diff --git a/poetry.lock b/poetry.lock index 3c52b3b5..c1d873ae 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "added-value" @@ -92,13 +92,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p [[package]] name = "authlib" -version = "1.3.1" +version = "1.3.0" description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." optional = false python-versions = ">=3.8" files = [ - {file = "Authlib-1.3.1-py2.py3-none-any.whl", hash = "sha256:d35800b973099bbadc49b42b256ecb80041ad56b7fe1216a362c7943c088f377"}, - {file = "authlib-1.3.1.tar.gz", hash = "sha256:7ae843f03c06c5c0debd63c9db91f9fda64fa62a42a77419fa15fbb7e7a58917"}, + {file = "Authlib-1.3.0-py2.py3-none-any.whl", hash = "sha256:9637e4de1fb498310a56900b3e2043a206b03cb11c05422014b0302cbc814be3"}, + {file = "Authlib-1.3.0.tar.gz", hash = "sha256:959ea62a5b7b5123c5059758296122b57cd2585ae2ed1c0622c21b371ffdae06"}, ] [package.dependencies] @@ -120,13 +120,13 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "bandit" -version = "1.7.9" +version = "1.7.8" description = "Security oriented static analyser for python code." optional = false python-versions = ">=3.8" files = [ - {file = "bandit-1.7.9-py3-none-any.whl", hash = "sha256:52077cb339000f337fb25f7e045995c4ad01511e716e5daac37014b9752de8ec"}, - {file = "bandit-1.7.9.tar.gz", hash = "sha256:7c395a436743018f7be0a4cbb0a4ea9b902b6d87264ddecf8cfdc73b4f78ff61"}, + {file = "bandit-1.7.8-py3-none-any.whl", hash = "sha256:509f7af645bc0cd8fd4587abc1a038fc795636671ee8204d502b933aee44f381"}, + {file = "bandit-1.7.8.tar.gz", hash = "sha256:36de50f720856ab24a24dbaa5fee2c66050ed97c1477e0a1159deab1775eab6b"}, ] [package.dependencies] @@ -174,17 +174,6 @@ files = [ {file = "billiard-4.2.0.tar.gz", hash = "sha256:9a3c3184cb275aa17a732f93f65b20c525d3d9f253722d26a82194803ade5a2c"}, ] -[[package]] -name = "blinker" -version = "1.8.2" -description = "Fast, simple object-to-object and broadcast signaling" -optional = false -python-versions = ">=3.8" -files = [ - {file = 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-3169,20 +3136,20 @@ test = ["websockets"] [[package]] name = "werkzeug" -version = "2.3.8" +version = "2.2.3" description = "The comprehensive WSGI web application library." optional = false -python-versions = ">=3.8" +python-versions = ">=3.7" files = [ - {file = "werkzeug-2.3.8-py3-none-any.whl", hash = "sha256:bba1f19f8ec89d4d607a3bd62f1904bd2e609472d93cd85e9d4e178f472c3748"}, - {file = "werkzeug-2.3.8.tar.gz", hash = "sha256:554b257c74bbeb7a0d254160a4f8ffe185243f52a52035060b761ca62d977f03"}, + {file = "Werkzeug-2.2.3-py3-none-any.whl", hash = "sha256:56433961bc1f12533306c624f3be5e744389ac61d722175d543e1751285da612"}, + {file = "Werkzeug-2.2.3.tar.gz", hash = "sha256:2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe"}, ] [package.dependencies] MarkupSafe = ">=2.1.1" [package.extras] -watchdog = ["watchdog (>=2.3)"] +watchdog = ["watchdog"] [[package]] name = "xmltodict" @@ -3198,4 +3165,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "58ff8e56ad701a8cda42215ba47057dd79e85b0d989a6b274ca7b7aa9c616620" +content-hash = "5360faeac82607ad994db4eac1f2a80dc823b930ba697b84e0bba299b9cac893" diff --git a/pyproject.toml b/pyproject.toml index 1f5b98d7..49795030 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ version = "0.1.0" [tool.poetry.dependencies] boto3 = "1.34.104" foca = "^0.13.0" -kubernetes = "^30.1.0" +kubernetes = "^29.0.0" python = "^3.11" requests = ">=2.20.0" urllib3 = "^2.2.2" diff --git a/tesk/api/ga4gh/tes/controllers.py b/tesk/api/ga4gh/tes/controllers.py index 73dc388d..109e4092 100644 --- a/tesk/api/ga4gh/tes/controllers.py +++ b/tesk/api/ga4gh/tes/controllers.py @@ -7,8 +7,8 @@ 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.api.kubernetes.convert.converter import TesKubernetesConverter +from tesk.api.kubernetes.convert.template import KubernetesTemplateSupplier from tesk.exceptions import BadRequest, InternalServerError from tesk.utils import get_custom_config @@ -43,7 +43,10 @@ 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() + tes_task = TesTask(**request_body) + namespace = "tesk" + task_creater = CreateTesTask(tes_task, namespace) + task_creater.response() 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 a6f76398..3fb29b38 100644 --- a/tesk/api/ga4gh/tes/task/create_task.py +++ b/tesk/api/ga4gh/tes/task/create_task.py @@ -5,9 +5,9 @@ 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 +from tesk.api.kubernetes.convert.converter import TesKubernetesConverter from tesk.constants import TeskConstants +from tesk.exceptions import KubernetesError logger = logging.getLogger(__name__) @@ -33,8 +33,9 @@ def __init__(self, task: TesTask, namespace=TeskConstants.tesk_namespace): def create_task(self): """Create TES task.""" attempts_no = 0 - while attempts_no > self.constants.job_create_attempts_no: + while attempts_no < self.constants.job_create_attempts_no: try: + attempts_no += 1 resources = self.task.resources if resources and resources.ram_gb: @@ -49,28 +50,27 @@ def create_task(self): ) ) + task_master_config_map = ( + self.tes_kubernetes_converter.from_tes_task_to_k8s_config_map( + self.task, + task_master_job, + # user + ) + ) + _ = self.kubernetes_client_wrapper.create_config_map( + task_master_config_map + ) + created_job = self.kubernetes_client_wrapper.create_job(task_master_job) + print(task_master_config_map) print(task_master_job) - - # 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) + return created_job.metadata.name 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) diff --git a/tesk/api/kubernetes/convert/__init__.py b/tesk/api/kubernetes/convert/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tesk/api/kubernetes/converter.py b/tesk/api/kubernetes/convert/converter.py similarity index 55% rename from tesk/api/kubernetes/converter.py rename to tesk/api/kubernetes/convert/converter.py index 54fc9630..fac4889b 100644 --- a/tesk/api/kubernetes/converter.py +++ b/tesk/api/kubernetes/convert/converter.py @@ -1,40 +1,57 @@ """Module for converting TES tasks to Kubernetes jobs.""" +import base64 import gzip import json import logging +from decimal import Decimal from io import BytesIO +from typing import Any from kubernetes.client import ( V1ConfigMap, V1ConfigMapVolumeSource, + V1Container, + V1EnvVar, V1ObjectMeta, + V1ResourceRequirements, V1Volume, ) from kubernetes.client.models import V1Job +from kubernetes.utils.quantity import parse_quantity # type: ignore 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.api.kubernetes.convert.data.job import Job +from tesk.api.kubernetes.convert.data.task import Task +from tesk.api.kubernetes.convert.executor_command_wrapper import ExecutorCommandWrapper +from tesk.api.kubernetes.convert.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 +from tesk.utils import get_taskmaster_env_property, pydantic_model_list_json logger = logging.getLogger(__name__) class TesKubernetesConverter: + """Convert TES requests to Kubernetes resources.""" + def __init__(self, namespace=TeskConstants.tesk_namespace): """Initialize the converter.""" self.taskmaster_env_properties: TaskmasterEnvProperties = ( get_taskmaster_env_property() ) + self.template_supplier = KubernetesTemplateSupplier( + namespace=namespace + # security_context=security_context + ) self.constants = Constants() self.k8s_constants = K8sConstants() self.namespace = namespace - # TODO: Add user to the mmethod when auth implemented in FOCA + # TODO: Add user to the method when auth implemented in FOCA def from_tes_task_to_k8s_job(self, task: TesTask): + """Convert TES task to Kubernetes job.""" taskmsater_job: V1Job = KubernetesTemplateSupplier( self.namespace ).task_master_template() @@ -48,6 +65,8 @@ def from_tes_task_to_k8s_job(self, task: TesTask): if taskmsater_job.metadata.labels is None: taskmsater_job.metadata.labels = {} + # taskmsater_job.metadata.name = task.name + taskmsater_job.metadata.annotations[self.constants.ann_testask_name_key] = ( task.name ) @@ -84,21 +103,30 @@ def from_tes_task_to_k8s_job(self, task: TesTask): def from_tes_task_to_k8s_config_map( self, task: TesTask, + job: V1Job, # user, - job, - ): + ) -> V1ConfigMap: + """Create a Kubernetes ConfigMap from a TES task.""" task_master_config_map = V1ConfigMap( metadata=V1ObjectMeta(name=job.metadata.name) ) + + task_master_config_map.metadata.labels = ( + task_master_config_map.metadata.labels or {} + ) + task_master_config_map.metadata.annotations = ( + task_master_config_map.metadata.annotations or {} + ) + task_master_config_map.metadata.annotations[ self.constants.ann_testask_name_key - ] = task["name"] + ] = 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"]: + 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"] + ] = task.tags["GROUP_NAME"] # elif user["is_member"]: # task_master_config_map.metadata.labels[self.constants.label_groupname_key] = user[ # "any_group" @@ -107,30 +135,42 @@ def from_tes_task_to_k8s_config_map( executors_as_jobs = [ self.from_tes_executor_to_k8s_job( task_master_config_map.metadata.name, - task["name"], + task.name, executor, idx, - task["resources"], + task.resources, # user, ) - for idx, executor in enumerate(task["executors"]) + for idx, executor in enumerate(task.executors) ] - task_master_input = { - "inputs": task.inputs or [], - "outputs": task.outputs or [], + task_master_input: dict[str, Any] = { + "inputs": pydantic_model_list_json(task.inputs) or [], + "outputs": pydantic_model_list_json(task.outputs) or [], "volumes": task.volumes or [], - "resources": {"disk_gb": task.resources.disk_gb or 10.0}, + "resources": {"disk_gb": float(task.resources.disk_gb) or 10.0}, } - task_master_input[self.constants.taskmaster_input_exec_key] = executors_as_jobs + task_master_input[self.constants.taskmaster_input_exec_key] = [ + exec_job.to_dict() for exec_job in executors_as_jobs + ] + + def decimal_to_float(obj): + if isinstance(obj, Decimal): + return float(obj) + raise TypeError - task_master_input_as_json = json.dumps(task_master_input) + taskmaster_input_as_json = json.loads( + json.dumps(task_master_input, default=decimal_to_float) + ) 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")) + json_data = json.dumps(taskmaster_input_as_json) + gzip_file.write(json_data.encode("utf-8")) task_master_config_map.binary_data = { - f"{self.constants.taskmaster_input}.gz": obj.getvalue() + f"{self.constants.taskmaster_input}.gz": base64.b64encode( + obj.getvalue() + ).decode("utf-8") } except Exception as e: logger.info( @@ -140,7 +180,6 @@ def from_tes_task_to_k8s_config_map( return task_master_config_map - def from_tes_executor_to_k8s_job( self, generated_task_id: str, @@ -151,38 +190,58 @@ def from_tes_executor_to_k8s_job( # user: User ) -> V1Job: # Get new template executor Job object - job = self.executor_template_supplier() - + job: V1Job = self.template_supplier.executor_template() + # Set executors name based on taskmaster's job name - Job(job).change_job_name(Task(generated_task_id).get_executor_name(executor_index)) - + Job(job).change_job_name( + # Task(job, generated_task_id).get_executor_name(executor_index) + "newname" + ) + # 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.labels[self.constants.label_testask_id_key] = generated_task_id + job.metadata.labels[self.constants.label_execno_key] = str(executor_index) + # job.metadata.labels[self.constants.label_userid_key] = user.username + job.metadata.annotations = job.metadata.annotations or {} - job.metadata.annotations["tesTaskName"] = tes_task_name - - container = job.spec.template.spec.containers[0] - + job.metadata.annotations[self.constants.ann_testask_name_key] = tes_task_name + + container: V1Container = job.spec.template.spec.containers[0] + + # TODO: Not sure what to do with this # Convert potential TRS URI into docker image - container.image = self.trs_client.get_docker_image_for_tool_version_uri(executor.image) - + # container.image = self.trs_client.get_docker_image_for_tool_version_uri( + # executor.image + # ) + + if not container.command: + container.command = [] # Map executor's command to job container's command - for command in ExecutorCommandWrapper(executor).get_commands_with_stream_redirects(): - container.add_command_item(command) - + for command in ExecutorCommandWrapper( + executor + ).get_commands_with_stream_redirects(): + container.command.append(command) + if executor.env: - container.env = [V1EnvVar(name=key, value=value) for key, value in executor.env.items()] - + container.env = [ + V1EnvVar(name=key, value=value) for key, value in executor.env.items() + ] + else: + container.env = [] + container.working_dir = executor.workdir - + + container.resources = V1ResourceRequirements(requests={}) + if resources.cpu_cores: - container.resources.requests['cpu'] = QuantityFormatter().parse(str(resources.cpu_cores)) - + container.resources.requests["cpu"] = parse_quantity( + str(resources.cpu_cores) + ) + if resources.ram_gb: - container.resources.requests['memory'] = QuantityFormatter().parse(f"{resources.ram_gb:.6f}Gi") - + container.resources.requests["memory"] = parse_quantity( + f"{resources.ram_gb:.6f}Gi" + ) + return job diff --git a/tesk/api/kubernetes/convert/data/__init__.py b/tesk/api/kubernetes/convert/data/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tesk/api/kubernetes/convert/data/job.py b/tesk/api/kubernetes/convert/data/job.py new file mode 100644 index 00000000..5df1c2ac --- /dev/null +++ b/tesk/api/kubernetes/convert/data/job.py @@ -0,0 +1,48 @@ +"""A container for a single Kubernetes job object (can be both a taskmaster and an executor) and its list of worker pods (Kubernetes Pod objects).""" + +from typing import List, Optional + +from kubernetes.client import V1Job, V1Pod + + +class Job: + """A container for a single Kubernetes job object (can be both a taskmaster and an executor) and its list of worker pods (Kubernetes Pod objects)""" + + def __init__(self, job: V1Job): + """Initializes the Job with a Kubernetes job object.""" + self.job: V1Job = job + self.pods: List[V1Pod] = [] + + def get_job(self) -> V1Job: + """Returns the Kubernetes job object.""" + return self.job + + def add_pod(self, pod: V1Pod): + """Adds a single pod to the list (without any duplication checks).""" + # TODO: This doesn't take care of duplication, use set on id or name + self.pods.append(pod) + + def has_pods(self) -> bool: + """Checks if the job has any pods.""" + return bool(self.pods) + + def get_first_pod(self) -> Optional[V1Pod]: + """Returns arbitrarily chosen pod from the list (currently the first one added) or None if the job has no pods.""" + if not self.has_pods(): + return None + return self.pods[0] + + def get_pods(self) -> List[V1Pod]: + """Returns the list of job pods in the order of addition to the list or an empty list if no pods.""" + return self.pods + + def change_job_name(self, new_name: str): + """Changes the job name, as well as the names in its metadata and container specs.""" + self.job.metadata.name = new_name + self.job.spec.template.metadata.name = new_name + if self.job.spec.template.spec.containers: + self.job.spec.template.spec.containers[0].name = new_name + + def get_job_name(self) -> Optional[str]: + """Returns the job name.""" + return self.job.metadata.name diff --git a/tesk/api/kubernetes/convert/data/task.py b/tesk/api/kubernetes/convert/data/task.py new file mode 100644 index 00000000..67058769 --- /dev/null +++ b/tesk/api/kubernetes/convert/data/task.py @@ -0,0 +1,65 @@ +"""A composite that represents Kubernetes object's graph of a single TES task. + +- Taskmaster job with its pods. +- Executor jobs with its pods. +""" + +import re +from typing import Dict, List, Optional + +from kubernetes.client.models import V1Job, V1ObjectMeta + +from tesk.api.kubernetes.constants import Constants +from tesk.api.kubernetes.convert.data.job import Job + + +class Task: + """Task is a composite that represents Kubernetes object's graph of a single TES task.""" + + def __init__( + self, taskmaster: Optional[Job] = None, taskmaster_name: Optional[str] = None + ): + if taskmaster: + self.taskmaster = taskmaster + elif taskmaster_name: + job = V1Job(metadata=V1ObjectMeta(name=taskmaster_name)) + self.taskmaster = Job(job) + else: + raise ValueError("Either taskmaster or taskmaster_name must be provided") + + self.executors_by_name: Dict[str, Job] = {} + self.output_filer: Optional[Job] = None + self.constants = Constants() + + def add_executor(self, executor: Job): + self.executors_by_name.setdefault(executor.get_job().metadata.name, executor) + + def set_output_filer(self, filer: Job): + self.output_filer = filer + + def get_taskmaster(self) -> Job: + return self.taskmaster + + def get_executors(self) -> List[Job]: + return sorted(self.executors_by_name.values(), key=self.extract_executor_number) + + def get_last_executor(self) -> Optional[Job]: + if not self.executors_by_name: + return None + executors = self.get_executors() + return executors[-1] if executors else None + + def get_output_filer(self) -> Optional[Job]: + return