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mg-tool-api

Introduction

This library implements the specifications detailed in the current version (23/09/2016) of the Deliverable 6.1 document: "Design of computational architecture of software modules" (http://bit.ly/MuGD6_1). It extends the above document with the aim to provide a simple programming paradigm to develop tools for the MuG VRE.

The main goals that this proposal aims to achieve are:

  1. Achieve horizontal interoperability by defining a "Tool" as a specific functionality with precise inputs and outputs, which must both comply with the Data Management Plan (DMP). Tools are implemented as a thin wrappers over existing software, in order to facilitate integrating existing tools in the VRE.

  2. Achieve vertical interoperability by using COMPSs, and allowing developers to specify the execution enviroment requirements for each tool by using COMPSs "constraints" decorator.

  3. Provide a unified, simple paradigm to access the diverse data storage facilities defined in the DMP, by wrapping data in Python objects (see "Resource" below) that implement a common API that abstracts the details of data retrieval; this also makes changes in the DMP transparent to the tools.

  4. Simplify the construction of workflows, by conceiving tools such that it is straightforward to combine them in workflows, using COMPSs "task" decorator and the COMPSs runtime as the workflow scheduler.

Implementation overview

  1. Tool: Is the top-level wrapper for tools within the VRE; each tool is defined by its input and output formats, and by its specific requirements on the execution environment. Tools should implement a "run" method, that defines operations needed to get from input to output. The "run" method calls other methods which are decorated using PyCOMPSs "@task" and "@constraints", allowing tool developers to define the workflow and execution environment.

  2. App: Is the main entry point to the tools layer of the VRE; it deals with heterogeneity in the way Tools are run, in terms of filesystem access, runtime environment, error reporting, and more. Therefore, Apps are compatible with all Tools. Apps implement a "launch" method, which prepares and runs a single instance of Tool. The "apps" module provides some example Apps for straightforward cases:

    • LocalApp: uses the MuG DMP API to retrieve file names that are assumed to be locally accessible;

    • PyCOMPSsApp: specific for Tools using PyCOMPSs;

    • WorkflowApp: inherits from both of the above, and implements the ability to unstage intermediate outputs.

  3. mug_datatypes: A repository of all data types available in MuG; it should closely mirror the contents of the DMP.

  4. mug_conversion: A library containing commodity functions to perform frequently needed conversion operations to and from the formats defined in the DMP. Tool developers can also implement their own conversion operations when missing from this library.

  5. Error handling: as a first attempt, the Tool catches all pertinent exceptions, while others not related to the Tool should not be caught. The Tool also takes care of attaching error information to the output resource.

See the documentation for the classes for more information.

Examples

The "examples" module contains usage examples.

The "summer.py" example implements a workflow using PyCOMPSs.