diff --git a/README.md b/README.md index 0dd388e..211572e 100644 --- a/README.md +++ b/README.md @@ -66,3 +66,17 @@ and the taskmaster ends, completing the task. need either an FTP account or a PVC that can be accessed from within or from outside of the cluster by the workflow manager (more in the [deployment](deployment/documentation/deployment.md) page). + +### Environment Variables + +| **Environment Variable** | **Default Value** | **Description** | +|-------------------------------------------------|----------------------------------------------------|------------------------------------------------| +| `TESK_API_TASKMASTER_FILER_IMAGE_NAME` | `docker.io/elixircloud/tesk-core-filer` | Name of the filer image | +| `TESK_API_TASKMASTER_FILER_IMAGE_VERSION` | `latest` | Version of the filer image | +| `TESK_API_TASKMASTER_IMAGE_NAME` | `docker.io/elixircloud/tesk-core-taskmaster` | Name of the taskmaster image | +| `TESK_API_TASKMASTER_IMAGE_VERSION` | `latest` | Version of the taskmaster image | +| `TESK_API_K8S_NAMESPACE` | `tesk` | Namespace in which TESK creates K8s resources | +| `TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME` | `taskmaster` | Taskmaster service account name | +| `ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT` | `6` | Backoff limit for taskmaster execution | +| `FILER_BACKOFF_LIMIT` | `2` | Backoff limit for filer job | +| `EXECUTOR_BACKOFF_LIMIT` | `2` | Backoff limit for executor job | \ No newline at end of file diff --git a/docs/source/pages/tesk/tesk.api.ga4gh.rst b/docs/source/pages/tesk/tesk.api.ga4gh.rst new file mode 100644 index 0000000..8c96efd --- /dev/null +++ b/docs/source/pages/tesk/tesk.api.ga4gh.rst @@ -0,0 +1,18 @@ +tesk.api.ga4gh package +====================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + tesk.api.ga4gh.tes + +Module contents +--------------- + +.. automodule:: tesk.api.ga4gh + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tesk/tesk.api.ga4gh.tes.rst b/docs/source/pages/tesk/tesk.api.ga4gh.tes.rst new file mode 100644 index 0000000..9081843 --- /dev/null +++ b/docs/source/pages/tesk/tesk.api.ga4gh.tes.rst @@ -0,0 +1,37 @@ +tesk.api.ga4gh.tes package +========================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + tesk.api.ga4gh.tes.service_info + +Submodules +---------- + +tesk.api.ga4gh.tes.controllers module +------------------------------------- + +.. automodule:: tesk.api.ga4gh.tes.controllers + :members: + :undoc-members: + :show-inheritance: + +tesk.api.ga4gh.tes.models module +-------------------------------- + +.. automodule:: tesk.api.ga4gh.tes.models + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: tesk.api.ga4gh.tes + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tesk/tesk.api.ga4gh.tes.service_info.rst b/docs/source/pages/tesk/tesk.api.ga4gh.tes.service_info.rst new file mode 100644 index 0000000..6df50f4 --- /dev/null +++ b/docs/source/pages/tesk/tesk.api.ga4gh.tes.service_info.rst @@ -0,0 +1,21 @@ +tesk.api.ga4gh.tes.service\_info package +======================================== + +Submodules +---------- + +tesk.api.ga4gh.tes.service\_info.service\_info module +----------------------------------------------------- + +.. automodule:: tesk.api.ga4gh.tes.service_info.service_info + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: tesk.api.ga4gh.tes.service_info + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tesk/tesk.api.rst b/docs/source/pages/tesk/tesk.api.rst new file mode 100644 index 0000000..e9d2f31 --- /dev/null +++ b/docs/source/pages/tesk/tesk.api.rst @@ -0,0 +1,18 @@ +tesk.api package +================ + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + tesk.api.ga4gh + +Module contents +--------------- + +.. automodule:: tesk.api + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tesk/tesk.k8s.rst b/docs/source/pages/tesk/tesk.k8s.rst new file mode 100644 index 0000000..6756e05 --- /dev/null +++ b/docs/source/pages/tesk/tesk.k8s.rst @@ -0,0 +1,29 @@ +tesk.k8s package +================ + +Submodules +---------- + +tesk.k8s.constants module +------------------------- + +.. automodule:: tesk.k8s.constants + :members: + :undoc-members: + :show-inheritance: + +tesk.k8s.wrapper module +----------------------- + +.. automodule:: tesk.k8s.wrapper + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: tesk.k8s + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tesk/tesk.rst b/docs/source/pages/tesk/tesk.rst index b023c8f..9b4aede 100644 --- a/docs/source/pages/tesk/tesk.rst +++ b/docs/source/pages/tesk/tesk.rst @@ -7,8 +7,53 @@ Subpackages .. toctree:: :maxdepth: 4 + tesk.api + tesk.k8s tesk.services +Submodules +---------- + +tesk.app module +--------------- + +.. automodule:: tesk.app + :members: + :undoc-members: + :show-inheritance: + +tesk.constants module +--------------------- + +.. automodule:: tesk.constants + :members: + :undoc-members: + :show-inheritance: + +tesk.custom\_config module +-------------------------- + +.. automodule:: tesk.custom_config + :members: + :undoc-members: + :show-inheritance: + +tesk.exceptions module +---------------------- + +.. automodule:: tesk.exceptions + :members: + :undoc-members: + :show-inheritance: + +tesk.utils module +----------------- + +.. automodule:: tesk.utils + :members: + :undoc-members: + :show-inheritance: + Module contents --------------- diff --git a/poetry.lock b/poetry.lock index c1d873a..1e03734 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. 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-3165,4 +3259,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "5360faeac82607ad994db4eac1f2a80dc823b930ba697b84e0bba299b9cac893" +content-hash = "4b2902fcbf88e46455b2c2a5046ae600b27b3223e955bfd298dcc75905d2b5ae" diff --git a/pyproject.toml b/pyproject.toml index 4979503..ae2a83c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,7 @@ boto3 = "1.34.104" foca = "^0.13.0" kubernetes = "^29.0.0" python = "^3.11" -requests = ">=2.20.0" +werkzeug = "==2.2.3" # Remove when FOCA updates this dependency. urllib3 = "^2.2.2" [tool.poetry.group.docs.dependencies] diff --git a/tesk/constants.py b/tesk/constants.py new file mode 100644 index 0000000..5508eb2 --- /dev/null +++ b/tesk/constants.py @@ -0,0 +1,78 @@ +"""Tesk scoped constants.""" + +import os + +from pydantic import BaseModel + + +class TeskConstants(BaseModel): + """Tesk's K8s scoped constants. + + Attributes: + FILER_IMAGE_NAME: Name of the filer image + FILER_IMAGE_VERSION: Version of the filer image + TASKMASTER_IMAGE_NAME: Name of the taskmaster image + TASKMASTER_IMAGE_VERSION: Version of the taskmaster image + TESK_NAMESPACE: Namespace in which api will create K8s resources from TES + request + TASKMASTER_SERVICE_ACCOUNT_NAME: Taskmaster service account name + TASKMASTER_ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT: Backoff limit for taskmaster env + FILER_BACKOFF_LIMIT: Backoff limit got filer job + EXECUTOR_BACKOFF_LIMIT: Backoff limit for executor job + + Note: + Below are the mentioned environment variable with which these constants can be + configured, otherwise mentioned default will be assigned. + + variable: + ENV_VARIABLE = default + + FILER_IMAGE_NAME: + TESK_API_TASKMASTER_FILER_IMAGE_NAME = docker.io/elixircloud/tesk-core-filer + FILER_IMAGE_VERSION: + TESK_API_TASKMASTER_FILER_IMAGE_VERSION = latest + TASKMASTER_IMAGE_NAME: + TESK_API_TASKMASTER_IMAGE_NAME = docker.io/elixircloud/tesk-core-taskmaster + TASKMASTER_IMAGE_VERSION: + TESK_API_TASKMASTER_IMAGE_VERSION = latest + TESK_NAMESPACE: + TESK_API_K8S_NAMESPACE = tesk + TASKMASTER_SERVICE_ACCOUNT_NAME: + TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME = taskmaster + TASKMASTER_ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT: + ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT = 6 + FILER_BACKOFF_LIMIT: + FILER_BACKOFF_LIMIT = 2 + EXECUTOR_BACKOFF_LIMIT: + EXECUTOR_BACKOFF_LIMIT = 2 + """ + + FILER_IMAGE_NAME: str = os.getenv( + "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" + ) + TASKMASTER_IMAGE_NAME: str = os.getenv( + "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_ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT: str = os.getenv( + "ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT", "6" + ) + FILER_BACKOFF_LIMIT: str = os.getenv("FILER_BACKOFF_LIMIT", "2") + EXECUTOR_BACKOFF_LIMIT: str = os.getenv("EXECUTOR_BACKOFF_LIMIT", "2") + + class Config: + """Configuration for class.""" + + frozen = True + + +tesk_constants = TeskConstants() diff --git a/tesk/exceptions.py b/tesk/exceptions.py index 367064f..d0aa727 100644 --- a/tesk/exceptions.py +++ b/tesk/exceptions.py @@ -7,6 +7,7 @@ OAuthProblem, Unauthorized, ) +from kubernetes.client.exceptions import ApiException from werkzeug.exceptions import ( BadRequest, InternalServerError, @@ -18,6 +19,10 @@ class ConfigNotFoundError(FileNotFoundError): """Configuration file not found error.""" +class KubernetesError(ApiException): + """Kubernetes error.""" + + # exceptions raised in app context exceptions = { Exception: { diff --git a/tesk/k8s/__init__.py b/tesk/k8s/__init__.py new file mode 100644 index 0000000..d14cbc3 --- /dev/null +++ b/tesk/k8s/__init__.py @@ -0,0 +1 @@ +"""Kubernetes API module for TESK.""" diff --git a/tesk/k8s/constants.py b/tesk/k8s/constants.py new file mode 100644 index 0000000..d0f32a9 --- /dev/null +++ b/tesk/k8s/constants.py @@ -0,0 +1,238 @@ +"""Constants for Kubernetes API.""" + +from enum import Enum +from typing import Set + +from pydantic import BaseModel + + +class JobConstants(BaseModel): + """Constants related to job and tasks. + + Attributes: + TASKMASTER_INPUT = ENV var that serves as taskmaster script input (JSON + format) + TASKMASTER_INPUT_EXEC_KEY = Key in JSON taskmaster input, which holds list + of executors + VOLUME_NAME = Volume name + JOB_CREATE_ATTEMPTS_NO = Number of attempts of job creation in case of name + collision + JOB_NAME_TASKM_PREFIX = Constant prefix of taskmaster's job name (== TES + task ID) + JOB_NAME_EXEC_PREFIX = Part of executor's job name, that follows + taskmaster's name + JOB_NAME_TASKM_RAND_PART_LENGTH = No of bytes of random part of task + master's name (which end up encoded to hex) + JOB_NAME_EXEC_NO_LENGTH = No of digits reserved for executor number in + executor's job name. Ends up padded with '0' for numbers < 10 + JOB_NAME_FILER_SUF = Output filer name suffix + RESOURCE_DISK_DEFAULT: float = Default resource disk value + COMPLETED_STATES = TES task states, indicating task is not running and + cannot be cancelled + EXECUTOR_BACKOFF_LIMIT = Set a number of retries of a job execution. + FILER_BACKOFF_LIMIT = Set a number of retries of a filer job execution. + """ + + TASKMASTER_INPUT: str = "JSON_INPUT" + TASKMASTER_INPUT_EXEC_KEY: str = "executors" + VOLUME_NAME: str = "PVC" + JOB_CREATE_ATTEMPTS_NO: int = 5 + JOB_NAME_TASKM_PREFIX: str = "task-" + JOB_NAME_EXEC_PREFIX: str = "-ex-" + JOB_NAME_TASKM_RAND_PART_LENGTH: int = 4 + JOB_NAME_EXEC_NO_LENGTH: int = 2 + JOB_NAME_FILER_SUF: str = "-outputs-filer" + RESOURCE_DISK_DEFAULT: float = 0.1 + COMPLETED_STATES: Set[str] = { + "CANCELED", + "COMPLETE", + "EXECUTOR_ERROR", + "SYSTEM_ERROR", + } + EXECUTOR_BACKOFF_LIMIT: str = "EXECUTOR_BACKOFF_LIMIT" + FILER_BACKOFF_LIMIT: str = "FILER_BACKOFF_LIMIT" + + class Config: + """Configuration for class.""" + + frozen = True + + +class AnnotationConstants(BaseModel): + """Constants related to Kubernetes annotations. + + Attributes: + ANN_TESTASK_NAME_KEY = Key of the annotation, that stores name of TES task + in both taskmaster's job and executor's jobs + ANN_JSON_INPUT_KEY = Key of the annotation, that stores whole input TES + task serialized to JSON + """ + + ANN_TESTASK_NAME_KEY: str = "tes-task-name" + ANN_JSON_INPUT_KEY: str = "json-input" + + class Config: + """Configuration for class.""" + + frozen = True + + +class LabelConstants(BaseModel): + """Constants related to Kubernetes labels. + + Attributes: + LABEL_TESTASK_ID_KEY = Key of the label, that stores taskmaster's name (== + TES task generated ID) in executor jobs + LABEL_JOBTYPE_KEY = Key of the label, that stores type of a job (taskmaster + or executor) + LABEL_JOBTYPE_VALUE_TASKM = Value of the label with taskmaster's job type + LABEL_JOBTYPE_VALUE_EXEC = Value of the label with executor's job type + LABEL_EXECNO_KEY = Key of the label, that holds executor number for + executor jobs + LABEL_TASKSTATE_KEY = Key of the label, that holds executor's state + LABEL_TASKSTATE_VALUE_CANC = Value of the label, that holds executor's + Cancelled state + LABEL_USERID_KEY = Key of the label, that holds user id + LABEL_GROUPNAME_KEY = Key of the label, that holds user's group name + """ + + LABEL_TESTASK_ID_KEY: str = "taskmaster-name" + LABEL_JOBTYPE_KEY: str = "job-type" + LABEL_JOBTYPE_VALUE_TASKM: str = "taskmaster" + LABEL_JOBTYPE_VALUE_EXEC: str = "executor" + LABEL_EXECNO_KEY: str = "executor-no" + LABEL_TASKSTATE_KEY: str = "task-status" + LABEL_TASKSTATE_VALUE_CANC: str = "Cancelled" + LABEL_USERID_KEY: str = "creator-user-id" + LABEL_GROUPNAME_KEY: str = "creator-group-name" + + class Config: + """Configuration for class.""" + + frozen = True + + +class PathValidationConstants(BaseModel): + """Constants related to path validation. + + Attributes: + ABSOLUTE_PATH_REGEX = Pattern to validate path + ABSOLUTE_PATH_MESSAGE = Message for absolute path validation (to avoid + message.property) + """ + + ABSOLUTE_PATH_REGEXP: str = "^\\/.*" + ABSOLUTE_PATH_MESSAGE: str = "must be an absolute path" + + class Config: + """Configuration for class.""" + + frozen = True + + +class FTPConstants(BaseModel): + """Constants related to FTP configuration. + + Attributes: + FTP_SECRET_USERNAME_ENV = Environment variable name for FTP username + FTP_SECRET_PASSWORD_ENV = Environment variable name for FTP password + """ + + FTP_SECRET_USERNAME_ENV: str = "TESK_FTP_USERNAME" + FTP_SECRET_PASSWORD_ENV: str = "TESK_FTP_PASSWORD" + + class Config: + """Configuration for class.""" + + frozen = True + + +class PatchConstants(BaseModel): + """Constants related to patch operations. + + Attributes: + CANCEL_PATH = Patch object passed to job API, when cancelling task + """ + + CANCEL_PATCH: str = '{"metadata":{"labels":{"task-status":"Cancelled"}}}' + + class Config: + """Configuration for class.""" + + frozen = True + + +class K8sConstants(BaseModel): + """Constants related to Kubernetes. + + Attribute: + K8S_BATCH_API_VERSION: Kubernetes Batch API version + K8S_BATCH_API_JOB_TYPE: Kubernetes Job object type + JOB_RESTART_POLICY: Kubernetes Job restart policy + RESOURCE_CPU_KEY: Executor CPU resource label + RESOURCE_MEM_KEY: Executor memory resource label + RESOURCE_MEM_UNIT: Executor memory resource unit + RESOURCE_MEM_ONE_GB: One Gibibyte (Gi) in bytes + """ + + K8S_BATCH_API_VERSION: str = "batch/v1" + K8S_BATCH_API_JOB_TYPE: str = "Job" + JOB_RESTART_POLICY: str = "Never" + RESOURCE_CPU_KEY: str = "cpu" + RESOURCE_MEM_KEY: str = "memory" + RESOURCE_MEM_UNIT: str = "Gi" + RESOURCE_MEM_ONE_GB: int = 1073741824 + + class Config: + """Configuration for class.""" + + frozen = True + + class PodPhase(Enum): + """Pod state. + + Attribute: + PENDING = pending + """ + + PENDING = "Pending" + + class Config: + """Configuration for class.""" + + frozen = True + + def get_code(self) -> str: + """Return the pod state.""" + code: str = self.value + return code + + +class TeskK8sConstants(BaseModel): + """All the constants related to k8s and job creation. + + Attributes: + job_constants + annotation_constants + label_constants + path_validation_constants + ftp_constants + patch_constants + k8s_constants + """ + + job_constants: JobConstants = JobConstants() + annotation_constants: AnnotationConstants = AnnotationConstants() + label_constants: LabelConstants = LabelConstants() + path_validation_constants: PathValidationConstants = PathValidationConstants() + ftp_constants: FTPConstants = FTPConstants() + patch_constants: PatchConstants = PatchConstants() + k8s_constants: K8sConstants = K8sConstants() + + class Config: + """Configuration for class.""" + + frozen = True + + +tesk_k8s_constants = TeskK8sConstants() diff --git a/tesk/k8s/wrapper.py b/tesk/k8s/wrapper.py new file mode 100644 index 0000000..80a7112 --- /dev/null +++ b/tesk/k8s/wrapper.py @@ -0,0 +1,318 @@ +"""Wrapper Abstraction of Kubernetes Python client API for TESK.""" + +import logging +from typing import Optional + +from kubernetes import client, config +from kubernetes.client import ( + V1ConfigMap, + V1Job, + V1JobList, + V1LabelSelector, + V1LimitRangeList, + V1PodList, +) +from kubernetes.utils.quantity import parse_quantity # type: ignore + +from tesk.constants import tesk_constants +from tesk.exceptions import KubernetesError, NotFound +from tesk.k8s.constants import tesk_k8s_constants + +logger = logging.getLogger(__name__) + + +class KubernetesClientWrapper: + """Kubernetes client wrapper class.""" + + def __init__(self): + """Initialize the Kubernetes client wrapper.""" + config.load_kube_config() + self.batch_api = client.BatchV1Api() + self.core_api = client.CoreV1Api() + self.namespace = tesk_constants.TESK_NAMESPACE + self.tesk_k8s_constant = tesk_k8s_constants + + def create_job(self, job: V1Job) -> V1Job: + """Create a job in the Kubernetes cluster. + + Returns: + Job object created in the Kubernetes cluster. + """ + try: + v1_job: V1Job = self.batch_api.create_namespaced_job( + namespace=self.namespace, body=job + ) + return v1_job + except KubernetesError as e: + logger.error(f"Exception when creating job: {e}") + raise + + def create_config_map(self, config_map: V1ConfigMap) -> V1ConfigMap: + """Create a config map in the Kubernetes cluster. + + Args: + config_map: ConfigMap object to create. + """ + try: + v1_config_map: V1ConfigMap = self.core_api.create_namespaced_config_map( + namespace=self.namespace, body=config_map + ) + return v1_config_map + except KubernetesError as e: + logger.error(f"Exception when creating config map: {e}") + raise + + def read_taskmaster_job(self, task_id: str) -> V1Job: + """Read a taskmaster