[ome-devel] OMERO Importer / Bio-Formats / BD Pathway

[Chris Allan]

On 7 Jan 2010, at 15:00, Garbett, Shawn P wrote:

>> On 6 Jan 2010, at 17:24, Shawn Garbett wrote:
>>> I have submitted a rudimentary importer for a BD Pathway (main
>>> feature lacking is proper z-stack support) to the Bio-Formats
>>> project for the 4.2 release. I need to use this in OMERO Importer as
>>> a demo. I did the naive approach and just switch the bio-formats jar
>>> to the ones I'd built. The first problem I encountered was I can't
>>> select the "experiment.exp" file from OMERO Importer.
>>>
>>> How can I get OMERO Importer to recognize loading this file?
>
> On Thursday, January 07, 2010 8:40 AM, Chris Allan wrote:
>> I assume you have add a reader and modified readers.txt?
>
> Yes. But as always, I will double check this. I think it's something  
> in the OMERO importer GUI that is only allowing certain extensions.  
> I found a "file filter" stack that had a list of the ones that it  
> allows in the importer code. I'm going to fiddle with that.

The importer has its own version of readers.txt in order to filter out  
some file formats that do not make sense in the context of OMERO as a  
system. You'll need to replace the readers.txt in OmeroImporter.jar if  
you've added a new reader. It's path is "ome/formats/importer/ 
importer_readers.txt".

>
>>>
>>> I've also tried building my own version of OMERO and had no luck.
>>> That was in a previous email. The only suggestion I got was I had an
>>> older version of python.
>>
>> Just looking back at the ome-devel history, it appears that Josh had
>> some questions for you. Did you discuss this offline with him? Do you
>> have more details on your environment to give us?
>
> Josh and I emailed back and forth, and he suggested it was my Python  
> version. I installed Snow Leopard figuring it would update some of  
> these core libraries/interpreters on the box, and made a second try.  
> It worked like a charm after that.

Great.

>
> Shawn

-Chris