From 40e2136e96efef1da93b7a3c3c12e9ef4f1acc88 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Fri, 9 Aug 2024 11:11:32 +0530 Subject: [PATCH 01/20] feat: add k8s client wrapper and needed constants --- tesk/api/kubernetes/__init__.py | 1 + tesk/api/kubernetes/constants.py | 166 ++++++++++++++++ tesk/api/kubernetes/wrapper.py | 332 +++++++++++++++++++++++++++++++ tesk/constants.py | 33 +++ tesk/exceptions.py | 11 + 5 files changed, 543 insertions(+) create mode 100644 tesk/api/kubernetes/__init__.py create mode 100644 tesk/api/kubernetes/constants.py create mode 100644 tesk/api/kubernetes/wrapper.py create mode 100644 tesk/constants.py diff --git a/tesk/api/kubernetes/__init__.py b/tesk/api/kubernetes/__init__.py new file mode 100644 index 0000000..d14cbc3 --- /dev/null +++ b/tesk/api/kubernetes/__init__.py @@ -0,0 +1 @@ +"""Kubernetes API module for TESK.""" diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py new file mode 100644 index 0000000..4386b34 --- /dev/null +++ b/tesk/api/kubernetes/constants.py @@ -0,0 +1,166 @@ +"""Constants for Kubernetes API.""" + +from enum import Enum +from typing import Set + +from pydantic import BaseModel, Field + + +class Constants(BaseModel): + """Constants related to job and tasks.""" + + taskmaster_input: str = Field( + default="JSON_INPUT", + description="ENV var that serves as taskmaster script input (JSON format)", + ) + taskmaster_input_exec_key: str = Field( + default="executors", + description="Key in JSON taskmaster input, which holds list of executors", + ) + volume_name: str = Field(default="PVC", description="Volume name") + job_create_attempts_no: int = Field( + default=5, + description="Number of attempts of job creation in case of name collision", + ) + job_name_taskm_prefix: str = Field( + default="task-", + description="Constant prefix of taskmaster's job name (== TES task ID)", + ) + job_name_exec_prefix: str = Field( + default="-ex-", + description="Part of executor's job name, that follows taskmaster's name", + ) + job_name_taskm_rand_part_length: int = Field( + default=4, + description=( + "No of bytes of random part of task master's name (which end up " + "encoded to hex)" + ), + ) + job_name_exec_no_length: int = Field( + default=2, + description="No of digits reserved for executor number in executor's job name." + " Ends up padded with '0' for numbers < 10", + ) + job_name_filer_suf: str = Field( + default="-outputs-filer", description="Output filer name suffix" + ) + ann_testask_name_key: str = Field( + default="tes-task-name", + description=( + "Key of the annotation, that stores name of TES task in both taskmaster's " + "job and executor's jobs" + ), + ) + ann_json_input_key: str = Field( + default="json-input", + description="Key of the annotation, that stores whole input TES task serialized" + " to JSON", + ) + label_testask_id_key: str = Field( + default="taskmaster-name", + description="Key of the label, that stores taskmaster's name (==TES task " + "generated ID) in executor jobs", + ) + label_jobtype_key: str = Field( + default="job-type", + description="Key of the label, that stores type of a job (taskmaster or " + "executor)", + ) + label_jobtype_value_taskm: str = Field( + default="taskmaster", + description="Value of the label with taskmaster's job type", + ) + label_jobtype_value_exec: str = Field( + default="executor", description="Value of the label with executor's job type" + ) + label_execno_key: str = Field( + default="executor-no", + description="Key of the label, that holds executor number for executor jobs", + ) + label_taskstate_key: str = Field( + default="task-status", + description="Key of the label, that holds executor's state", + ) + label_taskstate_value_canc: str = Field( + default="Cancelled", + description="Value of the label, that holds executor's Cancelled state", + ) + label_userid_key: str = Field( + default="creator-user-id", description="Key of the label, that holds user id" + ) + label_groupname_key: str = Field( + default="creator-group-name", + description="Key of the label, that holds user's group name", + ) + absolute_path_regexp: str = Field( + default="^\\/.*", description="Pattern to validate paths" + ) + absolute_path_message: str = Field( + default="must be an absolute path", + description="Message for absolute path validation (to avoid " + "message.properties)", + ) + resource_disk_default: float = Field( + default=0.1, description="Default resource disk value" + ) + completed_states: Set[str] = Field( + default={"CANCELED", "COMPLETE", "EXECUTOR_ERROR", "SYSTEM_ERROR"}, + description="TES task states, indicating task is not running and cannot be " + "cancelled", + ) + ftp_secret_username_env: str = Field( + default="TESK_FTP_USERNAME", + description="Name of taskmaster's ENV variable with username of FTP account " + "used for storage", + ) + ftp_secret_password_env: str = Field( + default="TESK_FTP_PASSWORD", + description="Name of taskmaster's ENV variable with password of FTP account " + "used for storage", + ) + cancel_patch: str = Field( + default='{"metadata":{"labels":{"task-status":"Cancelled"}}}', + description="Patch object passed to job API, when cancelling task", + ) + executor_backoff_limit: str = Field( + default="EXECUTOR_BACKOFF_LIMIT", + description="Set a number of retries of a job execution.", + ) + filer_backoff_limit: str = Field( + default="FILER_BACKOFF_LIMIT", + description="Set a number of retries of a filer job execution.", + ) + + +class K8sConstants(BaseModel): + """Constants related to Kubernetes.""" + + k8s_batch_api_version: str = Field( + default="batch/v1", description="Kubernetes Batch API version" + ) + k8s_batch_api_job_type: str = Field( + default="Job", description="Kubernetes Job object type" + ) + job_restart_policy: str = Field( + default="Never", description="Kubernetes Job restart policy" + ) + resource_cpu_key: str = Field("cpu", description="Executor CPU resource label") + resource_mem_key: str = Field( + default="memory", description="Executor memory resource label" + ) + resource_mem_unit: str = Field( + default="Gi", description="Executor memory resource unit" + ) + resource_mem_one_gb: int = Field( + default=1073741824, description="One Gibibyte (Gi) in bytes" + ) + + class PodPhase(Enum): + """Pod state.""" + + PENDING = "Pending" + + def get_code(self) -> str: + """Return the pod state.""" + return self.value diff --git a/tesk/api/kubernetes/wrapper.py b/tesk/api/kubernetes/wrapper.py new file mode 100644 index 0000000..f97e78a --- /dev/null +++ b/tesk/api/kubernetes/wrapper.py @@ -0,0 +1,332 @@ +"""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.api.kubernetes.constants import Constants +from tesk.constants import TeskConstants +from tesk.exceptions import KubernetesError, NotFound + +logger = logging.getLogger(__name__) + + +class KubernetesClientWrapper: + """Kubernetes client wrapper class.""" + + def __init__(self): + """Initialize the Kubernetes client wrapper. + + Args: + namespace: Namespace to use for Kubernetes. + """ + config.load_kube_config() + self.batch_api = client.BatchV1Api() + self.core_api = client.CoreV1Api() + self.namespace = TeskConstants.tesk_namespace + self.constant = 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.constant.label_jobtype_key in job.metadata.labels + and job.metadata.labels[self.constant.label_jobtype_key] + == self.constant.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, + # user: str + ) -> 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. + # user: User identifier. + + Returns: + Job list of Taskmaster jobs that user is allowed to see. + """ + # TODO: Implement this method when auth is implemented in FOCA. + label_selector = ( + f"{self.constant.label_jobtype_key}" + "=" + f"{self.constant.label_jobtype_value_taskm}" + ) + # if user.get_label_selector(): + # label_selector += f",{user.get_label_selector()}" + + result: V1JobList = self.list_jobs(page_token, label_selector, items_per_page) + + # if user.is_member_in_non_managed_groups(): + # filtered_job_list = [ + # job for job in result.items + # if user.is_group_manager( + # job.metadata.labels.get(self.constant.label_groupname_key) + # ) or user.get_username() + # == job.metadata.labels.get(self.constant.label_userid_key) + # ] + # result.items = filtered_job_list + + return result + + def list_single_task_executor_jobs(self, task_id: str) -> V1JobList: + """List single task executor job.""" + label_selector = (self.constant.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.constant.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.constant.label_jobtype_key + + "=" + + self.constant.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.constant.label_jobtype_key + + "=" + + self.constant.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.constant.