job from the Kubernetes cluster. + + task_id: Task identifier. + + Returns: + Job object read from the Kubernetes cluster + + Raises: + Exception: If the task is not found. + """ + try: + job: V1Job = self.batch_api.read_namespaced_job( + name=task_id, namespace=self.namespace + ) + if ( + job.metadata + and job.metadata.labels + and self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_KEY + in job.metadata.labels + and job.metadata.labels[ + self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_KEY + ] + == self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_VALUE_TASKM + ): + return job + except KubernetesError as e: + if e.status != NotFound.code: + logger.error(f"Exception when reading job: {e}") + raise + raise Exception(f"Task {task_id} not found") + + def list_jobs( + self, page_token: Optional[str] = None, label_selector=None, limit=None + ): + """List jobs in the Kubernetes cluster. + + Args: + page_token: pageToken supplied by user (from previous result; points to + next page of results) + label_selector: Label selector to filter jobs. + limit: Maximum number of jobs to return. + """ + try: + return self.batch_api.list_namespaced_job( + namespace=self.namespace, + label_selector=label_selector, + limit=limit, + _continue=page_token, + ) + except KubernetesError as e: + logger.error(f"Exception when listing jobs: {e}") + raise + + def list_limits(self, label_selector=None, limit=None) -> V1LimitRangeList: + """List limit ranges in the Kubernetes cluster. + + Args: + label_selector: Label selector to filter limit ranges. + limit: Maximum number of limit ranges to return. + """ + try: + limits: V1LimitRangeList = self.core_api.list_namespaced_limit_range( + namespace=self.namespace, label_selector=label_selector, limit=limit + ) + return limits + except KubernetesError as e: + logger.error(f"Exception when listing limits: {e}") + raise + + def minimum_ram_gb(self) -> float: + """Get the minimum amount of RAM in the cluster. + + Returns: + Minimum amount of RAM in the cluster in GB. + """ + try: + min_ram = 0 + limits = self.list_limits().items + for limit in limits: + if limit.spec: + for item in limit.spec.limits: + if item.min and "memory" in item.min: + mem_quantity = item.min["memory"] + mem_bytes = self.quantity_to_bytes(mem_quantity) + min_ram = max(min_ram, mem_bytes) + return min_ram / (1024**3) + 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.""" + parsed_quantity: int = parse_quantity(quantity) + return parsed_quantity + + def list_all_taskmaster_jobs_for_user( + self, + page_token: str, + items_per_page: int, + ) -> V1JobList: + """Gets all Taskmaster job objects, a User is allowed to see. + + Args: + page_token: pageToken supplied by user (from previous result; points to + next page of results) + items_per_page: Value submitted by user, limiting number of results. + + Returns: + Job list of Taskmaster jobs that user is allowed to see. + """ + label_selector = ( + f"{self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_KEY}" + "=" + f"{self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_VALUE_TASKM}" + ) + + result: V1JobList = self.list_jobs(page_token, label_selector, items_per_page) + + return result + + def list_single_task_executor_jobs(self, task_id: str) -> V1JobList: + """List single task executor job.""" + label_selector = ( + self.tesk_k8s_constant.label_constants.LABEL_TESTASK_ID_KEY + "=" + task_id, + ) + job_list: V1JobList = self.list_jobs(label_selector=label_selector) + return job_list + + def get_single_task_output_filer_job(self, task_id: str) -> Optional[V1Job]: + """Get single task