WIP

README.md

@@ -55,6 +55,32 @@ After the last executor, the `filer` is called once more to process the outputs
 and push them to remote locations from the PVC. The PVC is the scrubbed, deleted
 and the taskmaster ends, completing the task.
 
+┌─────────────────────────────────────────────────────────┐
+│                         Kubernetes                      │
+│                                                         │
+│  ┌────────────────────────────┐  ┌───────────────────┐  │
+│  │ Secret: ftp-secret         │  │ ConfigMap/PVC     │  │
+│  │ - username                 │  │ - JSON_INPUT.gz   │  │
+│  │ - password                 │  │                   │  │
+│  └──────────▲─────────────────┘  └───────▲───────────┘  │
+│             │                            |              │
+│             │                            |              │
+│             │                            |              │
+│   ┌─────────┴────────────────────────────┴────────────┐ │
+│   │                Job: taskmaster                    │ │
+│   │ ┌───────────────────────────────────────────────┐ │ │
+│   │ │ Pod: taskmaster                               │ │ │
+│   │ │ - Container: taskmaster                       │ │ │
+│   │ │   - Env: TESK_FTP_USERNAME                    │ │ │
+│   │ │   - Env: TESK_FTP_PASSWORD                    │ │ │
+│   │ │   - Args: -f /jsoninput/JSON_INPUT.gz         │ │ │
+│   │ │   - Mounts: /podinfo                          │ │ │
+│   │ │             /jsoninput                        │ │ │
+│   │ └───────────────────────────────────────────────┘ │ │
+│   └───────────────────────────────────────────────────┘ │
+│                                                         │
+└─────────────────────────────────────────────────────────┘
+
 ## Requirements
 
 - A working [Kubernetes](https://kubernetes.io/) cluster version 1.9 and later.

deployment/charts/tesk/values.yaml

@@ -9,7 +9,7 @@ host_name: ""
 #
 
 # 'openstack' or 's3'
-storage: none
+storage: s3
 
 # Configurable storage class.
 storageClass:

tesk/api/ga4gh/tes/controllers.py

@@ -6,6 +6,7 @@
 
 from tesk.api.ga4gh.tes.models import TesTask
 from tesk.api.ga4gh.tes.service_info.service_info import ServiceInfo
+from tesk.api.ga4gh.tes.task.create_task import CreateTesTask
 from tesk.api.kubernetes.converter import TesKubernetesConverter
 from tesk.api.kubernetes.template import KubernetesTemplateSupplier
 from tesk.exceptions import BadRequest, InternalServerError
@@ -42,6 +43,7 @@ def CreateTask(**kwargs) -> dict:  # type: ignore
         if request_body is None:
             logger("Nothing recieved in request body.")
             raise BadRequest("No request body recieved.")
+        CreateTesTask(TesTask(**request_body)).create_task()
     except Exception as e:
         raise InternalServerError from e
 

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

@@ -21,7 +21,6 @@ def __init__(self, task: TesTask, namespace=TeskConstants.tesk_namespace):
 
         Args:
           task: TES task to create.
-          user: User who creates the task.
           namespace: Kubernetes namespace where the task is created.
         """
         self.task = task
@@ -45,10 +44,13 @@ def create_task(self):
 
                 task_master_job = (
                     self.tes_kubernetes_converter.from_tes_task_to_k8s_job(
-                        self.task, self.user
+                        self.task,
+                        # self.user
                     )
                 )
 
+                print(task_master_job)
+
                 # TODO: Create ConfigMap
                 # TODO: Create Job
                 # TODO Return created job

tesk/api/kubernetes/converter.py

@@ -13,7 +13,7 @@
 )
 from kubernetes.client.models import V1Job
 
-from tesk.api.ga4gh.tes.models import TesTask
+from tesk.api.ga4gh.tes.models import TesExecutor, TesResources, TesTask
 from tesk.api.kubernetes.constants import Constants, K8sConstants
 from tesk.api.kubernetes.template import KubernetesTemplateSupplier
 from tesk.constants import TeskConstants
@@ -26,7 +26,6 @@
 class TesKubernetesConverter:
     def __init__(self, namespace=TeskConstants.tesk_namespace):
         """Initialize the converter."""
-        self.taskmaster_template: V1Job = get_taskmaster_template()
         self.taskmaster_env_properties: TaskmasterEnvProperties = (
             get_taskmaster_env_property()
         )
@@ -82,54 +81,108 @@ def from_tes_task_to_k8s_job(self, task: TesTask):
 
