Glossary

This glossary defines key terms and acronyms found in the Poiesis documentation. It covers both Poiesis-specific components and general concepts relevant to the Task Execution Service (TES).

Poiesis Components

Core services and components that make up the Poiesis system.

Poiesis

Poiesis is a Kubernetes-native implementation of the Task Execution Service (TES) specification. It's designed to efficiently run computational tasks within containerized environments on Kubernetes clusters.

Task Orchestrator (TOrc)

TOrc is the Poiesis component that manages the setup and initialization phase of a task. It ensures all necessary Kubernetes resources (like PVCs) and dependencies are correctly provisioned before the task execution begins.

Task Input Filer (TIF)

TIF is the Poiesis service responsible for importing input data required by a task. It fetches files from user-specified storage locations (supporting protocols like S3, HTTPS, direct content, local paths, etc.) and makes them available to the task executor.

Task Execution And Monitor (TExAM)

TExAM oversees the lifecycle of computational tasks within Poiesis. It handles submission, scheduling, resource allocation, monitoring execution progress and logs, and managing results. TExAM is responsible for launching the actual Task Executor (TE).

Task Executor (TE)

TE is the component directly responsible for executing the commands defined within a task. It runs within a Kubernetes Pod and performs the actual computational work, utilizing the inputs prepared by TIF and generating outputs handled by TOF.

Task Output Filer (TOF)

TOF is the Poiesis service that handles the export of output data generated by a task. After task completion, TOF uploads specified files to the user's desired storage location, using various supported protocols based on the user's request.

General Concepts

Fundamental terms related to container orchestration and task execution used in the context of Poiesis and TES.

Task Execution Service (TES)

TES is a standard specification developed by the Global Alliance for Genomics and Health (GA4GH) for a RESTful API to submit, manage, and monitor batch execution tasks. Poiesis implements this standard.

More Information

You can find the official TES specification on GitHub.

Container

A container is a lightweight, standalone, executable package of software that includes everything needed to run it: code, runtime, system tools, system libraries, and settings. Containers isolate software from its environment, ensuring consistent operation. Popular containerization technology includes Docker.

Task

In the context of TES, a task represents a single unit of computational work. It's defined by its inputs (files, parameters), outputs (expected files, logs), execution commands (typically run inside a container), and resource requirements (CPU, RAM, disk).

More Information

Check the task schema (tesTask) on the bottom section of the API Reference page.

Kubernetes (K8s)

Kubernetes (often abbreviated as K8s) is an open-source platform for automating the deployment, scaling, and management of containerized applications. Poiesis leverages Kubernetes to manage its components and execute tasks efficiently.

More Information

Learn more at the official Kubernetes website.

Kubernetes Job

A Kubernetes Job is a controller object that creates one or more Pods and ensures that a specified number of them successfully terminate. Jobs are ideal for running batch processes or finite tasks to completion. Poiesis may use Jobs as part of its task execution mechanism.

Kubernetes Pod

A Pod is the smallest and simplest deployable unit in the Kubernetes object model. It represents a single instance of a running process in your cluster and can contain one or more containers, along with shared storage (Volumes) and network resources.

Kubernetes Persistent Volume Claim (PVC)

A Persistent Volume Claim (PVC) is a request for storage by a user within Kubernetes. Pods can request specific storage resources (like size and access modes) through PVCs, which are then fulfilled by Persistent Volumes (PVs) available in the cluster. Poiesis uses PVCs to provide persistent storage for tasks when needed.