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 diff --git a/tesk/constants.py b/tesk/constants.py new file mode 100644 index 0000000..cdd3321 --- /dev/null +++ b/tesk/constants.py @@ -0,0 +1,33 @@ +"""Tesk scoped constants.""" + +import os + + +class TeskConstants: + """Tesk's K8s scoped constants.""" + + 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") + # FIXME: IDK what to do with this + tesk_api_taskmaster_environment_filer_backoff_limit: str = os.getenv( + "TESK_API_TASKMASTER_ENVIRONMENT_FILER_BACKOFF_LIMIT", "6" + ) diff --git a/tesk/exceptions.py b/tesk/exceptions.py index 367064f..a6af9a1 100644 --- a/tesk/exceptions.py +++ b/tesk/exceptions.py @@ -1,5 +1,7 @@ """App exceptions.""" +from http import HTTPStatus + from connexion.exceptions import ( BadRequestProblem, ExtraParameterProblem, @@ -7,6 +9,7 @@ OAuthProblem, Unauthorized, ) +from kubernetes.client.exceptions import ApiException from werkzeug.exceptions import ( BadRequest, InternalServerError, @@ -71,3 +74,11 @@ class ConfigNotFoundError(FileNotFoundError): # exceptions raised outside of app context class ValidationError(Exception): """Value or object is not compatible with required type or schema.""" + + +class KubernetesError(ApiException): + """Kubernetes error.""" + + def is_object_name_duplicated(self) -> bool: + """Check if object name is duplicated.""" + return self.status == HTTPStatus.CONFLICT From 3e865497f09f0fada0292353df3756856800bf95 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Fri, 9 Aug 2024 18:40:07 +0530 Subject: [PATCH 02/20] chore: categorise consts --- tesk/api/kubernetes/constants.py | 75 ++++++++++++++++++++++++-------- tesk/api/kubernetes/wrapper.py | 62 ++++++++++---------------- 2 files changed, 80 insertions(+), 57 deletions(-) diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index 4386b34..91af8ad 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -6,7 +6,7 @@ from pydantic import BaseModel, Field -class Constants(BaseModel): +class JobConstants(BaseModel): """Constants related to job and tasks.""" taskmaster_input: str = Field( @@ -45,6 +45,27 @@ class Constants(BaseModel): job_name_filer_suf: str = Field( default="-outputs-filer", description="Output filer name suffix" ) + resource_disk_default: float = Field( + default=0.1, description="Default resource disk value" + ) + completed_states: Set[str] = Field( + default={"CANCELED", "COMPLETE", "EXECUTOR_ERROR", "SYSTEM_ERROR"}, + description="TES task states, indicating task is not running and cannot be " + "cancelled", + ) + executor_backoff_limit: str = Field( + default="EXECUTOR_BACKOFF_LIMIT", + description="Set a number of retries of a job execution.", + ) + filer_backoff_limit: str = Field( + default="FILER_BACKOFF_LIMIT", + description="Set a number of retries of a filer job execution.", + ) + + +class AnnotationConstants(BaseModel): + """Constants related to Kubernetes annotations.""" + ann_testask_name_key: str = Field( default="tes-task-name", description=( @@ -57,6 +78,11 @@ class Constants(BaseModel): description="Key of the annotation, that stores whole input TES task serialized" " to JSON", ) + + +class LabelConstants(BaseModel): + """Constants related to Kubernetes labels.""" + label_testask_id_key: str = Field( default="taskmaster-name", description="Key of the label, that stores taskmaster's name (==TES task " @@ -93,6 +119,11 @@ class Constants(BaseModel): default="creator-group-name", description="Key of the label, that holds user's group name", ) + + +class PathValidationConstants(BaseModel): + """Constants related to path validation.""" + absolute_path_regexp: str = Field( default="^\\/.*", description="Pattern to validate paths" ) @@ -101,14 +132,11 @@ class Constants(BaseModel): description="Message for absolute path validation (to avoid " "message.properties)", ) - resource_disk_default: float = Field( - default=0.1, description="Default resource disk value" - ) - completed_states: Set[str] = Field( - default={"CANCELED", "COMPLETE", "EXECUTOR_ERROR", "SYSTEM_ERROR"}, - description="TES task states, indicating task is not running and cannot be " - "cancelled", - ) + + +class FTPConstants(BaseModel): + """Constants related to FTP configuration.""" + ftp_secret_username_env: str = Field( default="TESK_FTP_USERNAME", description="Name of taskmaster's ENV variable with username of FTP account " @@ -119,18 +147,15 @@ class Constants(BaseModel): description="Name of taskmaster's ENV variable with password of FTP account " "used for storage", ) + + +class PatchConstants(BaseModel): + """Constants related to patch operations.""" + cancel_patch: str = Field( default='{"metadata":{"labels":{"task-status":"Cancelled"}}}', description="Patch object passed to job API, when cancelling task", ) - executor_backoff_limit: str = Field( - default="EXECUTOR_BACKOFF_LIMIT", - description="Set a number of retries of a job execution.", - ) - filer_backoff_limit: str = Field( - default="FILER_BACKOFF_LIMIT", - description="Set a number of retries of a filer job execution.", - ) class K8sConstants(BaseModel): @@ -145,7 +170,9 @@ class K8sConstants(BaseModel): job_restart_policy: str = Field( default="Never", description="Kubernetes Job restart policy" ) - resource_cpu_key: str = Field("cpu", description="Executor CPU resource label") + resource_cpu_key: str = Field( + default="cpu", description="Executor CPU resource label" + ) resource_mem_key: str = Field( default="memory", description="Executor memory resource label" ) @@ -164,3 +191,15 @@ class PodPhase(Enum): def get_code(self) -> str: """Return the pod state.""" return self.value + + +class Constants(BaseModel): + """All the constants related to k8s and job creation.""" + + 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() diff --git a/tesk/api/kubernetes/wrapper.py b/tesk/api/kubernetes/wrapper.py index f97e78a..1299a79 100644 --- a/tesk/api/kubernetes/wrapper.py +++ b/tesk/api/kubernetes/wrapper.py @@ -25,11 +25,7 @@ class KubernetesClientWrapper: """Kubernetes client wrapper class.""" def __init__(self): - """Initialize the Kubernetes client wrapper. - - Args: - namespace: Namespace to use for Kubernetes. - """ + """Initialize the Kubernetes client wrapper.""" config.load_kube_config() self.batch_api = client.BatchV1Api() self.core_api = client.CoreV1Api() @@ -40,7 +36,7 @@ def create_job(self, job: V1Job) -> V1Job: """Create a job in the Kubernetes cluster. Returns: - Job object created in the Kubernetes cluster. + Job object created in the Kubernetes cluster. """ try: v1_job: V1Job = self.batch_api.create_namespaced_job( @@ -72,10 +68,10 @@ def read_taskmaster_job(self, task_id: str) -> V1Job: task_id: Task identifier. Returns: - Job object read from the Kubernetes cluster + Job object read from the Kubernetes cluster Raises: - Exception: If the task is not found. + Exception: If the task is not found. """ try: job: V1Job = self.batch_api.read_namespaced_job( @@ -84,9 +80,10 @@ def read_taskmaster_job(self, task_id: str) -> V1Job: if ( job.metadata and job.metadata.labels - and self.constant.label_jobtype_key in job.metadata.labels - and job.metadata.labels[self.constant.label_jobtype_key] - == self.constant.label_jobtype_value_taskm + and self.constant.label_constants.label_jobtype_key + in job.metadata.labels + and job.metadata.labels[self.constant.label_constants.label_jobtype_key] + == self.constant.label_constants.label_jobtype_value_taskm ): return job except KubernetesError as e: @@ -101,10 +98,10 @@ def list_jobs( """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. + 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( @@ -166,7 +163,6 @@ def list_all_taskmaster_jobs_for_user( self, page_token: str, items_per_page: int, - # user: str ) -> V1JobList: """Gets all Taskmaster job objects, a User is allowed to see. @@ -174,37 +170,25 @@ def list_all_taskmaster_jobs_for_user( 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. - # user: User identifier. Returns: Job list of Taskmaster jobs that user is allowed to see. """ - # TODO: Implement this method when auth is implemented in FOCA. label_selector = ( - f"{self.constant.label_jobtype_key}" + f"{self.constant.label_constants.label_jobtype_key}" "=" - f"{self.constant.label_jobtype_value_taskm}" + f"{self.constant.label_constants.label_jobtype_value_taskm}" ) - # if user.get_label_selector(): - # label_selector += f",{user.get_label_selector()}" result: V1JobList = self.list_jobs(page_token, label_selector, items_per_page) - # if user.is_member_in_non_managed_groups(): - # filtered_job_list = [ - # job for job in result.items - # if user.is_group_manager( - # job.metadata.labels.get(self.constant.label_groupname_key) - # ) or user.get_username() - # == job.metadata.labels.get(self.constant.label_userid_key) - # ] - # result.items = filtered_job_list - return result def list_single_task_executor_jobs(self, task_id: str) -> V1JobList: """List single task executor job.""" - label_selector = (self.constant.label_testask_id_key + "=" + task_id,) + label_selector = ( + self.constant.label_constants.label_testask_id_key + "=" + task_id, + ) job_list: V1JobList = self.list_jobs(label_selector=label_selector) return job_list @@ -212,7 +196,7 @@ 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.constant.job_name_filer_suf, + name=task_id + self.constant.job_constants.job_name_filer_suf, namespace=self.namespace, ) return job @@ -225,9 +209,9 @@ def get_single_task_output_filer_job(self, task_id: str) -> Optional[V1Job]: def list_all_taskmaster_jobs(self) -> V1JobList: """List all taskmaster jobs in the Kubernetes cluster.""" label_selector = ( - self.constant.label_jobtype_key + self.constant.label_constants.label_jobtype_key + "=" - + self.constant.label_jobtype_value_taskm + + self.constant.label_constants.label_jobtype_value_taskm ) job_list: V1JobList = self.list_jobs(label_selector=label_selector) return job_list @@ -235,16 +219,16 @@ def list_all_taskmaster_jobs(self) -> V1JobList: def list_all_task_executor_jobs(self) -> V1JobList: """List all executor jobs in the Kubernetes cluster.""" label_selector = ( - self.constant.label_jobtype_key + self.constant.label_constants.label_jobtype_key + "=" - + self.constant.label_jobtype_value_exec + + self.