Merge pull request #26 from NII-DG/patch-for-sapporo

Patch for demo using Sapporo

.gitignore

@@ -165,3 +165,7 @@ cython_debug/
 # ---
 
 **/ro-crate-metadata.json
+sapporo_example/run
+sapporo_example/results
+sapporo_example/ro-crate-metadata.json
+sapporo_example/ro-crate-metadata_failed.json

sapporo_example/compose.yml

@@ -0,0 +1,32 @@
+version: "3.5"
+services:
+  nii-dg:
+    build:
+      context: ..
+      dockerfile: Dockerfile-api
+    image: nii-dg
+    container_name: nii-dg
+    ports:
+      - 0.0.0.0:5000:5000
+    restart: on-failure
+    networks:
+      - nii-dg-network
+  sapporo-service:
+    image: ghcr.io/sapporo-wes/sapporo-service:1.4.9
+    container_name: sapporo-service
+    volumes:
+      - ${PWD}/run:${PWD}/run
+      - /var/run/docker.sock:/var/run/docker.sock
+      - /tmp:/tmp
+    environment:
+      - SAPPORO_DEBUG=False
+      - SAPPORO_RUN_DIR=${PWD}/run
+    ports:
+      - 0.0.0.0:1122:1122
+    restart: on-failure
+    networks:
+      - nii-dg-network
+
+networks:
+  nii-dg-network:
+    name: nii-dg-network

sapporo_example/download_results.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+import argparse
+import json
+from pathlib import Path
+from typing import List
+from urllib.request import urlopen
+
+
+def fetch_output_file_list(run_id: str, endpoint: str) -> List[str]:
+    with urlopen(f"{endpoint.rstrip('/')}/runs/{run_id}") as response:
+        result = json.load(response)
+        return [output["file_name"] for output in result["outputs"]]
+
+
+def download_results(endpoint: str, run_id: str, output_dir: Path) -> None:
+    output_dir.mkdir(parents=True, exist_ok=True)
+    output_file_list = fetch_output_file_list(run_id, endpoint)
+
+    for output_file in output_file_list:
+        with urlopen(f"{endpoint.rstrip('/')}/runs/{run_id}/data/outputs/{output_file}") as response:
+            file_path = output_dir.joinpath("outputs").joinpath(output_file).resolve()
+            file_path.parent.mkdir(parents=True, exist_ok=True)
+            with open(file_path, "wb") as f:
+                f.write(response.read())
+
+    # download run_request.json
+    with urlopen(f"{endpoint.rstrip('/')}/runs/{run_id}/data/run_request.json") as response:
+        file_path = output_dir.joinpath("run_request.json").resolve()
+        with open(file_path, "wb") as f:
+            f.write(response.read())
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("endpoint", help="The endpoint to send the request (default: http://localhost:1122)",
+                        default="http://localhost:1122", nargs="?")
+    parser.add_argument("run_id", help="The RUN_ID of the executed workflow")
+    parser.add_argument("output_dir", help="The output directory to save the results (default: ./results)",
+                        default="./results", nargs="?")
+    args = parser.parse_args()
+
+    download_results(args.endpoint, args.run_id, Path(args.output_dir).resolve())
+
+
+if __name__ == "__main__":
+    main()

sapporo_example/execute_workflow.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+import argparse
+import json
+from urllib.parse import urlencode
+from urllib.request import Request, urlopen
+
+
+def execute_workflow(endpoint: str) -> None:
+    data = {
+        "workflow_params": json.dumps({
+            "fastq_1": {"location": "ERR034597_1.small.fq.gz", "class": "File"},
+            "fastq_2": {"location": "ERR034597_2.small.fq.gz", "class": "File"},
+            "nthreads": 2
+        }),
+        "workflow_type": "CWL",
+        "workflow_type_version": "v1.0",
+        "workflow_url": "https://raw.githubusercontent.com/sapporo-wes/sapporo-service/main/tests/resources/cwltool/trimming_and_qc.cwl",
+        "workflow_engine_name": "cwltool",
+        "workflow_attachment": json.dumps([
+            {"file_url": "https://raw.githubusercontent.com/sapporo-wes/sapporo-service/main/tests/resources/cwltool/ERR034597_2.small.fq.gz", "file_name": "ERR034597_2.small.fq.gz"},
+            {"file_url": "https://raw.githubusercontent.com/sapporo-wes/sapporo-service/main/tests/resources/cwltool/ERR034597_1.small.fq.gz", "file_name": "ERR034597_1.small.fq.gz"}
+        ])
+    }
+
+    data = urlencode(data).encode("utf-8")  # type: ignore
+    headers = {"Content-Type": "application/x-www-form-urlencoded"}
+    # remove trailing slash from endpoint
+    request = Request(f"{endpoint.rstrip('/')}/runs", data=data, headers=headers)  # type: ignore
+
+    with urlopen(request) as response:
+        result = json.load(response)
+        print(result)
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("endpoint", help="The endpoint to send the request (default: http://localhost:1122)",
+                        default="http://localhost:1122", nargs="?")
+    args = parser.parse_args()
+    execute_workflow(args.endpoint)
+
+
+if __name__ == "__main__":
+    main()