From 944328a100074213f848663f38893c2ab7d92899 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 3 Sep 2024 07:38:59 +0200
Subject: [PATCH] update scripts

---
 scripts/create_component/create_python_method.sh | 0
 scripts/create_component/create_python_metric.sh | 0
 scripts/create_component/create_r_method.sh      | 0
 scripts/create_component/create_r_metric.sh      | 0
 scripts/create_datasets/resources.sh             | 2 +-
 scripts/run_benchmark/run.sh                     | 6 ++++++
 src/workflows/process_datasets/config.vsh.yaml   | 2 --
 src/workflows/run_benchmark/config.vsh.yaml      | 2 --
 src/workflows/run_benchmark/main.nf              | 5 +----
 9 files changed, 8 insertions(+), 9 deletions(-)
 mode change 100644 => 100755 scripts/create_component/create_python_method.sh
 mode change 100644 => 100755 scripts/create_component/create_python_metric.sh
 mode change 100644 => 100755 scripts/create_component/create_r_method.sh
 mode change 100644 => 100755 scripts/create_component/create_r_metric.sh
 mode change 100644 => 100755 scripts/run_benchmark/run.sh

diff --git a/scripts/create_component/create_python_method.sh b/scripts/create_component/create_python_method.sh
old mode 100644
new mode 100755
diff --git a/scripts/create_component/create_python_metric.sh b/scripts/create_component/create_python_metric.sh
old mode 100644
new mode 100755
diff --git a/scripts/create_component/create_r_method.sh b/scripts/create_component/create_r_method.sh
old mode 100644
new mode 100755
diff --git a/scripts/create_component/create_r_metric.sh b/scripts/create_component/create_r_metric.sh
old mode 100644
new mode 100755
diff --git a/scripts/create_datasets/resources.sh b/scripts/create_datasets/resources.sh
index 92b6d6f..ac2bc9d 100755
--- a/scripts/create_datasets/resources.sh
+++ b/scripts/create_datasets/resources.sh
@@ -4,7 +4,7 @@ cat > /tmp/params.yaml << 'HERE'
 input_states: s3://openproblems-data/resources/datasets/**/state.yaml
 rename_keys: 'input:output_dataset'
 output_state: "state.yaml"
-settings: '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}'
+settings: '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_state": "$id/state.yaml"}'
 publish_dir: s3://openproblems-data/resources/task_label_projection/datasets/
 HERE
 
diff --git a/scripts/run_benchmark/run.sh b/scripts/run_benchmark/run.sh
old mode 100644
new mode 100755
index 58d9d3b..cffcf27
--- a/scripts/run_benchmark/run.sh
+++ b/scripts/run_benchmark/run.sh
@@ -21,3 +21,9 @@ tw launch https://github.com/openproblems-bio/task_label_projection.git \
   --entry-name auto \
   --config common/nextflow_helpers/labels_tw.config \
   --labels task_label_projection,full
+
+# sync
+aws s3 sync \
+  s3://openproblems-data/resources/task_label_projection/results/ \
+  resources/results/ \
+  --delete --dryrun
diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml
index 41387f7..38d7e57 100644
--- a/src/workflows/process_datasets/config.vsh.yaml
+++ b/src/workflows/process_datasets/config.vsh.yaml
@@ -12,8 +12,6 @@ resources:
 dependencies:
   - name: schema/verify_data_structure
     repository: core
-  - name: h5ad/extract_uns_metadata
-    repository: core
   - name: data_processors/process_dataset
 
 runners:
diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
index b291a2d..521502b 100644
--- a/src/workflows/run_benchmark/config.vsh.yaml
+++ b/src/workflows/run_benchmark/config.vsh.yaml
@@ -62,8 +62,6 @@ resources:
     path: /_viash.yaml
 
 dependencies:
-  - name: schema/verify_data_structure
-    repository: core
   - name: h5ad/extract_uns_metadata
     repository: core
   - name: control_methods/majority_vote
diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
index 3e3970f..8c471a3 100644
--- a/src/workflows/run_benchmark/main.nf
+++ b/src/workflows/run_benchmark/main.nf
@@ -169,10 +169,7 @@ workflow run_wf {
       def metric_configs_file = tempFile("metric_configs.yaml")
       metric_configs_file.write(metric_configs_yaml_blob)
 
-      def viash_file = meta.resources_dir.resolve("_viash.yaml")
-      def viash_file_content = toYamlBlob(readYaml(viash_file).info)
-      def task_info_file = tempFile("task_info.yaml")
-      task_info_file.write(viash_file_content)
+      def task_info_file = meta.resources_dir.resolve("_viash.yaml")
 
       // store the scores in a file
       def score_uns = states.collect{it.score_uns}