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.constant.label_jobtype_key + label_selector = "!" + self.constant.label_constants.label_jobtype_key job_list: V1JobList = self.list_jobs(label_selector=label_selector) return job_list From 6b00c2b48e9ecf0b6928b27a9085b994704027e8 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Tue, 20 Aug 2024 10:19:33 +0530 Subject: [PATCH 03/20] chore: rename consts. --- tesk/api/kubernetes/constants.py | 2 +- tesk/api/kubernetes/wrapper.py | 30 ++++++++++++++++-------------- tesk/constants.py | 4 ---- 3 files changed, 17 insertions(+), 19 deletions(-) diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index 91af8ad..efe7977 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -193,7 +193,7 @@ def get_code(self) -> str: return self.value -class Constants(BaseModel): +class TeskK8sConstants(BaseModel): """All the constants related to k8s and job creation.""" job_constants: JobConstants = JobConstants() diff --git a/tesk/api/kubernetes/wrapper.py b/tesk/api/kubernetes/wrapper.py index 1299a79..94123bc 100644 --- a/tesk/api/kubernetes/wrapper.py +++ b/tesk/api/kubernetes/wrapper.py @@ -14,7 +14,7 @@ ) from kubernetes.utils.quantity import parse_quantity # type: ignore -from tesk.api.kubernetes.constants import Constants +from tesk.api.kubernetes.constants import TeskK8sConstants from tesk.constants import TeskConstants from tesk.exceptions import KubernetesError, NotFound @@ -30,7 +30,7 @@ def __init__(self): self.batch_api = client.BatchV1Api() self.core_api = client.CoreV1Api() self.namespace = TeskConstants.tesk_namespace - self.constant = Constants() + self.tesk_k8s_constant = TeskK8sConstants() def create_job(self, job: V1Job) -> V1Job: """Create a job in the Kubernetes cluster. @@ -80,10 +80,12 @@ def read_taskmaster_job(self, task_id: str) -> V1Job: if ( job.metadata and job.metadata.labels - and self.constant.label_constants.label_jobtype_key + and self.tesk_k8s_constant.label_constants.label_jobtype_key in job.metadata.labels - and job.metadata.labels[self.constant.label_constants.label_jobtype_key] - == self.constant.label_constants.label_jobtype_value_taskm + 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: @@ -175,9 +177,9 @@ def list_all_taskmaster_jobs_for_user( Job list of Taskmaster jobs that user is allowed to see. """ label_selector = ( - f"{self.constant.label_constants.label_jobtype_key}" + f"{self.tesk_k8s_constant.label_constants.label_jobtype_key}" "=" - f"{self.constant.label_constants.label_jobtype_value_taskm}" + f"{self.tesk_k8s_constant.label_constants.label_jobtype_value_taskm}" ) result: V1JobList = self.list_jobs(page_token, label_selector, items_per_page) @@ -187,7 +189,7 @@ def list_all_taskmaster_jobs_for_user( def list_single_task_executor_jobs(self, task_id: str) -> V1JobList: """List single task executor job.""" label_selector = ( - self.constant.label_constants.label_testask_id_key + "=" + task_id, + 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 @@ -196,7 +198,7 @@ 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.constant.job_constants.job_name_filer_suf, + name=task_id + self.tesk_k8s_constant.job_constants.job_name_filer_suf, namespace=self.namespace, ) return job @@ -209,9 +211,9 @@ def get_single_task_output_filer_job(self, task_id: str) -> Optional[V1Job]: def list_all_taskmaster_jobs(self) -> V1JobList: """List all taskmaster jobs in the Kubernetes cluster.""" label_selector = ( - self.constant.label_constants.label_jobtype_key + self.tesk_k8s_constant.label_constants.label_jobtype_key + "=" - + self.constant.label_constants.label_jobtype_value_taskm + + self.tesk_k8s_constant.label_constants.label_jobtype_value_taskm ) job_list: V1JobList = self.list_jobs(label_selector=label_selector) return job_list @@ -219,16 +221,16 @@ def list_all_taskmaster_jobs(self) -> V1JobList: def list_all_task_executor_jobs(self) -> V1JobList: """List all executor jobs in the Kubernetes cluster.""" label_selector = ( - self.constant.label_constants.label_jobtype_key + self.tesk_k8s_constant.label_constants.label_jobtype_key + "=" - + self.constant.label_constants.label_jobtype_value_exec + + 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.constant.label_constants.label_jobtype_key + label_selector = "!" + self.tesk_k8s_constant.label_constants.label_jobtype_key job_list: V1JobList = self.list_jobs(label_selector=label_selector) return job_list diff --git a/tesk/constants.py b/tesk/constants.py index cdd3321..5224462 100644 --- a/tesk/constants.py +++ b/tesk/constants.py @@ -27,7 +27,3 @@ class TeskConstants: ) filer_backoff_limit: str = os.getenv("FILER_BACKOFF_LIMIT", "2") executor_backoff_limit: str = os.getenv("EXECUTOR_BACKOFF_LIMIT", "2") - # FIXME: IDK what to do with this - tesk_api_taskmaster_environment_filer_backoff_limit: str = os.getenv( - "TESK_API_TASKMASTER_ENVIRONMENT_FILER_BACKOFF_LIMIT", "6" - ) From 0d408e41febfe2a901b4ce1310e30b95186e77c4 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Tue, 20 Aug 2024 10:44:22 +0530 Subject: [PATCH 04/20] chore: fix safety error by updating requests, and lock werkeug. --- poetry.lock | 2092 +++++++++++++++++++++++++----------------------- pyproject.toml | 3 +- 2 files changed, 1093 insertions(+), 1002 deletions(-) diff --git a/poetry.lock b/poetry.lock index c1d873a..886f706 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" @@ -73,32 +73,32 @@ files = [ [[package]] name = "attrs" -version = "23.2.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, - {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, + {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, + {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, ] [package.extras] -cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] -dev = ["attrs[tests]", "pre-commit"] -docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] -tests = ["attrs[tests-no-zope]", "zope-interface"] -tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] -tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] +benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"] +tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] [[package]] name = "authlib" -version = "1.3.0" +version = "1.3.1" description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." optional = false python-versions = ">=3.8" files = [ - {file = "Authlib-1.3.0-py2.py3-none-any.whl", hash = "sha256:9637e4de1fb498310a56900b3e2043a206b03cb11c05422014b0302cbc814be3"}, - {file = "Authlib-1.3.0.tar.gz", hash = "sha256:959ea62a5b7b5123c5059758296122b57cd2585ae2ed1c0622c21b371ffdae06"}, + {file = "Authlib-1.3.1-py2.py3-none-any.whl", hash = "sha256:d35800b973099bbadc49b42b256ecb80041ad56b7fe1216a362c7943c088f377"}, + {file = "authlib-1.3.1.tar.gz", hash = "sha256:7ae843f03c06c5c0debd63c9db91f9fda64fa62a42a77419fa15fbb7e7a58917"}, ] [package.dependencies] @@ -106,13 +106,13 @@ cryptography = "*" [[package]] name = "babel" -version = "2.15.0" +version = "2.16.