feat: create task

Author: JaeAeich

deployment/config.yaml

@@ -48,6 +48,78 @@ api:
           swagger_ui: True
           serve_spec: True
 
+custom:
+  taskmaster_template:
+    apiVersion: batch/v1
+    kind: Job
+    metadata:
+      name: taskmaster
+      labels:
+        app: taskmaster
+    spec:
+      template:
+        metadata:
+          name: taskmaster
+        spec:
+          serviceAccountName: default
+          containers:
+          - name: taskmaster
+            image: eu.gcr.io/tes-wes/taskmaster:v0.0.5.2
+            args:
+            - -f
+            - /jsoninput/JSON_INPUT.gz
+            env:
+            - name: TESK_FTP_USERNAME
+              valueFrom:
+                secretKeyRef:
+                  name: ftp-secret
+                  key: username
+                  optional: true
+            - name: TESK_FTP_PASSWORD
+              valueFrom:
+                secretKeyRef:
+                  name: ftp-secret
+                  key: password
+                  optional: true
+            volumeMounts:
+            - name: podinfo
+              mountPath: /podinfo
+              readOnly: true
+            - name: jsoninput
+              mountPath: /jsoninput
+              readOnly: true
+          volumes:
+          - name: podinfo
+            downwardAPI:
+              items:
+              - path: labels
+                fieldRef:
+                  fieldPath: metadata.labels
+          restartPolicy: Never
+  taskmaster_env_properties:
+    # Taskmaster image name
+    imageName: eu.gcr.io/tes-wes/taskmaster
+    # Taskmaster image version
+    imageVersion: v0.10.0
+    # Filer image name
+    filerImageName: eu.gcr.io/tes-wes/filer
+    # Filer image version
+    filerImageVersion: v0.10.0
+    # Test FTP account settings
+    ftp:
+      # Name of the secret with FTP account credentials
+      secretName: account-secret
+      # If FTP account enabled (based on non-emptiness of secretName)
+      enabled: false
+    # If verbose (debug) mode of taskmaster is on (passes additional flag to taskmaster and sets image pull policy to Always)
+    debug: false
+    # Environment variables, that will be passed to taskmaster
+    environment:
+      key: value
+    # Service Account name for taskmaster
+    serviceAccountName: default
+
+
 # Logging configuration
 # Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.LogConfig
 log:

poetry.lock

@@ -30,7 +30,7 @@ version = "0.1.0"
 [tool.poetry.dependencies]
 boto3 = "1.34.104"
 foca = "^0.13.0"
-kubernetes = "^29.0.0"
+kubernetes = "^30.1.0"
 python = "^3.11"
 requests = ">=2.20.0"
 urllib3 = "^2.2.1"

pyproject.toml

@@ -2,9 +2,15 @@
 
 import logging
 
-# from connexion import request  # type: ignore
 from foca.utils.logging import log_traffic  # type: ignore
 
+from tesk.api.kubernetes.template import KubernetesTemplateSupplier
+from tesk.api.ga4gh.tes.models import TesTask
+from tesk.utils import get_custom_config
+from tesk.api.kubernetes.converter import TesKubernetesConverter
+
+# from tesk.api.ga4gh.tes.task.create_task import CreateTask as TaskCreater
+
 # Get logger instance
 logger = logging.getLogger(__name__)
 
@@ -24,13 +30,22 @@ def CancelTask(id, *args, **kwargs) -> dict:  # type: ignore
 
 # POST /tasks
 @log_traffic
-def CreateTask(*args, **kwargs) -> dict:  # type: ignore
+def CreateTask(**kwargs) -> dict:  # type: ignore
     """Create task.
 
     Args:
         *args: Variable length argument list.
         **kwargs: Arbitrary keyword arguments.
     """
+    request_body = kwargs["body"]
+    create_task_request = TesTask(**request_body)
+    user = {
+        "username": "test",
+        "is_member": True,
+        "any_group": "test_group",
+    }
+    tkc = TesKubernetesConverter().from_tes_task_to_k8s_job(create_task_request, user)
+    print(tkc)
     pass
 
 

tesk/api/ga4gh/tes/controllers.py

@@ -0,0 +1 @@
+"""Task API controller logic."""

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

@@ -0,0 +1,77 @@
+"""TESK API module for creating a task."""
+
+import logging
+
+from tesk.api.ga4gh.tes.models import TesTask
+from tesk.api.kubernetes.client_wrapper import KubernetesClientWrapper
+from tesk.api.kubernetes.constants import Constants
+from tesk.api.kubernetes.converter import TesKubernetesConverter
+from tesk.exceptions import KubernetesError
+
+logger = logging.getLogger(__name__)
+
+
+class CreateTesTask:
+    """Create TES task."""
+
+    def __init__(self, task: TesTask, user=None, namespace="default"):
+        """Initialize the CreateTask class.
+
+        Args:
+          task: TES task to create.
+          user: User who creates the task.
+          namespace: Kubernetes namespace where the task is created.
+        """
+        self.task = task
+        self.user = user
+        self.kubernetes_client_wrapper = KubernetesClientWrapper()
+        self.namespace = namespace
+        self.tes_kubernetes_converter = TesKubernetesConverter(self.namespace)
+        self.constants = Constants()
+
+    def create_task(self):
+        """Create TES task."""
+        attempts_no = 0
+        while True:
+            try:
+                resources = self.task.resources
+
+                if resources and resources.ram_gb:
+                    minimum_ram_gb = self.kubernetes_client_wrapper.minimum_ram_gb()
+                    if resources.ram_gb < minimum_ram_gb:
+                        self.task.resources.ram_gb = minimum_ram_gb
+
+                task_master_job = (
+                    self.tes_kubernetes_converter.from_tes_task_to_k8s_job(
+                        self.task, self.user
+                    )
+                )
+                
+                # TODO: Create ConfigMap
+                # TODO: Create Job
+                # TODO Return created job
+                # task_master_config_map = converter.from_tes_task_to_k8s_config_map(
+                #     task, user, task_master_job
+                # )
+                # created_config_map = kubernetes_client_wrapper.create_config_map(
+                #     task_master_config_map
+                # )
+                # created_job = kubernetes_client_wrapper.create_job(task_master_job)
+                # return converter.from_k8s_job_to_tes_create_task_response(created_job)
+
+            except KubernetesError as e:
+                # Handle Kubernetes specific exceptions
+                if (
+                    not e.is_object_name_duplicated()
+                    or attempts_no >= self.constants.job_create_attempts_no
+                ):
+                    raise e
+                attempts_no += 1
+
+            except Exception as exc:
+                logging.error("ERROR: In createTask", exc_info=True)
+                raise exc
+
+    def response(self) -> dict:
+        """Create response."""
+        return self.create_task()

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

@@ -0,0 +1 @@
+"""Kubernetes API module."""