From 2429b0fdfc89f02a73af16191ecc358b8307014b Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Thu, 1 Aug 2024 16:55:00 +0530 Subject: [PATCH] WIP --- README.md | 26 ++ deployment/charts/tesk/values.yaml | 2 +- poetry.lock | 369 ++++++++++++------------- tesk/api/ga4gh/tes/controllers.py | 2 + tesk/api/ga4gh/tes/task/create_task.py | 6 +- tesk/api/kubernetes/converter.py | 159 +++++++---- tesk/api/kubernetes/template.py | 57 +++- tesk/constants.py | 25 +- tesk/custom_config.py | 29 ++ 9 files changed, 427 insertions(+), 248 deletions(-) diff --git a/README.md b/README.md index 0dd388ec..8f8b6ad6 100644 --- a/README.md +++ b/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. diff --git a/deployment/charts/tesk/values.yaml b/deployment/charts/tesk/values.yaml index dae8b617..e2a957c2 100644 --- a/deployment/charts/tesk/values.yaml +++ b/deployment/charts/tesk/values.yaml @@ -9,7 +9,7 @@ host_name: "" # # 'openstack' or 's3' -storage: none +storage: s3 # Configurable storage class. storageClass: diff --git a/poetry.lock b/poetry.lock index 717f28e5..3c52b3b5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "added-value" @@ -206,13 +206,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.34.145" -description = "Type annotations for boto3 1.34.145 generated with mypy-boto3-builder 7.25.0" +version = "1.34.151" +description = "Type annotations for boto3 1.34.151 generated with mypy-boto3-builder 7.25.0" optional = false python-versions = ">=3.8" files = [ - {file = "boto3_stubs-1.34.145-py3-none-any.whl", hash = "sha256:1303deb7d749a2c9bd5a30830e1d537c1474b70c5f429e3db9af5d3eaa7b9696"}, - {file = "boto3_stubs-1.34.145.tar.gz", hash = "sha256:2d15ccfc44407baae897d3a531f9eb0826e207d70e92f5268e8703139bec2dba"}, + {file = "boto3_stubs-1.34.151-py3-none-any.whl", hash = "sha256:7c74775d5bca4693c9695526b95c80a572d6e1bf8059249698abff9596268671"}, + {file = "boto3_stubs-1.34.151.tar.gz", hash = "sha256:8422368138fb74afb7c11965677726000c4d24b7b3b872d414f5c706372bf94f"}, ] [package.dependencies] @@ -225,7 +225,7 @@ accessanalyzer = 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"5360faeac82607ad994db4eac1f2a80dc823b930ba697b84e0bba299b9cac893" ->>>>>>> main +content-hash = "58ff8e56ad701a8cda42215ba47057dd79e85b0d989a6b274ca7b7aa9c616620" diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index 9b9f01a2..73dc388d 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/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 diff --git a/tesk/api/ga4gh/tes/task/create_task.py b/tesk/api/ga4gh/tes/task/create_task.py index c301d27b..a6f76398 100644 --- a/tesk/api/ga4gh/tes/task/create_task.py +++ b/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 diff --git a/tesk/api/kubernetes/converter.py b/tesk/api/kubernetes/converter.py index 0e5fee88..54fc9630 100644 --- a/tesk/api/kubernetes/converter.py +++ b/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 diff --git a/tesk/api/kubernetes/template.py b/tesk/api/kubernetes/template.py index d4dfc29a..d38cbb40 100644 --- a/tesk/api/kubernetes/template.py +++ b/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 diff --git a/tesk/constants.py b/tesk/constants.py index 641df53d..6ffaafae 100644 --- a/tesk/constants.py +++ b/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") diff --git a/tesk/custom_config.py b/tesk/custom_config.py index 279ebffd..112daf3e 100644 --- a/tesk/custom_config.py +++ b/tesk/custom_config.py @@ -20,6 +20,26 @@ class FtpConfig(BaseModel): ) +class ExecutorSecret(BaseModel): + """Executor secret configuration.""" + + name: Optional[str] = Field( + default=None, + description=( + "Name of a secret that will be mounted as volume to each executor. The same" + " name will be used for the secret and the volume" + ), + ) + mountPath: Optional[str] = Field( + default=None, + alias="mountPath", + description="The path where the secret will be mounted to executors", + ) + enabled: bool = Field( + default=False, description="Indicates whether the secret is enabled" + ) + + class TaskmasterEnvProperties(BaseModel): """Taskmaster environment properties model for the TESK.""" @@ -50,6 +70,15 @@ class TaskmasterEnvProperties(BaseModel): serviceAccountName: str = Field( default="default", description="Service Account name for taskmaster" ) + debug: bool = Field( + default=False, + description="If verbose (debug) mode of taskmaster is on (passes additional " + "flag to taskmaster and sets image pull policy to Always)", + ) + executorSecret: Optional[ExecutorSecret] = Field( + default=None, + description="Executor secret configuration" + ) class SecretKeyRef(BaseModel):