self.output_filer + + def extract_executor_number(self, executor: Job) -> int: + taskmaster_name = self.taskmaster.get_job_name() + prefix = taskmaster_name + self.constants.job_name_exec_prefix + match = re.match(f"{re.escape(prefix)}(\d+)", executor.get_job_name()) + if match: + return int(match.group(1)) + return float("inf") + + def get_executor_name(self, executor_index: int) -> str: + taskmaster_name = self.taskmaster.get_job_name() + return f"{taskmaster_name}{self.constants.job_name_exec_prefix}{str(executor_index).zfill(self.constants.job_name_exec_no_length)}" diff --git a/tesk/api/kubernetes/convert/executor_command_wrapper.py b/tesk/api/kubernetes/convert/executor_command_wrapper.py new file mode 100644 index 00000000..6fa088b0 --- /dev/null +++ b/tesk/api/kubernetes/convert/executor_command_wrapper.py @@ -0,0 +1,60 @@ +"""Wraps list of executor's command. + +Such that: +- If any of executor's stdin/stdout/stderr params is set, the command runs in shell +- Each part of the original command (single command/argument) that contained shell + special chars is surrounded by single quotes, plus single quote inside such string + are replaced with '"'"' sequence +- `stdin`, `stdout`, `stderr` streams are redirected to paths according to executors + params +""" + +import re +from typing import List + +from tesk.api.ga4gh.tes.models import TesExecutor + + +class ExecutorCommandWrapper: + SPECIAL_CHARS = re.compile(r"[ !\"#$&'()*;<>?\[\\`{|~\t\n]") + + def __init__(self, executor: TesExecutor): + self.executor = executor + + def get_commands_with_stream_redirects(self) -> List[str]: + result = [] + + if ( + not self.executor.stdin + and not self.executor.stdout + and not self.executor.stderr + ): + return self.executor.command + + result.append("/bin/sh") + result.append("-c") + + command_parts = [] + + for command_part in self.executor.command: + if self.SPECIAL_CHARS.search(command_part): + if "'" in command_part: + command_part = command_part.replace("'", "'\"'\"'") + command_part = f"'{command_part}'" + command_parts.append(command_part) + + if self.executor.stdin: + command_parts.append("<") + command_parts.append(self.executor.stdin) + + if self.executor.stdout: + command_parts.append(">") + command_parts.append(self.executor.stdout) + + if self.executor.stderr: + command_parts.append("2>") + command_parts.append(self.executor.stderr) + + result.append(" ".join(command_parts)) + + return result diff --git a/tesk/api/kubernetes/convert/taskmaster_env_properties.py b/tesk/api/kubernetes/convert/taskmaster_env_properties.py new file mode 100644 index 00000000..d0f7ef7d --- /dev/null +++ b/tesk/api/kubernetes/convert/taskmaster_env_properties.py @@ -0,0 +1,79 @@ +"""Taskmaster environment properties model for the TESK.""" + +from typing import Dict, Optional + +from pydantic import BaseModel, Field + +from tesk.constants import TeskConstants + + +class FtpConfig(BaseModel): + """Ftp configuration model for the TESK.""" + + secretName: Optional[str] = Field( + default=None, description="Name of the secret with FTP account credentials" + ) + enabled: bool = Field( + default=False, + description="If FTP account enabled (based on non-emptiness of secretName)", + ) + + +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.""" + + imageName: str = Field( + default=TeskConstants.taskmaster_image_name, + description="Taskmaster image name", + ) + imageVersion: str = Field( + default=TeskConstants.taskmaster_image_version, + description="Taskmaster image version", + ) + filerImageName: str = Field( + default=TeskConstants.filer_image_name, description="Filer image name" + ) + filerImageVersion: str = Field( + default=TeskConstants.filer_image_version, description="Filer image version" + ) + ftp: FtpConfig = Field(default=None, description="Test FTP account settings") + 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)", + ) + environment: Dict[str, str] = Field( + default={"key": "value"}, + description="Environment variables, that will be passed to taskmaster", + ) + 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" + ) diff --git a/tesk/api/kubernetes/template.py b/tesk/api/kubernetes/convert/template.py similarity index 96% rename from tesk/api/kubernetes/template.py rename to