         return taskmsater_job
 
-    # def from_tes_task_to_k8s_config_map(self, task, user, job):
-    #     task_master_config_map = V1ConfigMap(
-    #         metadata=V1ObjectMeta(name=job.metadata.name)
-    #     )
-    #     task_master_config_map.metadata.annotations[ANN_TESTASK_NAME_KEY] = task["name"]
-    #     task_master_config_map.metadata.labels[LABEL_USERID_KEY] = user["username"]
-
-    #     if "tags" in task and "GROUP_NAME" in task["tags"]:
-    #         task_master_config_map.metadata.labels[LABEL_GROUPNAME_KEY] = task["tags"][
-    #             "GROUP_NAME"
-    #         ]
-    #     elif user["is_member"]:
-    #         task_master_config_map.metadata.labels[LABEL_GROUPNAME_KEY] = user[
-    #             "any_group"
-    #         ]
-
-    #     executors_as_jobs = [
-    #         self.from_tes_executor_to_k8s_job(
-    #             task_master_config_map.metadata.name,
-    #             task["name"],
-    #             executor,
-    #             idx,
-    #             task["resources"],
-    #             user,
-    #         )
-    #         for idx, executor in enumerate(task["executors"])
-    #     ]
-
-    #     task_master_input = {
-    #         "inputs": task.get("inputs", []),
-    #         "outputs": task.get("outputs", []),
-    #         "volumes": task.get("volumes", []),
-    #         "resources": {"disk_gb": task["resources"].get("disk_gb", 10.0)},
-    #     }
-    #     task_master_input[TASKMASTER_INPUT_EXEC_KEY] = executors_as_jobs
-
-    #     task_master_input_as_json = json.dumps(task_master_input)
-    #     try:
-    #         with BytesIO() as obj:
-    #             with gzip.GzipFile(fileobj=obj, mode="wb") as gzip_file:
-    #                 gzip_file.write(task_master_input_as_json.encode("utf-8"))
-    #             task_master_config_map.binary_data = {
-    #                 f"{TASKMASTER_INPUT}.gz": obj.getvalue()
-    #             }
-    #     except Exception as e:
-    #         logger.info(
-    #             f"Compression of task {task_master_config_map.metadata.name} JSON configmap failed",
-    #             e,
-    #         )
-
-    #     return task_master_config_map
+    def from_tes_task_to_k8s_config_map(
+        self,
+        task: TesTask,
+        # user,
+        job,
+    ):
+        task_master_config_map = V1ConfigMap(
+            metadata=V1ObjectMeta(name=job.metadata.name)
+        )
+        task_master_config_map.metadata.annotations[
+            self.constants.ann_testask_name_key
+        ] = task["name"]
+        # task_master_config_map.metadata.labels[self.constants.label_userid_key] = user["username"]
+
+        if "tags" in task and "GROUP_NAME" in task["tags"]:
+            task_master_config_map.metadata.labels[
+                self.constants.label_groupname_key
+            ] = task["tags"]["GROUP_NAME"]
+        # elif user["is_member"]:
+        #     task_master_config_map.metadata.labels[self.constants.label_groupname_key] = user[
+        #         "any_group"
+        #     ]
+
+        executors_as_jobs = [
+            self.from_tes_executor_to_k8s_job(
+                task_master_config_map.metadata.name,
+                task["name"],
+                executor,
+                idx,
+                task["resources"],
+                # user,
+            )
+            for idx, executor in enumerate(task["executors"])
+        ]
+
+        task_master_input = {
+            "inputs": task.inputs or [],
+            "outputs": task.outputs or [],
+            "volumes": task.volumes or [],
+            "resources": {"disk_gb": task.resources.disk_gb or 10.0},
+        }
+        task_master_input[self.constants.taskmaster_input_exec_key] = executors_as_jobs
+
+        task_master_input_as_json = json.dumps(task_master_input)
+        try:
+            with BytesIO() as obj:
+                with gzip.GzipFile(fileobj=obj, mode="wb") as gzip_file:
+                    gzip_file.write(task_master_input_as_json.encode("utf-8"))
+                task_master_config_map.binary_data = {
+                    f"{self.constants.taskmaster_input}.gz": obj.getvalue()
+                }
+        except Exception as e:
+            logger.info(
+                f"Compression of task {task_master_config_map.metadata.name} JSON configmap failed",
+                e,
+            )
+
+        return task_master_config_map
+
+
+    def from_tes_executor_to_k8s_job(
+        self,
+        generated_task_id: str,
+        tes_task_name: str,
+        executor: TesExecutor,
+        executor_index: int,
+        resources: TesResources,
+        # user: User
+    ) -> V1Job:
+        # Get new template executor Job object
+        job = self.executor_template_supplier()
+
+        # Set executors name based on taskmaster's job name
+        Job(job).change_job_name(Task(generated_task_id).get_executor_name(executor_index))
+
+        # Put arbitrary labels and annotations
+        job.metadata.labels = job.metadata.labels or {}
+        job.metadata.labels["taskId"] = generated_task_id
+        job.metadata.labels["execNo"] = str(executor_index)
+        job.metadata.labels["userId"] = user.username
+
+        job.metadata.annotations = job.metadata.annotations or {}
+        job.metadata.annotations["tesTaskName"] = tes_task_name
+
+        container = job.spec.template.spec.containers[0]
+
+        # Convert potential TRS URI into docker image
+        container.image = self.trs_client.get_docker_image_for_tool_version_uri(executor.image)
+
+        # Map executor's command to job container's command
+        for command in ExecutorCommandWrapper(executor).get_commands_with_stream_redirects():
+            container.add_command_item(command)
+
+        if executor.env:
+            container.env = [V1EnvVar(name=key, value=value) for key, value in executor.env.items()]
+
+        container.working_dir = executor.workdir
+
+        if resources.cpu_cores:
+            container.resources.requests['cpu'] = QuantityFormatter().parse(str(resources.cpu_cores))
+
+        if resources.ram_gb:
+            container.resources.requests['memory'] = QuantityFormatter().parse(f"{resources.ram_gb:.6f}Gi")
+
+        return job

