From 304d7a97164bf5965912711958e7422255ca61d4 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Wed, 28 Aug 2024 04:24:42 +0200
Subject: [PATCH] update test resources

---
 scripts/generate_test_resource.sh | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/scripts/generate_test_resource.sh b/scripts/generate_test_resource.sh
index c197728f..fdfe225c 100755
--- a/scripts/generate_test_resource.sh
+++ b/scripts/generate_test_resource.sh
@@ -13,14 +13,29 @@ nextflow run . \
   --dataset_summary "MOBNEW" \
   --dataset_reference "..." \
   --dataset_organism "mus_musculus" \
+  --output_state '$id/state.yaml' \
   --publish_dir resources_test/datasets
 
+# run a method
 viash run src/methods/scdesign3/config.vsh.yaml -- \
   --input resources_test/datasets/MOBNEW/dataset_sp.h5ad \
   --output resources_test/datasets/MOBNEW/simulated_dataset.h5ad
 
-viash run src/metrics/ks_statistic/config.vsh.yaml -- \
+# process the simulated spatial dataset
+viash run src/process_datasets/generate_sim_spatialcluster/config.vsh.yaml -- \
+  --input_sp resources_test/datasets/MOBNEW/dataset_sp.h5ad \
+  --input_sp_sim resources_test/datasets/MOBNEW/simulated_dataset.h5ad \
+  --output_sp resources_test/datasets/MOBNEW/simulated_dataset_processed.h5ad
+
+# run a metric
+viash run src/metrics/ks_statistic_spatial/config.vsh.yaml -- \
   --input_spatial_dataset resources_test/datasets/MOBNEW/dataset_sp.h5ad \
   --input_singlecell_dataset resources_test/datasets/MOBNEW/dataset_sc.h5ad \
-  --input_simulated_dataset resources_test/datasets/MOBNEW/simulated_dataset.h5ad \
+  --input_simulated_dataset resources_test/datasets/MOBNEW/simulated_dataset_processed.h5ad \
   --output resources_test/datasets/MOBNEW/score.h5ad
+
+# sync the resources
+aws s3 sync --profile op \
+  resources_test \
+  s3://openproblems-data/resources_test/task_spatial_simulators \
+  --delete --dryrun