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" files = [ - {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, - {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, + {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, + {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, ] [package.extras] @@ -120,13 +120,13 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "bandit" -version = "1.7.8" +version = "1.7.9" description = "Security oriented static analyser for python code." optional = false python-versions = ">=3.8" files = [ - {file = "bandit-1.7.8-py3-none-any.whl", hash = "sha256:509f7af645bc0cd8fd4587abc1a038fc795636671ee8204d502b933aee44f381"}, - {file = "bandit-1.7.8.tar.gz", hash = "sha256:36de50f720856ab24a24dbaa5fee2c66050ed97c1477e0a1159deab1775eab6b"}, + {file = 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Subject: [PATCH 05/20] chore: remove deps --- poetry.lock | 342 ++++++++++++++++++++++++++----------------------- pyproject.toml | 2 - 2 files changed, 179 insertions(+), 165 deletions(-) diff --git a/poetry.lock b/poetry.lock index 886f706..c16d219 100644 --- a/poetry.lock +++ b/poetry.lock @@ -92,13 +92,13 @@ tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] [[package]] name = "authlib" -version = "1.3.1" +version = "1.3.2" 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-1.3.2-py2.py3-none-any.whl", hash = "sha256:ede026a95e9f5cdc2d4364a52103f5405e75aa156357e831ef2bfd0bc5094dfc"}, + {file = 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{file = "Werkzeug-2.2.3-py3-none-any.whl", hash = "sha256:56433961bc1f12533306c624f3be5e744389ac61d722175d543e1751285da612"}, - {file = "Werkzeug-2.2.3.tar.gz", hash = "sha256:2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe"}, + {file = "werkzeug-2.3.8-py3-none-any.whl", hash = "sha256:bba1f19f8ec89d4d607a3bd62f1904bd2e609472d93cd85e9d4e178f472c3748"}, + {file = "werkzeug-2.3.8.tar.gz", hash = "sha256:554b257c74bbeb7a0d254160a4f8ffe185243f52a52035060b761ca62d977f03"}, ] [package.dependencies] MarkupSafe = ">=2.1.1" [package.extras] -watchdog = ["watchdog"] +watchdog = ["watchdog (>=2.3)"] [[package]] name = "xmltodict" @@ -3255,4 +3271,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "ea95f3a062ecdf2de9296b690644b597ca0fcfb0b7932877ed57599e15c4b0df" +content-hash = "324bc125fd8051594e0d7b1e1a76d7fcf80c2a53509f8e6ae30f835f72e84cc4" diff --git a/pyproject.toml b/pyproject.toml index 8e530aa..2323e49 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,9 +32,7 @@ boto3 = "1.34.104" foca = "^0.13.0" kubernetes = "^29.0.0" python = "^3.11" -requests = ">=2.32.0" urllib3 = "^2.2.2" -werkzeug = "==2.2.3" [tool.poetry.group.docs.dependencies] added-value = "^0.24.0" From 292a10800f2aff28b2082dd009ba7c65caa4b5fb Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Mon, 2 Sep 2024 10:39:42 +0530 Subject: [PATCH 06/20] format consts --- tesk/api/kubernetes/constants.py | 346 +++++++++++++++++-------------- tesk/api/kubernetes/wrapper.py | 4 +- tesk/constants.py | 45 +++- 3 files changed, 234 insertions(+), 161 deletions(-) diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index efe7977..7306fc7 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -3,198 +3,222 @@ from enum import Enum from typing import Set -from pydantic import BaseModel, Field +from pydantic import BaseModel class JobConstants(BaseModel): - """Constants related to job and tasks.""" - - taskmaster_input: str = Field( - default="JSON_INPUT", - description="ENV var that serves as taskmaster script input (JSON format)", - ) - taskmaster_input_exec_key: str = Field( - default="executors", - description="Key in JSON taskmaster input, which holds list of executors", - ) - volume_name: str = Field(default="PVC", description="Volume name") - job_create_attempts_no: int = Field( - default=5, - description="Number of attempts of job creation in case of name collision", - ) - job_name_taskm_prefix: str = Field( - default="task-", - description="Constant prefix of taskmaster's job name (== TES task ID)", - ) - job_name_exec_prefix: str = Field( - default="-ex-", - description="Part of executor's job name, that follows taskmaster's name", - ) - job_name_taskm_rand_part_length: int = Field( - default=4, - description=( - "No of bytes of random part of task master's name (which end up " - "encoded to hex)" - ), - ) - job_name_exec_no_length: int = Field( - default=2, - description="No of digits reserved for executor number in executor's job name." - " Ends up padded with '0' for numbers < 10", - ) - job_name_filer_suf: str = Field( - default="-outputs-filer", description="Output filer name suffix" - ) - resource_disk_default: float = Field( - default=0.1, description="Default resource disk value" - ) - completed_states: Set[str] = Field( - default={"CANCELED", "COMPLETE", "EXECUTOR_ERROR", "SYSTEM_ERROR"}, - description="TES task states, indicating task is not running and cannot be " - "cancelled", - ) - executor_backoff_limit: str = Field( - default="EXECUTOR_BACKOFF_LIMIT", - description="Set a number of retries of a job execution.", - ) - filer_backoff_limit: str = Field( - default="FILER_BACKOFF_LIMIT", - description="Set a number of retries of a filer job execution.", - ) + """Constants related to job and tasks. + + Attributes: + taskmaster_input: str = ENV var that serves as taskmaster script input (JSON + format) + taskmaster_input_exec_key: str = Key in JSON taskmaster input, which holds list + of executors + volume_name: str = Volume name + job_create_attempts_no: int = Number of attempts of job creation in case of name + collision + job_name_taskm_prefix: str = Constant prefix of taskmaster's job name (== TES + task ID) + job_name_exec_prefix: str = Part of executor's job name, that follows + taskmaster's name + job_name_taskm_rand_part_length: int = No of bytes of random part of task + master's name (which end up encoded to hex) + job_name_exec_no_length: int = No of digits reserved for executor number in + executor's job name. Ends up padded with '0' for numbers < 10 + job_name_filer_suf: str = Output filer name suffix + resource_disk_default: float = Default resource disk value + completed_states: Set[str] = TES task states, indicating task is not running and + cannot be cancelled + executor_backoff_limit: str = Set a number of retries of a job execution. + filer_backoff_limit: str = 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.""" - - ann_testask_name_key: str = Field( - default="tes-task-name", - description=( - "Key of the annotation, that stores name of TES task in both taskmaster's " - "job and executor's jobs" - ), - ) - ann_json_input_key: str = Field( - default="json-input", - description="Key of the annotation, that stores whole input TES task serialized" - " to JSON", - ) + """Constants related to Kubernetes annotations. + + Attributes: + ann_testask_name_key: str = Key of the annotation, that stores name of TES task + in both taskmaster's job and executor's jobs + ann_json_input_key: str = 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.""" - - label_testask_id_key: str = Field( - default="taskmaster-name", - description="Key of the label, that stores taskmaster's name (==TES task " - "generated ID) in executor jobs", - ) - label_jobtype_key: str = Field( - default="job-type", - description="Key of the label, that stores type of a job (taskmaster or " - "executor)", - ) - label_jobtype_value_taskm: str = Field( - default="taskmaster", - description="Value of the label with taskmaster's job type", - ) - label_jobtype_value_exec: str = Field( - default="executor", description="Value of the label with executor's job type" - ) - label_execno_key: str = Field( - default="executor-no", - description="Key of the label, that holds executor number for executor jobs", - ) - label_taskstate_key: str = Field( - default="task-status", - description="Key of the label, that holds executor's state", - ) - label_taskstate_value_canc: str = Field( - default="Cancelled", - description="Value of the label, that holds executor's Cancelled state", - ) - label_userid_key: str = Field( - default="creator-user-id", description="Key of the label, that holds user id" - ) - label_groupname_key: str = Field( - default="creator-group-name", - description="Key of the label, that holds user's group name", - ) + """Constants related to Kubernetes labels. + + Attributes: + label_testask_id_key: str = Key of the label, that stores taskmaster's name (== + TES task generated ID) in executor jobs + label_jobtype_key: str = Key of the label, that stores type of a job (taskmaster + or executor) + label_jobtype_value_taskm: str = Value of the label with taskmaster's job type + label_jobtype_value_exec: str = Value of the label with executor's job type + label_execno_key: str = Key of the label, that holds executor number for + executor jobs + label_taskstate_key: str = Key of the label, that holds executor's state + label_taskstate_value_canc: str = Value of the label, that holds executor's + Cancelled state + label_userid_key: str = Key of the label, that holds user id + label_groupname_key: str = 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.""" + """Constants related to path validation. + + Attributes: + absolute_path_regex: str = Pattern to validate path + absolute_path_message: str = Message for absolute path validation (to avoid + message.property) + """ - absolute_path_regexp: str = Field( - default="^\\/.