tesk/api/kubernetes/template.py

@@ -4,7 +4,16 @@
 import uuid
 
 from kubernetes.client import (
+    V1Container,
     V1EnvVar,
+    V1JobSpec,
+    V1ObjectMeta,
+    V1PodSpec,
+    V1PodTemplateSpec,
+    V1ResourceRequirements,
+    V1SecretVolumeSource,
+    V1Volume,
+    V1VolumeMount,
 )
 from kubernetes.client.models import V1Job
 
@@ -19,7 +28,7 @@
 class KubernetesTemplateSupplier:
     """Templates for tasmaster's and executor's job object.."""
 
-    def __init__(self, namespace=TeskConstants.tesk_namespace):
+    def __init__(self, namespace=TeskConstants.tesk_namespace, security_context = None):
         """Initialize the converter."""
         self.taskmaster_template: V1Job = get_taskmaster_template()
         self.taskmaster_env_properties: TaskmasterEnvProperties = (
@@ -28,6 +37,7 @@ def __init__(self, namespace=TeskConstants.tesk_namespace):
         self.constants = Constants()
         self.k8s_constants = K8sConstants()
         self.namespace = namespace
+        self.security_context= security_context
 
     def get_task_master_name(self) -> str:
         """Generate a unique name for the taskmaster job."""
@@ -89,3 +99,48 @@ def task_master_template(self) -> V1Job:
                     )
 
         return job
+
+    def executor_template(self):
+        container = V1Container(resources=V1ResourceRequirements())
+
+        if self.taskmaster_env_properties.executorSecret is not None:
+            container.volume_mounts = [
+                V1VolumeMount(
+                    read_only=True,
+                    name=self.taskmaster_env_properties.executorSecret.name,
+                    mount_path=self.taskmaster_env_properties.executorSecret.mountPath,
+                )
+            ]
+
+        pod_spec = V1PodSpec(
+            containers=[container],
+            restart_policy=self.k8s_constants.job_restart_policy,
+        )
+
+        if self.security_context:
+            pod_spec.security_context = self.security_context
+
+        job = V1Job(
+            api_version=self.k8s_constants.k8s_batch_api_version,
+            kind=self.k8s_constants.k8s_batch_api_job_type,
+            metadata=V1ObjectMeta(
+                labels={
+                    self.constants.label_jobtype_key: self.constants.label_jobtype_value_exec
+                }
+            ),
+            spec=V1JobSpec(
+                template=V1PodTemplateSpec(metadata=V1ObjectMeta(), spec=pod_spec)
+            ),
+        )
+
+        if self.taskmaster_env_properties.executorSecret is not None:
+            job.spec.template.spec.volumes = [
+                V1Volume(
+                    name=self.taskmaster_env_properties.executorSecret.name,
+                    secret=V1SecretVolumeSource(
+                        secret_name=self.taskmaster_env_properties.executorSecret.name
+                    ),
+                )
+            ]
+
+        return job

tesk/constants.py

@@ -4,14 +4,27 @@
 
 
 class TeskConstants:
-    """Tesk scoped constants."""
+    """Tesk's K8s scoped constants."""
 
     filer_image_name: str = os.getenv(
-        "FILER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-filer"
+        "TESK_API_TASKMASTER_FILER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-filer"
+    )
+    filer_image_version: str = os.getenv(
+        "TESK_API_TASKMASTER_FILER_IMAGE_VERSION", "latest"
     )
-    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"
+        "TESK_API_TASKMASTER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-taskmaster"
+    )
+    taskmaster_image_version: str = os.getenv(
+        "TESK_API_TASKMASTER_IMAGE_VERSION", "latest"
+    )
+    tesk_namespace: str = os.getenv("TESK_API_K8S_NAMESPACE", "tesk")
+    taskmaster_service_account_name: str = os.getenv(
+        "TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME", "taskmaster"
+    )
+    taskmaster_environement_executor_backoff_limit: str = os.getenv(
+        "ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT", "2"
+    )
+    filer_environment_filer_backoff_limit: str = os.getenv(
+        "TESK_API_TASKMASTER_ENVIRONMENT_FILER_BACKOFF_LIMIT", "2"
     )
-    taskmaster_image_version: str = os.getenv("TASKMASTER_IMAGE_VERSION", "latest")
-    tesk_namespace: str = os.getenv("TESK_NAMESPACE", "tesk")