feat: curation update

Author: Szymon Szyszkowski

src/ot_orchestration/dags/gwas_curation_update.py

@@ -0,0 +1,40 @@
+"""DAG for updating GWAS Catalog curation table."""
+
+from __future__ import annotations
+
+from datetime import datetime
+from pathlib import Path
+
+from ot_orchestration.utils import common
+from ot_orchestration.utils.dataproc import (
+    create_cluster,
+    install_dependencies,
+    submit_step,
+)
+from airflow.models.dag import DAG
+from airflow.models.baseoperator import chain
+
+CLUSTER_NAME = "otg-gwascatalog-curation"
+RUN_DATE = datetime.today().strftime("%Y-%m-%d")
+
+with DAG(
+    dag_id=Path(__file__).stem,
+    description="Open Targets Genetics — GWAS Catalog curation update",
+    default_args=common.shared_dag_args,
+    **common.shared_dag_kwargs,
+):
+    update_gwas_curation = submit_step(
+        cluster_name=CLUSTER_NAME,
+        step_id="ot_gwas_catalog_study_curation",
+        task_id="gwas_catalog_curation_update",
+        other_args=[
+            f"step.gwas_catalog_study_curation_out=gs://genetics_etl_python_playground/input/v2d/GWAS_Catalog_study_curation_{RUN_DATE}.tsv",
+        ],
+    )
+
+    # DAG description:
+    chain(
+        create_cluster(CLUSTER_NAME, num_workers=2),
+        install_dependencies(CLUSTER_NAME),
+        update_gwas_curation,
+    )