*", description="Pattern to validate paths" - ) - absolute_path_message: str = Field( - default="must be an absolute path", - description="Message for absolute path validation (to avoid " - "message.properties)", - ) + 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.""" + """Constants related to FTP configuration. + + Attributes: + ftp_secret_username_env: str = Environment variable name for FTP username + ftp_secret_password_env: str = 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.""" - ftp_secret_username_env: str = Field( - default="TESK_FTP_USERNAME", - description="Name of taskmaster's ENV variable with username of FTP account " - "used for storage", - ) - ftp_secret_password_env: str = Field( - default="TESK_FTP_PASSWORD", - description="Name of taskmaster's ENV variable with password of FTP account " - "used for storage", - ) + frozen = True class PatchConstants(BaseModel): - """Constants related to patch operations.""" + """Constants related to patch operations. - cancel_patch: str = Field( - default='{"metadata":{"labels":{"task-status":"Cancelled"}}}', - description="Patch object passed to job API, when cancelling task", - ) + Attributes: + cancel_path: str = 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.""" - - k8s_batch_api_version: str = Field( - default="batch/v1", description="Kubernetes Batch API version" - ) - k8s_batch_api_job_type: str = Field( - default="Job", description="Kubernetes Job object type" - ) - job_restart_policy: str = Field( - default="Never", description="Kubernetes Job restart policy" - ) - resource_cpu_key: str = Field( - default="cpu", description="Executor CPU resource label" - ) - resource_mem_key: str = Field( - default="memory", description="Executor memory resource label" - ) - resource_mem_unit: str = Field( - default="Gi", description="Executor memory resource unit" - ) - resource_mem_one_gb: int = Field( - default=1073741824, description="One Gibibyte (Gi) in bytes" - ) + """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.""" + """Pod state. + + Attribute: + PENDING: str = pending + """ PENDING = "Pending" + class Config: + """Configuration for class.""" + + frozen = True + def get_code(self) -> str: """Return the pod state.""" return self.value class TeskK8sConstants(BaseModel): - """All the constants related to k8s and job creation.""" + """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() @@ -203,3 +227,11 @@ class TeskK8sConstants(BaseModel): 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/api/kubernetes/wrapper.py b/tesk/api/kubernetes/wrapper.py index 94123bc..23593b3 100644 --- a/tesk/api/kubernetes/wrapper.py +++ b/tesk/api/kubernetes/wrapper.py @@ -14,7 +14,7 @@ ) from kubernetes.utils.quantity import parse_quantity # type: ignore -from tesk.api.kubernetes.constants import TeskK8sConstants +from tesk.api.kubernetes.constants import tesk_k8s_constants from tesk.constants import TeskConstants from tesk.exceptions import KubernetesError, NotFound @@ -30,7 +30,7 @@ def __init__(self): self.batch_api = client.BatchV1Api() self.core_api = client.CoreV1Api() self.namespace = TeskConstants.tesk_namespace - self.tesk_k8s_constant = TeskK8sConstants() + self.tesk_k8s_constant = tesk_k8s_constants def create_job(self, job: V1Job) -> V1Job: """Create a job in the Kubernetes cluster. diff --git a/tesk/constants.py b/tesk/constants.py index 5224462..5df1c43 100644 --- a/tesk/constants.py +++ b/tesk/constants.py @@ -2,9 +2,50 @@ import os +from pydantic import BaseModel -class TeskConstants: - """Tesk's K8s scoped constants.""" + +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" From 48c8cd0fb9acc620eb24c2fe572adf6b5f6aeaf3 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Mon, 2 Sep 2024 10:42:47 +0530 Subject: [PATCH 07/20] add class config --- tesk/constants.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/tesk/constants.py b/tesk/constants.py index 5df1c43..54701b5 100644 --- a/tesk/constants.py +++ b/tesk/constants.py @@ -68,3 +68,8 @@ class TeskConstants(BaseModel): ) 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 From b611cab1ea4340bfaafdcae4ad26fee673eea087 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Mon, 2 Sep 2024 10:50:47 +0530 Subject: [PATCH 08/20] uppercase --- tesk/api/kubernetes/constants.py | 172 +++++++++++++++---------------- tesk/constants.py | 56 +++++----- 2 files changed, 115 insertions(+), 113 deletions(-) diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index 7306fc7..2470ace 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -10,47 +10,47 @@ class JobConstants(BaseModel): """Constants related to job and tasks. Attributes: - taskmaster_input: str = ENV var that serves as taskmaster script input (JSON + TASKMASTER_INPUT: str = ENV var that serves as taskmaster script input (JSON format) - taskmaster_input_exec_key: str = Key in JSON taskmaster input, which holds list + TASKMASTER_INPUT_EXEC_KEY: str = Key in JSON taskmaster input, which holds list of executors - volume_name: str = Volume name - job_create_attempts_no: int = Number of attempts of job creation in case of name + VOLUME_NAME: str = Volume name + JOB_CREATE_ATTEMPTS_NO: int = Number of attempts of job creation in case of name collision - job_name_taskm_prefix: str = Constant prefix of taskmaster's job name (== TES + JOB_NAME_TASKM_PREFIX: str = Constant prefix of taskmaster's job name (== TES task ID) - job_name_exec_prefix: str = Part of executor's job name, that follows + JOB_NAME_EXEC_PREFIX: str = Part of executor's job name, that follows taskmaster's name - job_name_taskm_rand_part_length: int = No of bytes of random part of task + JOB_NAME_TASKM_RAND_PART_LENGTH: int = No of bytes of random part of task master's name (which end up encoded to hex) - job_name_exec_no_length: int = No of digits reserved for executor number in + JOB_NAME_EXEC_NO_LENGTH: int = No of digits reserved for executor number in executor's job name. Ends up padded with '0' for numbers < 10 - job_name_filer_suf: str = Output filer name suffix - resource_disk_default: float = Default resource disk value - completed_states: Set[str] = TES task states, indicating task is not running and + JOB_NAME_FILER_SUF: str = Output filer name suffix + RESOURCE_DISK_DEFAULT: float = Default resource disk value + COMPLETED_STATES: Set[str] = TES task states, indicating task is not running and cannot be cancelled - executor_backoff_limit: str = Set a number of retries of a job execution. - filer_backoff_limit: str = Set a number of retries of a filer job execution. + EXECUTOR_BACKOFF_LIMIT: str = Set a number of retries of a job execution. + FILER_BACKOFF_LIMIT: str = 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] = { + 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" + EXECUTOR_BACKOFF_LIMIT: str = "EXECUTOR_BACKOFF_LIMIT" + FILER_BACKOFF_LIMIT: str = "FILER_BACKOFF_LIMIT" class Config: """Configuration for class.""" @@ -62,14 +62,14 @@ class AnnotationConstants(BaseModel): """Constants related to Kubernetes annotations. Attributes: - ann_testask_name_key: str = Key of the annotation, that stores name of TES task + ANN_TESTASK_NAME_KEY: str = Key of the annotation, that stores name of TES task in both taskmaster's job and executor's jobs - ann_json_input_key: str = Key of the annotation, that stores whole input TES + ANN_JSON_INPUT_KEY: str = 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" + ANN_TESTASK_NAME_KEY: str = "tes-task-name" + ANN_JSON_INPUT_KEY: str = "json-input" class Config: """Configuration for class.""" @@ -81,30 +81,30 @@ class LabelConstants(BaseModel): """Constants related to Kubernetes labels. Attributes: - label_testask_id_key: str = Key of the label, that stores taskmaster's name (== + LABEL_TESTASK_ID_KEY: str = Key of the label, that stores taskmaster's name (== TES task generated ID) in executor jobs - label_jobtype_key: str = Key of the label, that stores type of a job (taskmaster + LABEL_JOBTYPE_KEY: str = Key of the label, that stores type of a job (taskmaster or executor) - label_jobtype_value_taskm: str = Value of the label with taskmaster's job type - label_jobtype_value_exec: str = Value of the label with executor's job type - label_execno_key: str = Key of the label, that holds executor number for + LABEL_JOBTYPE_VALUE_TASKM: str = Value of the label with taskmaster's job type + LABEL_JOBTYPE_VALUE_EXEC: str = Value of the label with executor's job type + LABEL_EXECNO_KEY: str = Key of the label, that holds executor number for executor jobs - label_taskstate_key: str = Key of the label, that holds executor's state - label_taskstate_value_canc: str = Value of the label, that holds executor's + LABEL_TASKSTATE_KEY: str = Key of the label, that holds executor's state + LABEL_TASKSTATE_VALUE_CANC: str = Value of the label, that holds executor's Cancelled state - label_userid_key: str = Key of the label, that holds user id - label_groupname_key: str = Key of the label, that holds user's group name + LABEL_USERID_KEY: str = Key of the label, that holds user id + LABEL_GROUPNAME_KEY: str = 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" + 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.""" @@ -116,13 +116,13 @@ class PathValidationConstants(BaseModel): """Constants related to path validation. Attributes: - absolute_path_regex: str = Pattern to validate path - absolute_path_message: str = Message for absolute path validation (to avoid + ABSOLUTE_PATH_REGEX: str = Pattern to validate path + ABSOLUTE_PATH_MESSAGE: str = Message for absolute path validation (to avoid message.property) """ - absolute_path_regexp: str = "^\\/.*" - absolute_path_message: str = "must be an absolute path" + ABSOLUTE_PATH_REGEXP: str = "^\\/.