review

Author: JaeAeich

deployment/config.yaml

@@ -64,7 +64,7 @@ custom:
           serviceAccountName: default
           containers:
           - name: taskmaster
-            image: eu.gcr.io/tes-wes/taskmaster:v0.0.5.2
+            image: docker.io/elixircloud/tesk-core-taskmaster:v0.10.2
             args:
             - -f
             - /jsoninput/JSON_INPUT.gz
@@ -98,13 +98,13 @@ custom:
           restartPolicy: Never
   taskmaster_env_properties:
     # Taskmaster image name
-    imageName: eu.gcr.io/tes-wes/taskmaster
+    imageName: docker.io/elixircloud/tesk-core-taskmaster
     # Taskmaster image version
-    imageVersion: v0.10.0
+    imageVersion: latest
     # Filer image name
-    filerImageName: eu.gcr.io/tes-wes/filer
+    filerImageName: docker.io/elixircloud/tesk-core-filer
     # Filer image version
-    filerImageVersion: v0.10.0
+    filerImageVersion: latest
     # Test FTP account settings
     ftp:
       # Name of the secret with FTP account credentials

tesk/api/ga4gh/tes/controllers.py

@@ -8,7 +8,7 @@
 from tesk.api.ga4gh.tes.models import TesTask
 from tesk.utils import get_custom_config
 from tesk.api.kubernetes.converter import TesKubernetesConverter
-
+from tesk.exceptions import BadRequest, InternalServerError
 # from tesk.api.ga4gh.tes.task.create_task import CreateTask as TaskCreater
 
 # Get logger instance
@@ -37,16 +37,13 @@ def CreateTask(**kwargs) -> dict:  # type: ignore
         *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
+    try:
+        request_body = kwargs.get("body")
+        if request_body is None:
+            logger("Nothing recieved in request body.")
+            raise BadRequest("No request body recieved.")
+    except Exception as e:
+        raise InternalServerError from e
 
 
 # GET /tasks/service-info

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

@@ -7,14 +7,16 @@
 from tesk.api.kubernetes.constants import Constants
 from tesk.api.kubernetes.converter import TesKubernetesConverter
 from tesk.exceptions import KubernetesError
+from tesk.constants import TeskConstants
 
 logger = logging.getLogger(__name__)
 
 
 class CreateTesTask:
     """Create TES task."""
 
-    def __init__(self, task: TesTask, user=None, namespace="default"):
+    # TODO: Add user to the class when auth implemented in FOCA
+    def __init__(self, task: TesTask, namespace=TeskConstants.tesk_namespace):
         """Initialize the CreateTask class.
 
         Args:
@@ -23,7 +25,7 @@ def __init__(self, task: TesTask, user=None, namespace="default"):
           namespace: Kubernetes namespace where the task is created.
         """
         self.task = task
-        self.user = user
+        # self.user = user
         self.kubernetes_client_wrapper = KubernetesClientWrapper()
         self.namespace = namespace
         self.tes_kubernetes_converter = TesKubernetesConverter(self.namespace)
@@ -32,7 +34,7 @@ def __init__(self, task: TesTask, user=None, namespace="default"):
     def create_task(self):
         """Create TES task."""
         attempts_no = 0
-        while True:
+        while attempts_no > self.constants.job_create_attempts_no:
             try:
                 resources = self.task.resources
 
@@ -46,7 +48,7 @@ def create_task(self):
                         self.task, self.user
                     )
                 )
-                
+
                 # TODO: Create ConfigMap
                 # TODO: Create Job
                 # TODO Return created job

tesk/api/kubernetes/client_wrapper.py

@@ -7,6 +7,7 @@
 from kubernetes.client import V1ConfigMap, V1Job, V1LimitRangeList
 from kubernetes.utils.quantity import parse_quantity  # type: ignore
 
+from tesk.constants import TeskConstants
 from tesk.exceptions import KubernetesError, NotFound
 
 logger = logging.getLogger(__name__)
@@ -15,7 +16,7 @@
 class KubernetesClientWrapper:
     """Kubernetes client wrapper class."""
 
-    def __init__(self, namespace="tesk"):
+    def __init__(self, namespace=TeskConstants.tesk_namespace):
         """Initialize the Kubernetes client wrapper.
 
         Args:
@@ -132,9 +133,12 @@ def minimum_ram_gb(self) -> float:
                         mem_bytes = self.quantity_to_bytes(mem_quantity)
                         min_ram = max(min_ram, mem_bytes)
             return min_ram / (1024**3)
-        except Exception as e:
+        except (ValueError, TypeError) as e:
             logger.error(f"Error in minimum_ram_gb: {e}")
             return 0.0
+        except Exception as e:
+            logger.error(f"Unexpected error in minimum_ram_gb: {e}")
+            raise
 
     def quantity_to_bytes(self, quantity: str) -> int:
         """Convert quantity(resource) to bytes."""

