From e52d07e2e4f49a273a0296b3d9f3a3460cc05792 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Sun, 8 Sep 2024 08:25:42 +0200
Subject: [PATCH] fix scripts and submodule

---
 common                                  |  2 +-
 scripts/run_benchmark/run_full_local.sh |  5 ++++-
 scripts/run_benchmark/run_test_local.sh | 13 ++++++++++---
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/common b/common
index 1660eef..4343111 160000
--- a/common
+++ b/common
@@ -1 +1 @@
-Subproject commit 1660eef0b1172c1059270fff77f9abc0a5fc1ea4
+Subproject commit 4343111a4fd80f3bc6d38ec041131bb33d1bba0f
diff --git a/scripts/run_benchmark/run_full_local.sh b/scripts/run_benchmark/run_full_local.sh
index 4fc4b48..8c63393 100755
--- a/scripts/run_benchmark/run_full_local.sh
+++ b/scripts/run_benchmark/run_full_local.sh
@@ -21,6 +21,9 @@ exit 1
 
 set -e
 
+echo "Running benchmark on test data"
+echo "  Make sure to run 'scripts/project/build_all_docker_containers.sh'!"
+
 # generate a unique id
 RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
 publish_dir="resources/results/${RUN_ID}"
@@ -40,5 +43,5 @@ nextflow run openproblems-bio/task_template \
   -profile docker \
   -resume \
   -entry auto \
-  -c common/nextflow_helpers/labels.config \
+  -c common/nextflow_helpers/labels_ci.config \
   -params-file /tmp/params.yaml
diff --git a/scripts/run_benchmark/run_test_local.sh b/scripts/run_benchmark/run_test_local.sh
index 097a949..e549635 100755
--- a/scripts/run_benchmark/run_test_local.sh
+++ b/scripts/run_benchmark/run_test_local.sh
@@ -16,12 +16,19 @@ exit 1
 
 set -e
 
+echo "Running benchmark on test data"
+echo "  Make sure to run 'scripts/project/build_all_docker_containers.sh'!"
+
+# generate a unique id
+RUN_ID="testrun_$(date +%Y-%m-%d_%H-%M-%S)"
+publish_dir="resources/results/${RUN_ID}"
+
 # write the parameters to file
-cat > /tmp/params.yaml << 'HERE'
+cat > /tmp/params.yaml << HERE
 input_states: s3://openproblems-data/resources_test/task_template/**/state.yaml
 rename_keys: 'input_train:output_train;input_test:output_test;input_solution:output_solution'
 output_state: "state.yaml"
-publish_dir: s3://openproblems-nextflow/temp/task_template/
+publish_dir: "$publish_dir"
 HERE
 
 nextflow run . \
@@ -29,5 +36,5 @@ nextflow run . \
   -profile docker \
   -resume \
   -entry auto \
-  -c common/nextflow_helpers/labels.config \
+  -c common/nextflow_helpers/labels_ci.config \
   -params-file /tmp/params.yaml