[ome-users] OMERO with iRODS?

[Curtis Rueden]

Hi Harri,

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?
>

Sure, this is how we integrated Bio-Formats with the original C- and
Perl-driven OME server. The "OMEIS" process (written in C) just invoked a
particular Bio-Formats Java class responsible for parsing the file in
question. This Bio-Formats class then wrote the pixel out to a particular
binary file designated by OMEIS, and dumped the OME-XML metadata to stdout,
which the OME server's perl layer then consumed. Maybe sounds complicated,
but it worked like a charm!

The main thing is to create a Java helper class that behaves the way you
want. You then make a single system call from C to that class.

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
>

Since all you need to do is convert to OME-TIFF, system calls will be just
fine. The main advantage of the C++ bindings is the ability to perform very
granular operations (at the same level as the Java API), which is nice for
some applications.

You might even be able to get away with calling the Bio-Formats "bfconvert"
tool (loci.formats.tools.ImageConverter) without need for your own Java
helper class.

-Curtis

2010/10/22 Harri Jäälinoja <harri.jaalinoja at helsinki.fi>

> 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.
>>
>
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