Virtual Folder

Last updated 8 months ago

Introduction

"Virtual Folder" provides a unified access mechanism to files stored in a variety of locations including the local file system, and B2DROP and other cloud storage facilities. It is developed in work package WP6 by the West-Life H2020 project, which is running from 2015 to 2018. It provides application level services usable for structural biology use cases and follows the structural biology data lifecycle. Data management work package WP6 build on existing infrastructure for storing and accessing data to create a "Virtual Folder".

Usage

A public installation of the Virtual Folder is available at West-Life portal. Follow User's guide for further details how to use it.

Installation

Virtual Folder can be installed: 1. from source codes 2. from binaries at cernvm-fs 3. from cloud template, contextualized to binaries at cernvm-fs

For all the installation options follow: Installation guide.

Brief installation instruction from source codes

Recommended configuration for private deployment of virtual machine with Virtual Folder:

  • Minimal: 1 CPU, 2 GB RAM, 50GB disk space.

  • Recommended: 4 CPU, 8 GB RAM, 100 GB disk space

  • Desktop, Server OS: Windows (tested on Windows 7, Windows 2012), Linux (tested on Ubuntu 14.04 LTS, Ubuntu 16.04 LTS), VirtualBox 5.1.6+, Vagrant 1.8.6+

  • Cloud OS: OpenNebula, OpenStack, or any other supporting OVA images.

git clone https://github.com/h2020-westlife-eu/west-life-wp6
cd west-life-wp6
vagrant up

The new virtual machine can be accessed via web browser http://[vm.ip.address]:[port]/ By default, http://localhost:8080 Virtual folder provides WEBDAV API at http://[vm.ip.address]:[port]/webdav e.g. http://localhost:8080/webdav

Inside VM, the files of the current working directory of host are mounted into /vagrant and the repositories of virtual folder are accessible at /home/vagrant/work

Integration

The functionality of the Virtual Folder can be integrated into other portal or web application. The recommended method is to link the existing component using cross-document messaging mechanism - e.g. for picking a file from Virtual Folder by using the File Picker component.

Follow Integration guide for further details.

Development

In order to test, contribute to source codes and prepare virtual machine environment with source codes, follow Virtual Machines chapter.

Release Notes

  • 21/06/2018 - new features: Import Settings from another Virtual Folder instance,

    integration with West-Life SSO,

    generate obfuscated public webdav URL in order to prevent full path disclosure,

    added Jupyter notebook option to start instance on local deployment

    updated features: UI - basic UI as SPA with router navigation (#/setting #/filemanager), updated angular.js 1.6.10 used by EBI PDB components.

    Backend installation into standard linux paths - shared data at /srv/virtualfolder/, database at /var/lib/westlife/, configuration /etc/westlife/, logs /var/log/westlife/

  • 14/05/2018 - update docs to new gitbook system - no PDF, updated links.

  • 01/04/2018 - docs moved to westlife-docs repository, docs covering Virtual Folder, Virtual Machines and Repository

  • 28/06/2017 - UI improvement, docs in sync with gitbook and /doc folder in dev-docs branch

  • 23/06/2017 - added support for source code installation/binary installation

  • 01/05/2017 - Added Dataset demo integrates some web PDB components to visualize features of PDB and UniProt entries

  • 01/04/2017 - Added Upload Dir Picker component and updated integration guide

  • 07/03/2017 - public deployment integrated with SSO authentication ARIA at www.structuralbiology.eu

  • 25/11/2016 - Updated vagrant boxes to use uCernVM 2.7.7 bootloader, updated OVA images in https://appdb.egi.eu/store/vappliance/d6.1.virtualfoldervm/vaversion/latest and vagrant boxes, do "vagrant box update", bug fixes, consolidated initial web page and design, fixed/added background services

  • 26/10/2016 - moved VagrantFile to new repository https://github.com/h2020-westlife-eu/wp6-vm, updated base box with uCernVM2.7.4 bootloader for CernVM 4 fixes security bug 'dirty COW' and aufs bug in kernel, https://atlas.hashicorp.com/westlife-eu,

  • tested on Windows 7 64 bit, vagrant 1.8.6 + VirtualBox 5.1.6, vagrant 1.8.1, 1.8.4 + VirtualBox 5.0.26, note vagrant < 1.8.6 requires VirtualBox 5.0.x, doesn't require VirtualBox extension pack, download from https://www.virtualbox.org/wiki/Download_Old_Builds_5_0

  • tested on Ubuntu 14.04 LTS, default vagrant 1.4.3 needs to be updated to 1.8.6), default VirtualBox 4.3.36 works