[ome-users] Custom annotations absent in exported metadata

[Graham Klyne]

Ilya,

Thanks for this... all useful.

I'm about to take a 3-week break, but when I get back tackling this 
custom export of XML is top of my agenda, since we need it soon, and it 
it relates to some ther ideas we have.

Unfortunately, I'm not a great fan of Perl, being more of a Python 
and/or functional programming person myself.  So I would aim to keep my 
code involvement to the level of customizing/adapting existing 
scripts/modules rather than getting deep into the system.  But from your 
descriptions that's all that is needed, so that should be OK.

#g
--

Ilya Goldberg wrote:
> 
> On Aug 5, 2005, at 9:04 AM, Graham Klyne wrote:
> 
>> Ilya Goldberg wrote:
>>
>>> On Aug 4, 2005, at 6:52 AM, Graham Klyne wrote:
>>
>>
>> Although I've been trying to avoid getting into the OME code so far, 
>> this is an area where I feel that it would be reasonable to dig in to 
>> get the output we want.  For our purposes, a one-off specification of 
>> what needs to be exported would be fine (even best), and I don't think 
>> we really need a UI to control the details.
> 
> 
> Unfortunately, this is the state of OME development.  If you want custom 
> solutions often times that means writing custom code.  Obviously not 
> ideal, and we've been trying to do things in a way that would cover most 
> bases for most users.  Combined with trying very hard to make the code 
> easy to use if the only option is to modify code.
> 
>>
>> I assume I can create a new perl module in the appropriate CGI 
>> directory, and subsequently access the required data simply by using 
>> an appropriately constructed URI?
>>
>> The following information would help:
>> - is there a sample module that does something close to this?  The 
>> current export module described in your other message sounds as if it 
>> could be copied and adapted.
> 
> 
> The best place to start is definitely the current XML Export module: 
> src/perl2/OME/Web/XMLFileExport.pm
> The entire web UI is done using sub-classes of OME::Web (in 
> src/perl2/OME/Web.pm and the src/perl2/OME/Web/ directory tree)
> I would follow the same inheritance pattern and simply make a new class 
> similar to XMLFileExport - there's really no point to subclassing this 
> since its just an HTML interface for 
> src/perl2/OME/Tasks/OMEXMLImportExport.pm.  This 
> OME::Tasks::OMEXMLImportExport class performs the logic of gathering the 
> objects to export.  The export itself is performed by 
> OME::Tasks::OMEExport, which is the generalized exporter.
> 
> Since OMEXMLImportExport.pm just gathers objects and calls 
> OME::Tasks::OMEExport, the thing to do is copy the 
> OMEXMLImportExport->exportToXMLFile() method to your new class and 
> modify it to look for additional objects using a OME::Factory call 
> documented here:
> http://openmicroscopy.org/APIdocs/OME/Factory.html
> 
> 
>> - what would I need to tweak to get a link to this external export 
>> format placed on the image information page?  (Maybe HTML templates 
>> will be the best answer for this?)
> 
> 
> I'm guessing you want to set up your OME::Web::XMLFileExport variant to 
> export an image using a URL param with an Image ID.
> 
> We're about to send an announcement about the customized templates thing 
> (stay tuned).  You should be able to easily include a link to your 
> customized exporter from there.  You'll also be glad to know that your 
> request to allow changing the order of items in the annotation form is 
> specifically treated in the example of template customization.  
> Actually, so is introducing a hyperlink using one of the image 
> annotations (you'd just be using the ImageID in the template instead of 
> a categorization value to generate your export URL).
> 
> If you don't want to get into custom templates (though we'd appreciate 
> any feedback if you give it a whirl), you can modify the image detail 
> template here:
> src/html/Templates/Display/One/OME/Image/detail.tmpl
> Or, if you're using the 2.4.0 tar-ball, here:
> src/html/Templates/OME_Image_detail.tmpl
> 
> -Ilya
> 
> 
>>
>> #g
>>
>> -- 
>> Graham Klyne
>> Image Bioinformatics Research Group (http://www.bioimage.org/)
>> Department of Zoology, University of Oxford
>> South Parks Road, Oxford OX1 3PS, UK
>> E-mail: <Graham.Klyne at zoo.ox.ac.uk>
>> Direct phone: +44-(0)1865-281991
>> Departmental fax: +44-(0)1865-310447
>>
> 

-- 
Graham Klyne
Image Bioinformatics Research Group (http://www.bioimage.org/)
Department of Zoology, University of Oxford
South Parks Road, Oxford OX1 3PS, UK
E-mail: <Graham.Klyne at zoo.ox.ac.uk>
Direct phone: +44-(0)1865-281991
Departmental fax: +44-(0)1865-310447