From 5cf922d69f2a035fc0c53b4d04d76e3e44320ec2 Mon Sep 17 00:00:00 2001
From: Louis <louis.lacoste@agroparistech.fr>
Date: Mon, 13 Oct 2025 13:41:05 +0200
Subject: [PATCH] Perform file existence check in load script

---
 load-europe.R | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/load-europe.R b/load-europe.R
index 274e6b1..d722661 100644
--- a/load-europe.R
+++ b/load-europe.R
@@ -1,14 +1,18 @@
-library(MicroBioMap)
-library(phyloseq)
-library(mia)
+if (!file.exists("data/hmc-phyloseq-europe.Rds")) {
+    library(MicroBioMap)
+    library(phyloseq)
+    library(mia)
 
-cpd <- getCompendium()
-cpd_phyloseq <- convertToPhyloseq(x = cpd)
-sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe")
-rm(cpd)
-gc()
-sample_data(cpd_phyloseq)
-cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name))
-rm(cpd_phyloseq)
-gc()
-saveRDS(cpd_phyloseq_europe, "data/hmc-phyloseq-europe.Rds")
+    cpd <- getCompendium()
+    cpd_phyloseq <- convertToPhyloseq(x = cpd)
+    sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe")
+    rm(cpd)
+    gc()
+    sample_data(cpd_phyloseq)
+    cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name))
+    rm(cpd_phyloseq)
+    gc()
+    saveRDS(cpd_phyloseq_europe, "data/hmc-phyloseq-europe.Rds")
+} else {
+    cpd_phyloseq_europe <- readRDS("data/hmc-phyloseq-europe.Rds")
+}