roverlay

Overlay Research Object service

Author: Graham Klyne ([email protected])

The Overlay Research Object service is a web server that provides an easy, lightweight way to create Research Objects, primarily so that RO-based services can be used with arbitrary linked data.

The software consists of two components:

1. A Django-based web apoplication that provides a simple HTTP API for creating, deleting and accessing Overlay Research Objects.

2. A simple command-line tool, roverlay to provide access to the web service from a command shell, or from a shell script.

See https://github.com/wf4ever/ro-manager/blob/master/src/roverlay/roverlay.md for more details.

Installation and deployment

Dependencies

• Python 2.7.x
• Linux/Unix type system. This software has not been tested under Windows, but may work.
• Python pip utility
• git command line tool (depending on the installation option used).
• Commands are tested to run in a bash shell environment.
• The Overlay RO web service uses the Django web development framework, installation of which is covered below. The software has been developed and tested with Django version 1.5.1, but will hopefully also work with later releases.
• Various other Python packages that are located and installed by the pip and setup.py utilities.

Installation overview

Installation instructions assume a terminal interface and a bash command shell.

The first step for installing the checklist service is to install RO Manager. Then some additional supporting code needs to be installed, and the web service deployed and activated.

In the instructions that follow:

• software is the name of a directory where the Python virtual enviroment will be installed.
• pyenv is the name of python virtual environmewnt used. This is also used to name a subdirectory of software that holds the virtual environment files.
• workspace is the name of a workspace directory where the RO Manager software is copied.

RO Mananger

This is just a summary of the RO Manager installation. More detailed explanations can be found in https://github.com/wf4ever/ro-manager/blob/master/src/README.md. Installing RO Manager is sufficient to install the roverlay command line client.

The installation method suggested here uses git to pull the software from Github rather than installation from PyPI using pip. Either can be used, but with the suggested approach, it is easier to locate the Django utilities used to start the web service, the service log file, etc.

If not already existing, create the new virtual environment:

cd _software_
pip install virtualenv
virtualenv _pyenv_

Once created, activate this environment (using name of enviroment used in the original virtualenv command):

source _pyenv_/bin/activate

Install the RO Manager software package from github:

cd _workspace_
git clone https://github.com/wf4ever/ro-manager.git ro-manager
cd ro-manager/src
python setup.py build
python setup.py install
ro-manager-test

Overlay RO web service instalation and deploymemt

These are quick-start instructions, assuming that the RO Manager source package has been extracted into directory _workspace_. More details about the installation process are in https://github.com/wf4ever/ro-manager/blob/master/src/README.md.

First, ensure that the appropriate Python virtual environment is active; e.g.

source _pyenv_/bin/activate

The checklist evaluation service uses the Pyramid web application development framework (http://www.pylonsproject.org), which is installed thus:

pip install django

To activate the checklist web service, go to the RO Manager source directory and issue the command shown:

cd _workspace_/ro-manager/src/roverlay/rovweb
mkdir db
python manage.py syncdb
python manage.py runserver 0.0.0.0:8000

At this point, the Overlay RO service should to ready to receive HTTP requests on port 8000. Try starting a browser on the local machine, and displaying the page at http://localhost:8000 to confirm this.

Testing the deployed service

Switch to a new terminal session and activate the Python virtual environment into which RO Manager was installed. Should be able to run the command:

roverlay --help

A summary of usage options is displayed. Twy the following:

$ roverlay res1 res2 res3
http://localhost:8000/rovserver/ROs/127544b3/
$ roverlay -l
http://localhost:8000/rovserver/ROs/127544b3/
$ ro list http://localhost:8000/rovserver/ROs/127544b3/
file:///usr/workspace/wf4ever-ro-manager/src/roverlay/res1
file:///usr/workspace/wf4ever-ro-manager/src/roverlay/res2
file:///usr/workspace/wf4ever-ro-manager/src/roverlay/res3
$ roverlay -d http://localhost:8000/rovserver/ROs/127544b3/
RO http://localhost:8000/rovserver/ROs/127544b3/ deleted.
$ ro list http://localhost:8000/rovserver/ROs/127544b3/
Can't access RO manifest (404 NOT FOUND) for srsuri http://localhost:8000/rovserver/ROs/127544b3/
$ roverlay -l
$

Again, more details are at https://github.com/wf4ever/ro-manager/blob/master/src/README.md.

Related Publications

• Jun Zhao, Graham Klyne, Piotr Holubowicz, Raúl Palma, Stian Soiland-Reyes, Kristina Hettne, José Enrique Ruiz, Marco Roos, Kevin Page, José Manuel Gómez-Pérez, David De Roure, Carole Goble. RO-Manager: A Tool for Creating and Manipulating Research Objects to Support Reproducibility and Reuse in Sciences. The Second Linked Science Workshop at ISWC Boston, USA November, 2012
• Kevin Page, Raúl Palma, Piotr Holubowicz, Graham Klyne, Stian Soiland-Reyes, Don Cruickshank, Rafael González Cabero, Esteban García, David De Roure Cuesta, Jun Zhao, José Manuel Gómez-Pérez. From workflows to Research Objects: an architecture for preserving the semantics of science. The Second Linked Science Workshop at ISWC Boston, USA November, 2012

Acknowledgement

This software has been developed by University of Oxford as part of the Wf4Ever project.

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This work is licensed under a Creative Commons Attribution 2.0 UK: England & Wales License.