update scripts

openproblems-bio · Sep 3, 2024 · 944328a · 944328a
1 parent 2d85a7b
commit 944328a
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Showing 9 changed files with 8 additions and 9 deletions.
diff --git a/scripts/create_component/create_python_method.sh b/scripts/create_component/create_python_method.sh
diff --git a/scripts/create_component/create_python_metric.sh b/scripts/create_component/create_python_metric.sh
diff --git a/scripts/create_component/create_r_method.sh b/scripts/create_component/create_r_method.sh
diff --git a/scripts/create_component/create_r_metric.sh b/scripts/create_component/create_r_metric.sh
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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}