[CHANGE] Adding volume support to the generic cwl-dag DAG

airflow/dags/cwl_dag.py

@@ -6,7 +6,9 @@
 import json
 import uuid
 from datetime import datetime
+import os
 
+from airflow.operators.python import PythonOperator, get_current_context
 from airflow.models.param import Param
 from airflow.providers.cncf.kubernetes.operators.kubernetes_pod import KubernetesPodOperator
 from kubernetes.client import models as k8s
@@ -20,10 +22,12 @@
 # The Kubernetes namespace within which the Pod is run (it must already exist)
 POD_NAMESPACE = "airflow"
 
+# The path of the working directory where the CWL workflow is executed
+# (aka the starting directory for cwl-runner)
+WORKING_DIR = "/scratch"
+
 # Example arguments
-default_cwl_workflow = (
-    "https://raw.githubusercontent.com/unity-sds/sbg-workflows/main/preprocess/sbg-preprocess-workflow.cwl"
-)
+default_cwl_workflow = "https://raw.githubusercontent.com/unity-sds/sbg-workflows/main/preprocess/sbg-preprocess-workflow.cwl"
 default_args_as_json_dict = {
     "input_processing_labels": ["label1", "label2"],
     "input_cmr_stac": "https://cmr.earthdata.nasa.gov/search/granules.stac?collection_concept_id=C2408009906-LPCLOUD&temporal[]=2023-08-10T03:41:03.000Z,2023-08-10T03:41:03.000Z",
@@ -35,7 +39,11 @@
 }
 
 # Default DAG configuration
-dag_default_args = {"owner": "unity-sps", "depends_on_past": False, "start_date": datetime(2024, 1, 1, 0, 0)}
+dag_default_args = {
+    "owner": "unity-sps",
+    "depends_on_past": False,
+    "start_date": datetime(2024, 1, 1, 0, 0)
+}
 
 # The DAG
 dag = DAG(
@@ -63,6 +71,16 @@
 # Environment variables
 default_env_vars = {}
 
+# This task that creates the working directory on the shared volume
+def setup(ti=None, **context):
+    context = get_current_context()
+    dag_run_id = context["dag_run"].run_id
+    local_dir = os.path.dirname(f"/shared-task-data/{dag_run_id}")
+    os.makedirs(local_dir, exist_ok=True)
+
+
+setup_task = PythonOperator(task_id="Setup", python_callable=setup, dag=dag)
+
 # This section defines KubernetesPodOperator
 cwl_task = KubernetesPodOperator(
     namespace=POD_NAMESPACE,
@@ -76,6 +94,33 @@
         metadata=k8s.V1ObjectMeta(name="docker-cwl-pod-" + uuid.uuid4().hex),
     ),
     pod_template_file=POD_TEMPLATE_FILE,
-    arguments=["{{ params.cwl_workflow }}", "{{ params.args_as_json }}"],
+    arguments=["{{ params.cwl_workflow }}", "{{ params.args_as_json }}", WORKING_DIR],
     dag=dag,
+    volume_mounts=[
+        k8s.V1VolumeMount(name="workers-volume", mount_path=WORKING_DIR, sub_path="{{ dag_run.run_id }}")
+    ],
+    volumes=[
+        k8s.V1Volume(
+            name="workers-volume",
+            persistent_volume_claim=k8s.V1PersistentVolumeClaimVolumeSource(claim_name="kpo-efs"),
+        )
+    ],
 )
+
+def cleanup(**context):
+    dag_run_id = context["dag_run"].run_id
+    local_dir = f"/shared-task-data/{dag_run_id}"
+    if os.path.exists(local_dir):
+        shutil.rmtree(local_dir)
+        print(f"Deleted directory: {local_dir}")
+    else:
+        print(f"Directory does not exist, no need to delete: {local_dir}")
+
+
+cleanup_task = PythonOperator(
+    task_id="Cleanup",
+    python_callable=cleanup,
+    dag=dag,
+)
+
+setup_task >> cwl_task >> cleanup_task

airflow/dags/docker_cwl_pod.yaml

@@ -9,7 +9,7 @@ spec:
   containers:
   - name: cwl-docker
     # image: ghcr.io/unity-sds/unity-sps/sps-docker-cwl:2.0.0-alpha.1
-    image: ghcr.io/unity-sds/unity-sps/sps-docker-cwl:develop7
+    image: ghcr.io/unity-sds/unity-sps/sps-docker-cwl:develop8
     imagePullPolicy: Always
     command: ["/usr/share/cwl/docker_cwl_entrypoint.sh"]
     securityContext:

airflow/dags/sbg_preprocess_cwl_dag.py

@@ -90,7 +90,7 @@ def setup(ti=None, **context):
     arguments=["{{ params.cwl_workflow }}", "{{ti.xcom_pull(task_ids='Setup', key='cwl_args')}}", WORKING_DIR],
     dag=dag,
     volume_mounts=[
-        k8s.V1VolumeMount(name="workers-volume", mount_path="/scratch", sub_path="{{ dag_run.run_id }}")
+        k8s.V1VolumeMount(name="workers-volume", mount_path=WORKING_DIR, sub_path="{{ dag_run.run_id }}")
     ],
     volumes=[
         k8s.V1Volume(