*" + ABSOLUTE_PATH_MESSAGE: str = "must be an absolute path" class Config: """Configuration for class.""" @@ -134,12 +134,12 @@ class FTPConstants(BaseModel): """Constants related to FTP configuration. Attributes: - ftp_secret_username_env: str = Environment variable name for FTP username - ftp_secret_password_env: str = Environment variable name for FTP password + FTP_SECRET_USERNAME_ENV: str = Environment variable name for FTP username + FTP_SECRET_PASSWORD_ENV: str = Environment variable name for FTP password """ - ftp_secret_username_env: str = "TESK_FTP_USERNAME" - ftp_secret_password_env: str = "TESK_FTP_PASSWORD" + FTP_SECRET_USERNAME_ENV: str = "TESK_FTP_USERNAME" + FTP_SECRET_PASSWORD_ENV: str = "TESK_FTP_PASSWORD" class Config: """Configuration for class.""" @@ -151,10 +151,10 @@ class PatchConstants(BaseModel): """Constants related to patch operations. Attributes: - cancel_path: str = Patch object passed to job API, when cancelling task + CANCEL_PATH: str = Patch object passed to job API, when cancelling task """ - cancel_patch: str = '{"metadata":{"labels":{"task-status":"Cancelled"}}}' + CANCEL_PATCH: str = '{"metadata":{"labels":{"task-status":"Cancelled"}}}' class Config: """Configuration for class.""" @@ -166,22 +166,22 @@ 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: 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 + 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.""" @@ -211,22 +211,22 @@ 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 + 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() + 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.""" diff --git a/tesk/constants.py b/tesk/constants.py index 54701b5..a34a208 100644 --- a/tesk/constants.py +++ b/tesk/constants.py @@ -9,16 +9,16 @@ 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 + 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 + 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 @@ -27,49 +27,51 @@ class TeskConstants(BaseModel): variable: ENV_VARIABLE = default - filer_image_name: + FILER_IMAGE_NAME: TESK_API_TASKMASTER_FILER_IMAGE_NAME = docker.io/elixircloud/tesk-core-filer - filer_image_version: + FILER_IMAGE_VERSION: TESK_API_TASKMASTER_FILER_IMAGE_VERSION = latest - taskmaster_image_name: + TASKMASTER_IMAGE_NAME: TESK_API_TASKMASTER_IMAGE_NAME = docker.io/elixircloud/tesk-core-taskmaster - taskmaster_image_version: + TASKMASTER_IMAGE_VERSION: TESK_API_TASKMASTER_IMAGE_VERSION = latest - tesk_namespace: + TESK_NAMESPACE: TESK_API_K8S_NAMESPACE = tesk - taskmaster_service_account_name: + TASKMASTER_SERVICE_ACCOUNT_NAME: TESK_API_TASKMASTER_SERVICE_ACCOUNT_NAME = taskmaster - taskmaster_environment_executor_backoff_limit: + TASKMASTER_ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT: ENVIRONMENT_EXECUTOR_BACKOFF_LIMIT = 6 - filer_backoff_limit: + FILER_BACKOFF_LIMIT: FILER_BACKOFF_LIMIT = 2 - executor_backoff_limit: + EXECUTOR_BACKOFF_LIMIT: EXECUTOR_BACKOFF_LIMIT = 2 """ - filer_image_name: str = os.getenv( + FILER_IMAGE_NAME: str = os.getenv( "TESK_API_TASKMASTER_FILER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-filer" ) - filer_image_version: str = os.getenv( + FILER_IMAGE_VERSION: str = os.getenv( "TESK_API_TASKMASTER_FILER_IMAGE_VERSION", "latest" ) - taskmaster_image_name: str = os.getenv( + TASKMASTER_IMAGE_NAME: str = os.getenv( "TESK_API_TASKMASTER_IMAGE_NAME", "docker.io/elixircloud/tesk-core-taskmaster" ) - taskmaster_image_version: str = os.getenv( + 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_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( + 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") + 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() \ No newline at end of file From d0f2b547c8d6c9db1811bb2a08c0040fbd2c1f7c Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 4 Sep 2024 11:04:13 +0530 Subject: [PATCH 09/20] chore: remove datatype from pydocs --- tesk/api/kubernetes/constants.py | 58 ++++++++++++++++---------------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index 2470ace..e9f97d9 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -10,27 +10,27 @@ class JobConstants(BaseModel): """Constants related to job and tasks. Attributes: - TASKMASTER_INPUT: str = ENV var that serves as taskmaster script input (JSON + TASKMASTER_INPUT = ENV var that serves as taskmaster script input (JSON format) - TASKMASTER_INPUT_EXEC_KEY: str = Key in JSON taskmaster input, which holds list + TASKMASTER_INPUT_EXEC_KEY = Key in JSON taskmaster input, which holds list of executors - VOLUME_NAME: str = Volume name - JOB_CREATE_ATTEMPTS_NO: int = Number of attempts of job creation in case of name + VOLUME_NAME = Volume name + JOB_CREATE_ATTEMPTS_NO = Number of attempts of job creation in case of name collision - JOB_NAME_TASKM_PREFIX: str = Constant prefix of taskmaster's job name (== TES + JOB_NAME_TASKM_PREFIX = Constant prefix of taskmaster's job name (== TES task ID) - JOB_NAME_EXEC_PREFIX: str = Part of executor's job name, that follows + JOB_NAME_EXEC_PREFIX = Part of executor's job name, that follows taskmaster's name - JOB_NAME_TASKM_RAND_PART_LENGTH: int = No of bytes of random part of task + 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: int = No of digits reserved for executor number in + 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: str = Output filer name suffix + JOB_NAME_FILER_SUF = Output filer name suffix RESOURCE_DISK_DEFAULT: float = Default resource disk value - COMPLETED_STATES: Set[str] = TES task states, indicating task is not running and + COMPLETED_STATES = TES task states, indicating task is not running and cannot be cancelled - EXECUTOR_BACKOFF_LIMIT: str = Set a number of retries of a job execution. - FILER_BACKOFF_LIMIT: str = Set a number of retries of a filer job execution. + 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" @@ -62,9 +62,9 @@ class AnnotationConstants(BaseModel): """Constants related to Kubernetes annotations. Attributes: - ANN_TESTASK_NAME_KEY: str = Key of the annotation, that stores name of TES task + 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: str = Key of the annotation, that stores whole input TES + ANN_JSON_INPUT_KEY = Key of the annotation, that stores whole input TES task serialized to JSON """ @@ -81,19 +81,19 @@ class LabelConstants(BaseModel): """Constants related to Kubernetes labels. Attributes: - LABEL_TESTASK_ID_KEY: str = Key of the label, that stores taskmaster's name (== + LABEL_TESTASK_ID_KEY = Key of the label, that stores taskmaster's name (== TES task generated ID) in executor jobs - LABEL_JOBTYPE_KEY: str = Key of the label, that stores type of a job (taskmaster + LABEL_JOBTYPE_KEY = Key of the label, that stores type of a job (taskmaster or executor) - LABEL_JOBTYPE_VALUE_TASKM: str = Value of the label with taskmaster's job type - LABEL_JOBTYPE_VALUE_EXEC: str = Value of the label with executor's job type - LABEL_EXECNO_KEY: str = Key of the label, that holds executor number for + 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: str = Key of the label, that holds executor's state - LABEL_TASKSTATE_VALUE_CANC: str = Value of the label, that holds executor's + 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: str = Key of the label, that holds user id - LABEL_GROUPNAME_KEY: str = Key of the label, that holds user's group name + 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" @@ -116,8 +116,8 @@ class PathValidationConstants(BaseModel): """Constants related to path validation. Attributes: - ABSOLUTE_PATH_REGEX: str = Pattern to validate path - ABSOLUTE_PATH_MESSAGE: str = Message for absolute path validation (to avoid + ABSOLUTE_PATH_REGEX = Pattern to validate path + ABSOLUTE_PATH_MESSAGE = Message for absolute path validation (to avoid message.property) """ @@ -134,8 +134,8 @@ class FTPConstants(BaseModel): """Constants related to FTP configuration. Attributes: - FTP_SECRET_USERNAME_ENV: str = Environment variable name for FTP username - FTP_SECRET_PASSWORD_ENV: str = Environment variable name for FTP password + 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" @@ -151,7 +151,7 @@ class PatchConstants(BaseModel): """Constants related to patch operations. Attributes: - CANCEL_PATH: str = Patch object passed to job API, when cancelling task + CANCEL_PATH = Patch object passed to job API, when cancelling task """ CANCEL_PATCH: str = '{"metadata":{"labels":{"task-status":"Cancelled"}}}' @@ -192,7 +192,7 @@ class PodPhase(Enum): """Pod state. Attribute: - PENDING: str = pending + PENDING = pending """ PENDING = "Pending" From 1de65e1582c18c104d2935a805f1739f5ef57dab Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 4 Sep 2024 11:06:51 +0530 Subject: [PATCH 10/20] chore: fl and mypy --- tesk/api/kubernetes/constants.py | 5 +++-- tesk/constants.py | 3 ++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/tesk/api/kubernetes/constants.py b/tesk/api/kubernetes/constants.py index e9f97d9..e972248 100644 --- a/tesk/api/kubernetes/constants.py +++ b/tesk/api/kubernetes/constants.py @@ -40,7 +40,7 @@ class JobConstants(BaseModel): 