fix minor

Author: JaeAeich

deployment/config.yaml

@@ -126,7 +126,7 @@ custom:
     # Taskmaster image name
     imageName: docker.io/elixircloud/tesk-core-taskmaster
     # Taskmaster image version
-    imageVersion: fix-null-volumes3
+    imageVersion: fix-null-volumes5
     # Filer image name
     filerImageName: docker.io/elixircloud/tesk-core-filer
     # Filer image version

tesk/api/ga4gh/tes/task/create_task.py

@@ -7,7 +7,8 @@
 from tesk.api.ga4gh.tes.models import TesCreateTaskResponse, TesResources, TesTask
 from tesk.api.ga4gh.tes.task.task_request import TesTaskRequest
 from tesk.exceptions import KubernetesError
-
+import os
+from datetime import datetime
 logger = logging.getLogger(__name__)
 
 
@@ -36,7 +37,8 @@ def create_task(self) -> TesCreateTaskResponse:
             try:
                 attempts_no += 1
                 resources = self.task.resources
-
+                limits = self.kubernetes_client_wrapper.list_limits()
+                print("limits", limits)
                 minimum_ram_gb = self.kubernetes_client_wrapper.minimum_ram_gb()
 
                 if not self.task.resources:
@@ -49,22 +51,40 @@ def create_task(self) -> TesCreateTaskResponse:
                     # self.user
                 )
 
-                print(taskmaster_job)
                 taskmaster_config_map = (
                     self.tes_kubernetes_converter.from_tes_task_to_k8s_config_map(
                         self.task,
                         taskmaster_job,
                         # self.user
                     )
                 )
-                print(taskmaster_config_map)
 
-                # Create ConfigMap and Job
-                _ = self.kubernetes_client_wrapper.create_config_map(
-                    taskmaster_config_map
-                )
+                configmap = self.kubernetes_client_wrapper.create_config_map(taskmaster_config_map)
                 created_job = self.kubernetes_client_wrapper.create_job(taskmaster_job)
 
+                os.makedirs("/tmp/tesk", exist_ok=True)
+                output_log_path = f"/tmp/tesk/output-at-{datetime.now().strftime('%H:%M:%S')}.log"
+                with open(output_log_path, "w") as f:
+                    f.write("*********************************\n")
+                    f.write(f"Manifest consumed to create taskmaster job as {type(taskmaster_job)}\n")
+                    f.write(str(taskmaster_job) + "\n")
+                    f.write("*********************************\n")
+
+                    f.write("*********************************\n")
+                    f.write(f"Manifest consumed to create config map as {type(taskmaster_config_map)}\n")
+                    f.write(str(taskmaster_config_map) + "\n")
+                    f.write("*********************************\n")
+
+                    # Create ConfigMap and Job
+                    f.write("*********************************\n")
+                    f.write(f"Created ConfigMap as {type(configmap)}\n")
+                    f.write(str(configmap) + "\n")
+                    f.write("*********************************\n")
+                    
+                    f.write("*********************************\n")
+                    f.write(f"Created taskmaster job as {type(created_job)}\n")
+                    f.write(str(created_job) + "\n")
+                    f.write("*********************************\n")
                 assert created_job.metadata is not None
                 assert created_job.metadata.name is not None
 

tesk/api/kubernetes/convert/executor_command_wrapper.py

@@ -51,4 +51,4 @@ def get_commands_with_stream_redirects(self) -> List[str]:
 
         result.append(" ".join(command_parts))
 
-        return result
+        return result

tesk/api/kubernetes/convert/template.py

@@ -197,4 +197,6 @@ def get_executor_template_with_value_from_config(self) -> V1Job:
                 )
             ]
 
+        job.spec.template.spec.containers[0].restart_policy = "Never"
+
         return job

tesk/api/specs/task_execution_service.117cd92.openapi.yaml

@@ -582,7 +582,7 @@ components:
           type: integer
           description: Requested number of CPUs
           format: int32
-          example: 4
+          example: 1
         preemptible:
           type: boolean
           description: |-
@@ -595,12 +595,12 @@ components:
           type: number
           description: Requested RAM required in gigabytes (GB)
           format: double
-          example: 8
+          example: 1
         disk_gb:
           type: number
           description: Requested disk size in gigabytes (GB)
           format: double
-          example: 40
+          example: 2
         zones:
           type: array
           description: |-
@@ -610,7 +610,8 @@ components:
             priority queue to which the job is assigned.
           items:
             type: string
-          example: us-west-1
+          example: 
+            - us-west-1
         backend_parameters:
             type: object
             additionalProperties: