This library implements the specifications of a new tool in the openVRE enviroment. It provides a simple programming paradigm to develop tools for the VRE.
The main goals that this proposal aims to achieve are:
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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.
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Achieve vertical interoperability by using PyCOMPSs, and allowing developers to specify the execution enviroment requirements for each tool by using PyCOMPSs "constraints" decorator. Although written with task-based programming in mind, this library allows execution of Tools outside of the COMPSs runtime.
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Simplify the construction of workflows, by conceiving tools such that it is straightforward to combine them in Workflows; in particular by using PyCOMPSs "task" decorator and the PyCOMPSs runtime as the workflow scheduler.
The 'basic_modules' contains the basic entities of openvre-tool-api:
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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. See also Workflow.
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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:
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LocalApp: assumes files to be locally accessible;
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PyCOMPSsApp: specific for Tools using PyCOMPSs;
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WorkflowApp: inherits from both of the above, and implements the ability to run Workflows.
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JSONApp: inherits from WorkflowApp, and implements the ability to read run configuration from JSON files, and write results in a JSON file; JSON formats used are those provided, and accepted, by the VRE.
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Metadata: Class that contains extra information about files.
The 'utils' module contains useful functions for performing common tasks in Tool execution. In particular it contains 'logger', the logging facility of openvre-tool-api; it provides a unified way of sending messages to the VRE.
See the documentation for the classes for more information.
Directly from GitHub:
pip install git+https://github.com/inab/openvre-tool-api.gitThe repository vre_sample_tool showcase the functionalities of this wrapper by implementing a simple application. It consists on a CWL tool execution.