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_EXEC_NO_LENGTH: int = 2 JOB_NAME_FILER_SUF: str = "-outputs-filer" RESOURCE_DISK_DEFAULT: float = 0.1 COMPLETED_STATES: Set[str] = { @@ -204,7 +204,8 @@ class Config: def get_code(self) -> str: """Return the pod state.""" - return self.value + code: str = self.value + return code class TeskK8sConstants(BaseModel): diff --git a/tesk/constants.py b/tesk/constants.py index a34a208..5508eb2 100644 --- a/tesk/constants.py +++ b/tesk/constants.py @@ -74,4 +74,5 @@ class Config: frozen = True -tesk_constants = TeskConstants() \ No newline at end of file + +tesk_constants = TeskConstants() From 94891a850beaed0b5080182dc66b297416b494c9 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 4 Sep 2024 11:10:13 +0530 Subject: [PATCH 11/20] chore: add docs (autogen) --- docs/source/pages/tesk/tesk.api.ga4gh.rst | 18 ++++++++ docs/source/pages/tesk/tesk.api.ga4gh.tes.rst | 37 ++++++++++++++++ .../tesk/tesk.api.ga4gh.tes.service_info.rst | 21 +++++++++ .../source/pages/tesk/tesk.api.kubernetes.rst | 29 ++++++++++++ docs/source/pages/tesk/tesk.api.rst | 19 ++++++++ docs/source/pages/tesk/tesk.rst | 44 +++++++++++++++++++ 6 files changed, 168 insertions(+) create mode 100644 docs/source/pages/tesk/tesk.api.ga4gh.rst create mode 100644 docs/source/pages/tesk/tesk.api.ga4gh.tes.rst create mode 100644 docs/source/pages/tesk/tesk.api.ga4gh.tes.service_info.rst create mode 100644 docs/source/pages/tesk/tesk.api.kubernetes.rst create mode 100644 docs/source/pages/tesk/tesk.api.rst 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.kubernetes.rst b/docs/source/pages/tesk/tesk.api.kubernetes.rst new file mode 100644 index 0000000..06de122 --- /dev/null +++ b/docs/source/pages/tesk/tesk.api.kubernetes.rst @@ -0,0 +1,29 @@ +tesk.api.kubernetes package +=========================== + +Submodules +---------- + +tesk.api.kubernetes.constants module +------------------------------------ + +.. automodule:: tesk.api.kubernetes.constants + :members: + :undoc-members: + :show-inheritance: + +tesk.api.kubernetes.wrapper module +---------------------------------- + +.. automodule:: tesk.api.kubernetes.wrapper + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: tesk.api.kubernetes + :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..90ba935 --- /dev/null +++ b/docs/source/pages/tesk/tesk.api.rst @@ -0,0 +1,19 @@ +tesk.api package +================ + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + tesk.api.ga4gh + tesk.api.kubernetes + +Module contents +--------------- + +.. automodule:: tesk.api + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tesk/tesk.rst b/docs/source/pages/tesk/tesk.rst index b023c8f..9afd7a5 100644 --- a/docs/source/pages/tesk/tesk.rst +++ b/docs/source/pages/tesk/tesk.rst @@ -7,8 +7,52 @@ Subpackages .. toctree:: :maxdepth: 4 + tesk.api 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 --------------- From 35e5b940267ca0d417bf770f8ef223b40b3d976b Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 4 Sep 2024 18:01:50 +0530 Subject: [PATCH 12/20] chore: move k8s package to tesk scope --- tesk/{api => }/kubernetes/__init__.py | 0 tesk/{api => }/kubernetes/constants.py | 0 tesk/{api => }/kubernetes/wrapper.py | 2 +- 3 files changed, 1 insertion(+), 1 deletion(-) rename tesk/{api => }/kubernetes/__init__.py (100%) rename tesk/{api => }/kubernetes/constants.py (100%) rename tesk/{api => }/kubernetes/wrapper.py (99%) diff --git a/tesk/api/kubernetes/__init__.py b/tesk/kubernetes/__init__.py similarity index 100% rename from tesk/api/kubernetes/__init__.py rename to tesk/kubernetes/__init__.py diff --git a/tesk/api/kubernetes/constants.py b/tesk/kubernetes/constants.py similarity index 100% rename from tesk/api/kubernetes/constants.py rename to tesk/kubernetes/constants.py diff --git a/tesk/api/kubernetes/wrapper.py b/tesk/kubernetes/wrapper.py similarity index 99% rename from tesk/api/kubernetes/wrapper.py rename to tesk/kubernetes/wrapper.py index 23593b3..7f29361 100644 --- a/tesk/api/kubernetes/wrapper.py +++ b/tesk/kubernetes/wrapper.py @@ -14,9 +14,9 @@ ) from kubernetes.utils.quantity import parse_quantity # type: ignore -from tesk.api.kubernetes.constants import tesk_k8s_constants from tesk.constants import TeskConstants from tesk.exceptions import KubernetesError, NotFound +from tesk.kubernetes.constants import tesk_k8s_constants logger = logging.getLogger(__name__) From adda33e4f4dbce2e8ae634cd98f5ed77c47d0da6 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 4 Sep 2024 18:02:42 +0530 Subject: [PATCH 13/20] fix: docs --- .../source/pages/tesk/tesk.api.kubernetes.rst | 29 ------------------- docs/source/pages/tesk/tesk.api.rst | 1 - docs/source/pages/tesk/tesk.kubernetes.rst | 29 +++++++++++++++++++ docs/source/pages/tesk/tesk.rst | 1 + 4 files changed, 30 insertions(+), 30 deletions(-) delete mode 100644 docs/source/pages/tesk/tesk.api.kubernetes.rst create mode 100644 docs/source/pages/tesk/tesk.kubernetes.rst diff --git a/docs/source/pages/tesk/tesk.api.kubernetes.rst b/docs/source/pages/tesk/tesk.api.kubernetes.rst deleted file mode 100644 index 06de122..0000000 --- a/docs/source/pages/tesk/tesk.api.kubernetes.rst +++ /dev/null @@ -1,29 +0,0 @@ -tesk.api.kubernetes package -=========================== - -Submodules ----------- - -tesk.api.kubernetes.constants module ------------------------------------- - -.. automodule:: tesk.api.kubernetes.constants - :members: - :undoc-members: - :show-inheritance: - -tesk.api.kubernetes.wrapper module ----------------------------------- - -.. automodule:: tesk.api.kubernetes.wrapper - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: tesk.api.kubernetes - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/pages/tesk/tesk.api.rst b/docs/source/pages/tesk/tesk.api.rst index 90ba935..e9d2f31 100644 --- a/docs/source/pages/tesk/tesk.api.rst +++ b/docs/source/pages/tesk/tesk.api.rst @@ -8,7 +8,6 @@ Subpackages :maxdepth: 4 tesk.api.ga4gh - tesk.api.kubernetes Module contents --------------- diff --git a/docs/source/pages/tesk/tesk.kubernetes.rst b/docs/source/pages/tesk/tesk.kubernetes.rst new file mode 100644 index 0000000..332e72b --- /dev/null +++ b/docs/source/pages/tesk/tesk.kubernetes.rst @@ -0,0 +1,29 @@ +tesk.kubernetes package +======================= + +Submodules +---------- + +tesk.kubernetes.constants module +-------------------------------- + +.. automodule:: tesk.kubernetes.constants + :members: + :undoc-members: + :show-inheritance: + +tesk.kubernetes.wrapper module +------------------------------ + +.. automodule:: tesk.kubernetes.wrapper + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: tesk.kubernetes + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tesk/tesk.rst b/docs/source/pages/tesk/tesk.rst index 9afd7a5..9918ebd 100644 --- a/docs/source/pages/tesk/tesk.rst +++ b/docs/source/pages/tesk/tesk.rst @@ -8,6 +8,7 @@ Subpackages :maxdepth: 4 tesk.api + tesk.kubernetes tesk.services Submodules From 0e68713262cb91233e4ff1f731849d9c6a701e7f Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 4 Sep 2024 18:04:17 +0530 Subject: [PATCH 14/20] fix: revert deps --- poetry.lock | 2194 +++++++++++++++++++++++------------------------- pyproject.toml | 1 + 2 files changed, 1045 insertions(+), 1150 deletions(-) diff --git a/poetry.lock b/poetry.lock index c16d219..c1d873a 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" @@ -73,32 +73,32 @@ files = [ [[package]] name = "attrs" -version = "24.2.0" +version = "23.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, - {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, + {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, + {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, ] [package.extras] -benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"] -tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] +cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] +dev = ["attrs[tests]", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs[tests-no-zope]", "zope-interface"] +tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] +tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] [[package]] name = "authlib" -version = "1.3.2" +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-1.3.2-py2.py3-none-any.whl", hash = "sha256:ede026a95e9f5cdc2d4364a52103f5405e75aa156357e831ef2bfd0bc5094dfc"}, - {file = "authlib-1.3.2.tar.gz", hash = "sha256:4b16130117f9eb82aa6eec97f6dd4673c3f960ac0283ccdae2897ee4bc030ba2"}, + {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] @@ -106,13 +106,13 @@ cryptography = "*" [[package]] name = "babel" -version = "2.16.0" +version = "2.15.