tesk/api/kubernetes/convert/template.py index d38cbb40..45b7f1f4 100644 --- a/tesk/api/kubernetes/template.py +++ b/tesk/api/kubernetes/convert/template.py @@ -28,7 +28,7 @@ class KubernetesTemplateSupplier: """Templates for tasmaster's and executor's job object..""" - def __init__(self, namespace=TeskConstants.tesk_namespace, security_context = None): + 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 = ( @@ -37,7 +37,7 @@ def __init__(self, namespace=TeskConstants.tesk_namespace, security_context = No self.constants = Constants() self.k8s_constants = K8sConstants() self.namespace = namespace - self.security_context= security_context + self.security_context = security_context def get_task_master_name(self) -> str: """Generate a unique name for the taskmaster job.""" @@ -101,7 +101,7 @@ def task_master_template(self) -> V1Job: return job def executor_template(self): - container = V1Container(resources=V1ResourceRequirements()) + container = V1Container(name="executor", resources=V1ResourceRequirements()) if self.taskmaster_env_properties.executorSecret is not None: container.volume_mounts = [ diff --git a/tesk/custom_config.py b/tesk/custom_config.py index 112daf3e..78a285db 100644 --- a/tesk/custom_config.py +++ b/tesk/custom_config.py @@ -5,80 +5,9 @@ from pydantic import BaseModel, Field from tesk.api.ga4gh.tes.models import Service -from tesk.constants import TeskConstants - - -class FtpConfig(BaseModel): - """Ftp configuration model for the TESK.""" - - secretName: Optional[str] = Field( - default=None, description="Name of the secret with FTP account credentials" - ) - enabled: bool = Field( - default=False, - description="If FTP account enabled (based on non-emptiness of secretName)", - ) - - -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.""" - - imageName: str = Field( - default=TeskConstants.taskmaster_image_name, - description="Taskmaster image name", - ) - imageVersion: str = Field( - default=TeskConstants.taskmaster_image_version, - description="Taskmaster image version", - ) - filerImageName: str = Field( - default=TeskConstants.filer_image_name, description="Filer image name" - ) - filerImageVersion: str = Field( - default=TeskConstants.filer_image_version, description="Filer image version" - ) - ftp: FtpConfig = Field(default=None, description="Test FTP account settings") - 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)", - ) - environment: Dict[str, str] = Field( - default={"key": "value"}, - description="Environment variables, that will be passed to taskmaster", - ) - 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" - ) +from tesk.api.kubernetes.convert.taskmaster_env_properties import ( + TaskmasterEnvProperties, +) class SecretKeyRef(BaseModel): diff --git a/tesk/exceptions.py b/tesk/exceptions.py index add22fe0..155c228b 100644 --- a/tesk/exceptions.py +++ b/tesk/exceptions.py @@ -13,6 +13,7 @@ InternalServerError, NotFound, ) +from http import HTTPStatus class ConfigNotFoundError(FileNotFoundError): @@ -76,3 +77,7 @@ class ValidationError(Exception): class KubernetesError(ApiException): """Kubernetes error.""" + + def is_object_name_duplicated(self) -> bool: + """Check if object name is duplicated.""" + return self.status == HTTPStatus.CONFLICT diff --git a/tesk/utils.py b/tesk/utils.py index 8fef6e42..7b9ea2c2 100644 --- a/tesk/utils.py +++ b/tesk/utils.py @@ -2,7 +2,7 @@ import os from pathlib import Path -from typing import Optional +from typing import Any, List, Optional from foca import Foca from kubernetes.client.models import ( @@ -20,6 +20,7 @@ V1Volume, V1VolumeMount, ) +from pydantic import BaseModel from tesk.custom_config import ( Container, @@ -75,7 +76,6 @@ def get_taskmaster_template() -> V1Job: """ custom_conf = get_custom_config() try: - print(custom_conf.taskmaster_template) return job_to_v1job(custom_conf.taskmaster_template) except AttributeError: raise ConfigNotFoundError( @@ -189,3 +189,10 @@ def convert_job_metadata(job_metadata: JobMetadata) -> V1ObjectMeta: metadata=convert_job_metadata(job.metadata), spec=convert_job_spec(job.spec), ) + + +def pydantic_model_list_json(model_list: List[BaseModel]) -> List[dict[str, Any]]: + json_list = [] + for item in model_list: + json_list.append(item.json()) + return json_list