From a8fdd7f439aec0174ade6e4a2fe3385799afd042 Mon Sep 17 00:00:00 2001
From: Michael Dales <mwd24@cam.ac.uk>
Date: Tue, 25 Nov 2025 09:32:30 +0000
Subject: [PATCH] Add occurrence validation to run script

---
 requirements.txt |  2 +-
 scripts/run.sh   | 12 ++++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 8077573..d059589 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -7,7 +7,7 @@ pymer4
 pyproj
 scikit-image
 redlistapi
-yirgacheffe>=1.9
+yirgacheffe>=1.10
 aoh[validation]>=1.0
 
 # GDAL should be installed manually to match the version of the library installed on your machine
diff --git a/scripts/run.sh b/scripts/run.sh
index d88e05b..41ebeca 100755
--- a/scripts/run.sh
+++ b/scripts/run.sh
@@ -133,6 +133,18 @@ aoh-collate-data --aoh_results "${DATADIR}"/aohs/current/ \
 echo "Calculating model validation..."
 aoh-validate-prevalence --collated_aoh_data "${DATADIR}"/validation/aohs.csv \
                         --output "${DATADIR}"/validation/model_validation.csv
+for TAXA in "${TAXALIST[@]}"
+do
+    echo "Fetching GBIF data for ${TAXA}..."
+    aoh-fetch-gbif-data --collated_aoh_data "${DATADIR}"/validation/aohs.csv \
+                        --taxa "${TAXA}" \
+                        --output_dir "${DATADIR}"/validation/occurrences/"${TAXA}"
+    echo "Validating occurrences for ${TAXA}..."
+    aoh-validate-occurrences --gbif_data_path "${DATADIR}"/validation/occurrences/"${TAXA}" \
+                             --species_data "${DATADIR}"/species-info/"${TAXA}"/current/ \
+                             --aoh_results  "${DATADIR}"/aohs/current/"${TAXA}"/ \
+                             --output "${DATADIR}"/validation/occurrences/"${TAXA}".csv
+done
 
 # Threats
 echo "Generating threat task list..."