update scripts

_viash.yaml

@@ -29,3 +29,6 @@ info:
     - type: s3
       path: s3://openproblems-data/resources_test/common
       dest: resources_test/common
+    - type: s3
+      path: s3://openproblems-data/resources_test/datasets
+      dest: resources_test/datasets

scripts/create_resources/task_metadata.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# ensure that the command below is run from the root of the repository
+cd "$REPO_ROOT"
+
+set -e
+
+DATASETS_DIR="resources_test/batch_integration"
+OUTPUT_DIR="resources_test/common/task_metadata"
+
+if [ ! -d "$OUTPUT_DIR" ]; then
+  mkdir -p "$OUTPUT_DIR"
+fi
+
+echo ">> Running benchmark"
+# TODO: manually generate contents of output_dir
+export NXF_VER=22.04.5
+
+nextflow run . \
+  -main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \
+  -profile docker \
+  -resume \
+  -c src/wf_utils/labels_ci.config \
+  -with-trace \
+  -entry auto \
+  --input_states "$DATASETS_DIR/pancreas/state.yaml" \
+  --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \
+  --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml", "method_ids": ["bbknn", "mnnpy", "mnnr"]}' \
+  --publish_dir "$OUTPUT_DIR" \
+  --output_state "state.yaml"
+
+cp trace.txt "$OUTPUT_DIR/trace.txt"
+
+
+echo ">> Extracting method info"
+viash run src/common/process_task_results/get_method_info/config.vsh.yaml -- --input "$OUTPUT_DIR/method_configs.yaml" --output "$OUTPUT_DIR/method_info.json"
+
+
+echo ">> Uploading results to S3"
+aws s3 sync --profile op \
+  "resources_test/common/task_metadata/" \
+  "s3://openproblems-data/resources_test/common/task_metadata/" \
+  --delete --dryrun

scripts/sync_resources.sh

@@ -2,4 +2,4 @@
 
 set -e
 
-viash run src/common/sync_test_resources/config.vsh.yaml
+common/scripts/sync_resources