Set workflow parameters as CLI parameters

#46

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
         files: app
         args: [--check]
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.0.286'
+    rev: 'v0.0.287'
     hooks:
     -   id: ruff
 -   repo: https://github.com/PyCQA/isort

app/api/utils.py

@@ -160,8 +160,7 @@ async def start_workflow_execution(
 
     nextflow_command = nextflow_command_template.render(
         repo=git_repo,
-        params_file_name=params_file_name,
-        params_mount_path=settings.PARAMS_BUCKET_MOUNT_PATH,
+        parameters=parameters,
         execution_id=execution.execution_id,
         configuration=settings.NX_CONFIG,
         nx_bin=settings.NX_BIN,

app/check_slurm_connection.py

+import logging
+
+import httpx
+from fastapi import status
+from tenacity import after_log, before_log, retry, stop_after_attempt, wait_fixed
+
+from app.core.config import settings
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+max_tries = 60 * 3  # 3 minutes
+wait_seconds = 2
+
+
+@retry(
+    stop=stop_after_attempt(max_tries),
+    wait=wait_fixed(wait_seconds),
+    before=before_log(logger, logging.INFO),
+    after=after_log(logger, logging.WARN),
+)
+def init() -> None:
+    headers = {"X-SLURM-USER-TOKEN": settings.SLURM_TOKEN, "X-SLURM-USER-NAME": settings.SLURM_USER}
+
+    try:
+        response = httpx.get(
+            f"{settings.SLURM_ENDPOINT}slurm/v0.0.38/ping", timeout=5.0, follow_redirects=False, headers=headers
+        )
+        assert response.status_code == status.HTTP_200_OK
+    except Exception as e:
+        logger.error(e)
+        raise e
+
+
+def main() -> None:
+    logger.info("Check Slurm Cluster connection")
+    init()
+    logger.info("Slurm Cluster connection established")
+
+
+if __name__ == "__main__":
+    main()

mako_templates/nextflow_command.template

@@ -17,4 +17,6 @@ ${nx_bin} run ${repo.repo_url} \
 -c ${configuration} \
 % endif
 -revision ${repo.git_commit_hash} \
--params-file ${params_mount_path}/${params_file_name}
+% for param_name, param_value in parameters.items():
+--${param_name} "${param_value}" \
+% endfor

requirements-dev.txt

@@ -12,4 +12,4 @@ mypy>=1.5.0,<1.6.0
 boto3-stubs-lite[s3]>=1.28.0,<1.29.0
 types-requests
 # Miscellaneous
-pre-commit>=3.3.0,<3.4.0
+pre-commit>=3.4.0,<3.5.0

requirements.txt

@@ -2,7 +2,7 @@
 clowmdb>=2.2.0,<2.3.0
 
 # Webserver packages
-anyio>=3.7.0,<3.8.0
+anyio>=3.7.0,<4.0.0
 fastapi>=0.103.0,<0.104.0
 pydantic>=2.3.0,<2.4.0
 pydantic-settings

scripts/prestart.sh

@@ -2,5 +2,7 @@
 
 # Check Connection to Ceph RGW
 python app/check_ceph_connection.py
+# Check Connection to Slurm Cluster
+python app/check_slurm_connection.py
 # Let the DB start
 python app/check_database_connection.py