ascertainment))
 
-    y_t = obs_model()
+    y_t = obs_model() .|> y -> ismissing(y) ? missing : Int(y)
 
     #Return the sampled infections and observations
 
diff --git a/pipeline/test/pipeline/test_pipelinefunctions.jl b/pipeline/test/pipeline/test_pipelinefunctions.jl
index 76643496f..1a2b87d15 100644
--- a/pipeline/test/pipeline/test_pipelinefunctions.jl
+++ b/pipeline/test/pipeline/test_pipelinefunctions.jl
@@ -5,7 +5,7 @@
     truthdata = fetch.(truthdata_dg_task)
 
     @test length(truthdata) == 1
-    @test all([data["y_t"] isa Vector{Union{Missing, T}} where {T <: Real}
+    @test all([data["y_t"] isa Vector{Union{Missing, T}} where {T <: Integer}
                for data in truthdata])
 end