tesk/api/kubernetes/converter.py

@@ -16,14 +16,15 @@
 from tesk.api.ga4gh.tes.models import TesTask
 from tesk.api.kubernetes.constants import Constants, K8sConstants
 from tesk.api.kubernetes.template import KubernetesTemplateSupplier
+from tesk.constants import TeskConstants
 from tesk.custom_config import TaskmasterEnvProperties
 from tesk.utils import get_taskmaster_env_property, get_taskmaster_template
 
 logger = logging.getLogger(__name__)
 
 
 class TesKubernetesConverter:
-    def __init__(self, namespace="default"):
+    def __init__(self, namespace=TeskConstants.tesk_namespace):
         """Initialize the converter."""
         self.taskmaster_template: V1Job = get_taskmaster_template()
         self.taskmaster_env_properties: TaskmasterEnvProperties = (
@@ -33,7 +34,8 @@ def __init__(self, namespace="default"):
         self.k8s_constants = K8sConstants()
         self.namespace = namespace
 
-    def from_tes_task_to_k8s_job(self, task: TesTask, user):
+    # TODO: Add user to the mmethod when auth implemented in FOCA
+    def from_tes_task_to_k8s_job(self, task: TesTask):
         taskmsater_job: V1Job = KubernetesTemplateSupplier(
             self.namespace
         ).task_master_template()
@@ -50,18 +52,18 @@ def from_tes_task_to_k8s_job(self, task: TesTask, user):
         taskmsater_job.metadata.annotations[self.constants.ann_testask_name_key] = (
             task.name
         )
-        taskmsater_job.metadata.labels[self.constants.label_userid_key] = user[
-            "username"
-        ]
-
-        if task.tags and "GROUP_NAME" in task.tags:
-            taskmsater_job.metadata.labels[self.constants.label_userid_key] = task[
-                "tags"
-            ]["GROUP_NAME"]
-        elif user["is_member"]:
-            taskmsater_job.metadata.labels[self.constants.label_groupname_key] = user[
-                "any_group"
-            ]
+        # taskmsater_job.metadata.labels[self.constants.label_userid_key] = user[
+        #     "username"
+        # ]
+
+        # if task.tags and "GROUP_NAME" in task.tags:
+        #     taskmsater_job.metadata.labels[self.constants.label_userid_key] = task[
+        #         "tags"
+        #     ]["GROUP_NAME"]
+        # elif user["is_member"]:
+        #     taskmsater_job.metadata.labels[self.constants.label_groupname_key] = user[
+        #         "any_group"
+        #     ]
 
         try:
             taskmsater_job.metadata.annotations[self.constants.ann_json_input_key] = (

tesk/api/kubernetes/template.py

@@ -9,6 +9,7 @@
 from kubernetes.client.models import V1Job
 
 from tesk.api.kubernetes.constants import Constants, K8sConstants
+from tesk.constants import TeskConstants
 from tesk.custom_config import TaskmasterEnvProperties
 from tesk.utils import get_taskmaster_env_property, get_taskmaster_template
 
@@ -18,7 +19,7 @@
 class KubernetesTemplateSupplier:
     """Templates for tasmaster's and executor's job object.."""
 
-    def __init__(self, namespace="default"):
+    def __init__(self, namespace=TeskConstants.tesk_namespace):
         """Initialize the converter."""
         self.taskmaster_template: V1Job = get_taskmaster_template()
         self.taskmaster_env_properties: TaskmasterEnvProperties = (

tesk/constants.py

@@ -0,0 +1,17 @@
+"""Tesk scoped constants."""
+
+import os
+
+
+class TeskConstants:
+    """Tesk scoped constants."""
+
+    filer_image_name: str = os.getenv(
+        "FILER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-filer"
+    )
+    filer_image_version: str = os.getenv("FILER_IMAGE_VERSION", "latest")
+    taskmaster_image_name: str = os.getenv(
+        "TASKMASTER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-taskmaster"
+    )
+    taskmaster_image_version: str = os.getenv("TASKMASTER_IMAGE_VERSION", "latest")
+    tesk_namespace: str = os.getenv("TESK_NAMESPACE", "tesk")

tesk/custom_config.py

@@ -4,6 +4,8 @@
 
 from pydantic import BaseModel, Field
 
+from tesk.constants import TeskConstants
+
 
 class FtpConfig(BaseModel):
     """Ftp configuration model for the TESK."""
@@ -21,13 +23,19 @@ class TaskmasterEnvProperties(BaseModel):
     """Taskmaster environment properties model for the TESK."""
 
     imageName: str = Field(
-        default="eu.gcr.io/tes-wes/taskmaster", description="Taskmaster image name"
+        default=TeskConstants.taskmaster_image_name,
+        description="Taskmaster image name",
+    )
+    imageVersion: str = Field(
+        default=TeskConstants.taskmaster_image_version,
+        description="Taskmaster image version",
     )
-    imageVersion: str = Field(default="v0.10.0", description="Taskmaster image version")
     filerImageName: str = Field(
-        default="eu.gcr.io/tes-wes/filer", description="Filer image name"
+        default=TeskConstants.filer_image_name, description="Filer image name"
+    )
+    filerImageVersion: str = Field(
+        default=TeskConstants.filer_image_version, description="Filer image version"
     )
-    filerImageVersion: str = Field(default="v0.10.0", description="Filer image version")
     ftp: FtpConfig = Field(default=None, description="Test FTP account settings")
     debug: bool = Field(
         default=False,