wtsi-hgi/iquestFuse

Name: iquestFuse

Owner: Wellcome Trust Sanger Institute - Human Genetics Informatics

Description: iquest-like iRODS FUSE client (allows navigation of metadata via a virtual POSIX filesystem)

Created: 2014-06-19 15:08:17.0

Updated: 2014-06-19 19:37:11.0

Pushed: 2014-06-19 19:20:23.0

Homepage: null

Size: 192

Language: C

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README

iquestFuse

A Filesystem in USErspace (FUSE) filesystem to view data objects in an iRODS zone based on queries, in a manner similar to that provided by the iRODS i-command “iquest” (question (query)) utility.

Usage

unt
r mountpoint
st_fuse mountpoint

mount
rmount -u mountpoint 

To debug, you can mount with the iquestFuse client in the foreground using the -d option.

st_fuse -d mountpoint

Make sure you have authenticated to iRODS (e.g. using iinit or kinit) before running iquest_fuse or you will get an error.

Also make sure you have a working iRODS user environment file, either in ~/.irodsEnv or in a file referenced by the irodsEnvFile environment variable.

If you run iquest_fuse as above with no other options, it will mount the collection specified as irodsHome in your environment file. To mount with a different base directory, use the -c option.

For example, to mount the root collection, use:

st_fuse mountpoint -c /

After mounting a collection, you should be able to access the collection as you would with the standard irodsFs client. In addition, in each collection there is a special virtual directory created (by default named Q, but you can change this using the -i option to iquest_fuse) which you can use to perform a metadata search. This directory will not appear in directory listings by default (because it would be a disaster if one were to run a directory traversal (such as find) on it.

The virtual Q directory contains a list of all available metadata keys (including attributes and user AVUs), which are also indicated as virtual directories. Inside those virtual directories is another set of directories which are the available values. Inside each of those directories you should find all of the data objects and collections that match the query.

Prerequisites

iRODS - tested and working with 3.1

FUSE (http://fuse.sourceforge.net/) - tested with 2.9.3

Compiling

This directory should be placed within the source tree of an iRODS source distribution which has been configured and compiled.

iquestFuse should then be compiled, passing the location of a FUSE installation as the fuseHomeDir variable.

nfigure and compile iRODS
RODS
ripts/configure

eckout iquestFuse under clients/
lients
clone https://github.com/wtsi-hgi/iquestFuse.git
mpile iquestFuse
questFuse
 fuseHomeDir=/path/to/fuse-2.9.3

Notes

1. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads 'Copyright (c) 2005, 2007- 2009, 2011-2012' should be interpreted as being identical to a statement that reads 'Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012' and a copyright statement that reads “Copyright (c) 2005-2012' should be interpreted as being identical to a statement that reads 'Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012'.”