output filer job.""" + try: + job: V1Job = self.batch_api.read_namespaced_job( + name=task_id + self.tesk_k8s_constant.job_constants.JOB_NAME_FILER_SUF, + namespace=self.namespace, + ) + return job + except KubernetesError as e: + if e.status != NotFound.code: + logger.error(f"Exception when reading output filer job: {e}") + raise + return None + + def list_all_taskmaster_jobs(self) -> V1JobList: + """List all taskmaster jobs in the Kubernetes cluster.""" + label_selector = ( + self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_KEY + + "=" + + self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_VALUE_TASKM + ) + job_list: V1JobList = self.list_jobs(label_selector=label_selector) + return job_list + + def list_all_task_executor_jobs(self) -> V1JobList: + """List all executor jobs in the Kubernetes cluster.""" + label_selector = ( + self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_KEY + + "=" + + self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_VALUE_EXEC + ) + job_list: V1JobList = self.list_jobs(label_selector=label_selector) + return job_list + + def list_all_filer_jobs(self) -> V1JobList: + """List all output filer jobs in the Kubernetes cluster.""" + label_selector = "!" + self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_KEY + job_list: V1JobList = self.list_jobs(label_selector=label_selector) + return job_list + + def list_single_job_pods(self, job: V1Job) -> V1PodList: + """List pods associated with a single job. + + Args: + job: Job object to list pods for. + """ + try: + if ( + job.spec + and job.spec.selector + and isinstance(job.spec.selector, V1LabelSelector) + and job.spec.selector.match_labels + ): + label_selector = ",".join( + f"{k}={v}" for k, v in job.spec.selector.match_labels.items() + ) + namespaced_pods: V1PodList = self.core_api.list_namespaced_pod( + namespace=self.namespace, label_selector=label_selector + ) + return namespaced_pods + else: + logger.error("Job spec, selector, or match_labels is None or invalid") + return V1PodList(items=[]) + except KubernetesError as e: + logger.error(f"Exception when listing pods: {e}") + raise + + def list_all_job_pods(self): + """List all job pods.""" + label_selector = "job-name" + try: + return self.core_api.list_namespaced_pod( + namespace=self.namespace, label_selector=label_selector + ) + except KubernetesError as e: + logger.error(f"Couldn't list job of {self.namespace} namespace. {e}") + raise + + def read_pod_log(self, pod_name: str) -> Optional[str]: + """Read logs from a pod. + + Args: + pod_name: Name of the pod to read logs from. + """ + try: + pod_log: str = self.core_api.read_namespaced_pod_log( + name=pod_name, namespace=self.namespace + ) + return pod_log + except KubernetesError as e: + logger.error(f"Exception when reading pod log: {e}") + return None + + def label_job_as_cancelled(self, task_id: str) -> None: + """Label a job as cancelled. + + Args: + task_id: Task identifier. + """ + try: + patch = {"metadata": {"labels": {"status": "cancelled"}}} + self.batch_api.patch_namespaced_job( + name=task_id, namespace=self.namespace, body=patch + ) + except KubernetesError as e: + logger.error(f"Exception when labeling job as cancelled: {e}") + raise + + def label_pod_as_cancelled(self, pod_name: str) -> None: + """Label a pod as cancelled. + + Args: + pod_name: Pod name. + """ + try: + patch = {"metadata": {"labels": {"status": "cancelled"}}} + self.core_api.patch_namespaced_pod( + name=pod_name, namespace=self.namespace, body=patch + ) + except KubernetesError as e: + logger.error(f"Exception when labeling pod as cancelled: {e}") + raise