[ome-users] OMERO with iRODS?

[Harri Jäälinoja]

Hi Josh and others,

> Does iRODS have facilities for monitoring file access times and taking actions based on them? 

yes, seems so. The attributes that are stored in the iRODS database 
include timestamps for modification and creation, and I assume it is 
possible to use those for querying:
https://www.irods.org/index.php/icatAttributes

It is possible to create delayed or repeated rules, there is a server 
process that checks every two minutes if there is something to do. So 
one could run a job every day to move old files to another location for 
example.


> From the OMERO point-of-view, this sounds very straight-forward. The only issue I can think of off-hand is that OMERO.fs would have to handle the read-only status. I've added a story for this: http://trac.openmicroscopy.org.uk/omero/ticket/3162
> 
Thanks. This is my setup so far:

1. host1 (university general purpose server)
- iRODS main server, with iCAT database

2. host2 (Centos virtual server running in VMWare)
- OMERO
-- still need to enable OMERO.fs
- iRODS server 2, no database.
-- cannot connect to host1 iRODS, have to figure out why

Once I get host2 set up, I can start learning iRODS controls with some 
simple tests.

> This is certainly a much larger undertaking, and could possibly involve making Bio-Formats iRODS-aware (just glancing at Jargon -- it does provide a RandomAccessFile interface, so the necessary modifications may be limited). Perhaps there's a way using callbacks to do the reverse of dropbox? i.e. OMERO writes out to a location, and then iRODS takes control of that location on receiving notification?
> 
I think it might be possible to accomplish the reverse drop-box with 
either FUSE (Linux) or WebDAV (Windows, Linux, Mac):
https://www.irods.org/index.php/iRODS_FUSE
https://projects.arcs.org.au/trac/davis

It seems those will provide an area iRODS is aware of, or a drop-box 
into iRODS. I am not sure about this, though. For example, I was 
explained that WebDAV doesn't really make a folder where you can write, 
but rather just a GUI like WinSCP. I don't know about FUSE yet.

> That's of course difficult for everyone involved to say. When you've got both systems running, perhaps we could start with a very simple test, like opening a file stored in iRODS via Bio-Formats and converting it to OME-TIFF in iRODS. That would let us know if there are any barriers to moving forward.
> 
Making the conversion to OME-TIFF in iRODS requires some coding, the 
operation should be wrapped into a "microservice": 
https://www.irods.org/index.php/Micro-Services

Microservices are written in C. So we couldn't access the Bio-Formats 
C++ bindings from there. Maybe just use a system() call to run B-F?

I will let you know when I make progress.

Cheers,
Harri

>> Hoping to hear your comments!
>>
>> Best regards,
>> Harri
> 
> Cheers,
> ~Josh.