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" files = [ - {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, - {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, + {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, + {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, ] [package.extras] @@ -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 = "blinker-1.8.2-py3-none-any.whl", hash = "sha256:1779309f71bf239144b9399d06ae925637cf6634cf6bd131104184531bf67c01"}, - {file = "blinker-1.8.2.tar.gz", hash = "sha256:8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83"}, -] - [[package]] name = "boto3" version = "1.34.104" @@ -206,13 +195,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.35.10" -description = "Type annotations for boto3 1.35.10 generated with mypy-boto3-builder 7.26.1" +version = "1.34.115" +description = "Type annotations for boto3 1.34.115 generated with mypy-boto3-builder 7.24.0" optional = false python-versions = ">=3.8" files = [ - {file = "boto3_stubs-1.35.10-py3-none-any.whl", hash = "sha256:2c18c95acc7f13fd17ab48d309bcaeaffa7ac4ee3cccb600a027af62c0718da6"}, - {file = "boto3_stubs-1.35.10.tar.gz", hash = "sha256:29e7ab85fa7ecff571f696f8ca36034d56c7694b394f97b5f0ed1f2424935959"}, + {file = "boto3_stubs-1.34.115-py3-none-any.whl", hash = "sha256:fd06dc6cfb2503fcd4314e63d52eae4889f84e06ff4f92dca4a1f6cae68bfb00"}, + {file = "boto3_stubs-1.34.115.tar.gz", hash = "sha256:1d58dde687903e9b8cd01b2680219ace3981aab72f82165b58bb0a56cff2ce3f"}, ] [package.dependencies] @@ -221,405 +210,403 @@ types-s3transfer = "*" typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.12\""} [package.extras] -accessanalyzer = ["mypy-boto3-accessanalyzer 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2 files changed, 1150 insertions(+), 1045 deletions(-) diff --git a/poetry.lock b/poetry.lock index c1d873a..e3931ef 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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from connexion.exceptions import ( BadRequestProblem, ExtraParameterProblem, @@ -21,6 +19,10 @@ class ConfigNotFoundError(FileNotFoundError): """Configuration file not found error.""" +class KubernetesError(ApiException): + """Kubernetes error.""" + + # exceptions raised in app context exceptions = { Exception: { @@ -74,11 +76,3 @@ class ConfigNotFoundError(FileNotFoundError): # exceptions raised outside of app context class ValidationError(Exception): """Value or object is not compatible with required type or schema.""" - - -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/kubernetes/constants.py b/tesk/kubernetes/constants.py index e972248..d0f32a9 100644 --- a/tesk/kubernetes/constants.py +++ b/tesk/kubernetes/constants.py @@ -212,22 +212,22 @@ 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 + 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() + 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.""" diff --git a/tesk/kubernetes/wrapper.py b/tesk/kubernetes/wrapper.py index 7f29361..c52a0e4 100644 --- a/tesk/kubernetes/wrapper.py +++ b/tesk/kubernetes/wrapper.py @@ -14,7 +14,7 @@ ) from kubernetes.utils.quantity import parse_quantity # type: ignore -from tesk.constants import TeskConstants +from tesk.constants import tesk_constants from tesk.exceptions import KubernetesError, NotFound from tesk.kubernetes.constants import tesk_k8s_constants @@ -29,7 +29,7 @@ def __init__(self): config.load_kube_config() self.batch_api = client.BatchV1Api() self.core_api = client.CoreV1Api() - self.namespace = TeskConstants.tesk_namespace + self.namespace = tesk_constants.TESK_NAMESPACE self.tesk_k8s_constant = tesk_k8s_constants def create_job(self, job: V1Job) -> V1Job: @@ -80,12 +80,12 @@ def read_taskmaster_job(self, task_id: str) -> V1Job: if ( job.metadata and job.metadata.labels - and self.tesk_k8s_constant.label_constants.label_jobtype_key + 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_KEY ] - == self.tesk_k8s_constant.label_constants.label_jobtype_value_taskm + == self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_VALUE_TASKM ): return job except KubernetesError as e: @@ -177,9 +177,9 @@ def list_all_taskmaster_jobs_for_user( 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_KEY}" "=" - f"{self.tesk_k8s_constant.label_constants.label_jobtype_value_taskm}" + f"{self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_VALUE_TASKM}" ) result: V1JobList = self.list_jobs(page_token, label_selector, items_per_page) @@ -189,7 +189,7 @@ def list_all_taskmaster_jobs_for_user( 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, + 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 @@ -198,7 +198,7 @@ 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, + name=task_id + self.tesk_k8s_constant.job_constants.JOB_NAME_FILER_SUF, namespace=self.namespace, ) return job @@ -211,9 +211,9 @@ def get_single_task_output_filer_job(self, task_id: str) -> Optional[V1Job]: 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_KEY + "=" - + self.tesk_k8s_constant.label_constants.label_jobtype_value_taskm + + self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_VALUE_TASKM ) job_list: V1JobList = self.list_jobs(label_selector=label_selector) return job_list @@ -221,16 +221,16 @@ def list_all_taskmaster_jobs(self) -> V1JobList: 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_KEY + "=" - + self.tesk_k8s_constant.label_constants.label_jobtype_value_exec + + 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 + label_selector = "!" + self.tesk_k8s_constant.label_constants.LABEL_JOBTYPE_KEY job_list: V1JobList = self.list_jobs(label_selector=label_selector) return job_list From f44d90c2164286d3e03c6cae5c2279d0f2c8ef56 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 4 Sep 2024 19:14:19 +0530 Subject: [PATCH 17/20] minor --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 24d2597..1e03734 100644 --- a/poetry.lock +++ b/poetry.lock @@ -3259,4 +3259,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "ea95f3a062ecdf2de9296b690644b597ca0fcfb0b7932877ed57599e15c4b0df" +content-hash = "4b2902fcbf88e46455b2c2a5046ae600b27b3223e955bfd298dcc75905d2b5ae" From e3a658471939c0538137fb2be4d33f4604d65360 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Wed, 4 Sep 2024 19:33:40 +0530 Subject: [PATCH 18/20] change name of the package from kubernetes to k8s --- tesk/{kubernetes => k8s}/__init__.py | 0 tesk/{kubernetes => k8s}/constants.py | 0 tesk/{kubernetes => k8s}/wrapper.py | 2 +- 3 files changed, 1 insertion(+), 1 deletion(-) rename tesk/{kubernetes => k8s}/__init__.py (100%) rename tesk/{kubernetes => k8s}/constants.py (100%) rename tesk/{kubernetes => k8s}/wrapper.py (99%) diff --git a/tesk/kubernetes/__init__.py b/tesk/k8s/__init__.py similarity index 100% rename from tesk/kubernetes/__init__.py rename to tesk/k8s/__init__.py diff --git a/tesk/kubernetes/constants.py b/tesk/k8s/constants.py similarity index 100% rename from tesk/kubernetes/constants.py rename to tesk/k8s/constants.py diff --git a/tesk/kubernetes/wrapper.py b/tesk/k8s/wrapper.py similarity index 99% rename from tesk/kubernetes/wrapper.py rename to tesk/k8s/wrapper.py index c52a0e4..80a7112 100644 --- a/tesk/kubernetes/wrapper.py +++ b/tesk/k8s/wrapper.py @@ -16,7 +16,7 @@ from tesk.constants import tesk_constants from tesk.exceptions import KubernetesError, NotFound -from tesk.kubernetes.constants import tesk_k8s_constants +from tesk.k8s.constants import tesk_k8s_constants logger = logging.getLogger(__name__) From 23ac9e8a060fb2e09e5de8ddc8b02a5c955e6b49 Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Thu, 5 Sep 2024 15:36:38 +0530 Subject: [PATCH 19/20] reamde --- README.md | 14 +++++++++++ docs/source/pages/tesk/tesk.k8s.rst | 29 ++++++++++++++++++++++ docs/source/pages/tesk/tesk.kubernetes.rst | 29 ---------------------- docs/source/pages/tesk/tesk.rst | 2 +- 4 files changed, 44 insertions(+), 30 deletions(-) create mode 100644 docs/source/pages/tesk/tesk.k8s.rst delete mode 100644 docs/source/pages/tesk/tesk.kubernetes.rst 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.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.kubernetes.rst b/docs/source/pages/tesk/tesk.kubernetes.rst deleted file mode 100644 index 332e72b..0000000 --- a/docs/source/pages/tesk/tesk.kubernetes.rst +++ /dev/null @@ -1,29 +0,0 @@ -tesk.kubernetes package -======================= - -Submodules ----------- - -tesk.kubernetes.constants module --------------------------------- - -.. automodule:: tesk.kubernetes.constants - :members: - :undoc-members: - :show-inheritance: - -tesk.kubernetes.wrapper module ------------------------------- - -.. automodule:: tesk.kubernetes.wrapper - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: tesk.kubernetes - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/pages/tesk/tesk.rst b/docs/source/pages/tesk/tesk.rst index 9918ebd..9b4aede 100644 --- a/docs/source/pages/tesk/tesk.rst +++ b/docs/source/pages/tesk/tesk.rst @@ -8,7 +8,7 @@ Subpackages :maxdepth: 4 tesk.api - tesk.kubernetes + tesk.k8s tesk.services Submodules From dc0ba73c6cc1fa407467a4f4827e9901d37e5a5d Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Thu, 5 Sep 2024 15:42:07 +0530 Subject: [PATCH 20/20] werkzeug updates breaks the server --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a108ff2..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" -werkzeug = "==2.2.3" +werkzeug = "==2.2.3" # Remove when FOCA updates this dependency. urllib3 = "^2.2.2" [tool.poetry.group.docs.dependencies]