executor, add job status polling

closes #33

CHANGES.rst

@@ -1,6 +1,11 @@
 Changes
 =======
 
+Version 0.8.1 (UNRELEASED)
+---------------------------
+
+- Adds jobs status polling.
+
 Version 0.8.0 (2021-11-22)
 ---------------------------
 

reana_workflow_engine_snakemake/config.py

@@ -9,6 +9,7 @@
 """REANA Workflow Engine Snakemake configuration."""
 
 import os
+from enum import Enum
 
 MOUNT_CVMFS = os.getenv("REANA_MOUNT_CVMFS", "false")
 
@@ -20,3 +21,36 @@
 
 SNAKEMAKE_MAX_PARALLEL_JOBS = 100
 """Snakemake maximum number of jobs that can run in parallel."""
+
+
+# defined in reana-db component, in reana_db/models.py file as JobStatus
+class JobStatus(str, Enum):
+    """Enumeration of job statuses.
+
+    Example:
+        JobStatus.started == "started"  # True
+    """
+
+    # FIXME: this state is not defined in reana-db but returned by r-job-controller
+    started = "started"
+
+    created = "created"
+    running = "running"
+    finished = "finished"
+    failed = "failed"
+    stopped = "stopped"
+    queued = "queued"
+
+
+# defined in reana-db component, in reana_db/models.py file as RunStatus
+class RunStatus(Enum):
+    """Enumeration of possible run statuses of a workflow."""
+
+    created = 0
+    running = 1
+    finished = 2
+    failed = 3
+    deleted = 4
+    stopped = 5
+    queued = 6
+    pending = 7

reana_workflow_engine_snakemake/executor.py

@@ -11,6 +11,8 @@
 import os
 import subprocess
 import logging
+import time
+import threading
 from collections import namedtuple
 from typing import Callable
 
@@ -26,6 +28,8 @@
     LOGGING_MODULE,
     MOUNT_CVMFS,
     SNAKEMAKE_MAX_PARALLEL_JOBS,
+    JobStatus,
+    RunStatus,
 )
 from reana_workflow_engine_snakemake.utils import (
     publish_job_submission,
@@ -45,6 +49,11 @@
 class REANAClusterExecutor(GenericClusterExecutor):
     """REANA Cluster Snakemake executor implementation."""
 
+    def __init__(self, *args, **kwargs):
+        """Initialize REANA Cluster Snakemake executor. Start polling jobs."""
+        super().__init__(*args, **kwargs)
+        self._start_job_polling()
+
     def run(
         self,
         job: Job,
@@ -145,7 +154,8 @@ def run(
                 )
             )
 
-    def _get_container_image(self, job: Job) -> str:
+    @staticmethod
+    def _get_container_image(job: Job) -> str:
         if job.container_img_url:
             container_image = job.container_img_url.replace("docker://", "")
             log.info(f"Environment: {container_image}")
@@ -154,7 +164,7 @@ def _get_container_image(self, job: Job) -> str:
             log.info(f"No environment specified, falling back to: {container_image}")
         return container_image
 
-    def _handle_job_status(self, job, status):
+    def _handle_workflow_status(self, job, status: RunStatus):
         workflow_uuid = os.getenv("workflow_uuid", "default")
         job_id = job.reana_job_id
         log.info(f"{status} job: {job_id}")
@@ -163,11 +173,8 @@ def _handle_job_status(self, job, status):
                 **{status: {"total": 1, "job_ids": [job_id]}}
             )
         }
-        status_running = 1
-        status_failed = 3
-        status_mapping = {"finished": status_running, "failed": status_failed}
         self.publisher.publish_workflow_status(
-            workflow_uuid, status_mapping[status], message=message
+            workflow_uuid, status.value, message=message
         )
 
     def handle_job_success(self, job):
@@ -177,13 +184,36 @@ def handle_job_success(self, job):
             job, upload_remote=False, handle_log=False, handle_touch=True
         )
 
-        self._handle_job_status(job, "finished")
+        self._handle_workflow_status(job, RunStatus.running)
 
     def handle_job_error(self, job):
         """Override job error method to publish job status."""
         super().handle_job_error(job)
 
-        self._handle_job_status(job, "failed")
+        self._handle_workflow_status(job, RunStatus.failed)
+
+    def _get_job_status_from_controller(self, job_id: str) -> str:
+        response = self.rjc_api_client.check_status(job_id)
+        return response["status"]
+
+    def _poll_jobs(self):
+        while True:
+            with self.lock:
+                active_jobs = self.active_jobs
+
+            log.debug(f"Active jobs: {self.active_jobs}")
+            for active_job in active_jobs:
+                job_id = active_job.job.reana_job_id
+                status = self._get_job_status_from_controller(job_id)
+                if status == JobStatus.finished:
+                    self.handle_job_success(active_job.job)
+                elif status == JobStatus.failed:
+                    self.handle_job_error(active_job.job)
+
+            time.sleep(5)
+
+    def _start_job_polling(self):
+        threading.Thread(target=self._poll_jobs, daemon=True).start()
 
 
 def submit_job(rjc_api_client, publisher, job_request_body):