[ome-devel] new file formats

[Ilya Goldberg]

Hi Bernd
The command for command-line importing is
ome import
You can get help by saying
ome help import

You can register a new importer by adding your class (module name) to 
the list in the configuration table
psql ome
ome=# select value from configuration where name = 'import_formats';
then,
update configuration set value = '..... My::Module' where name = 
'import_formats';
where ..... is what was there before, and My::Module is your new 
importer.  Or, put it somewhere else in the list, like before the 
generic TIFF importer if your files are TIFF-based.  The importers are 
executed in sequence to "claim" a particular file.
The better way is to modify the $IMPORT_FORMATS variable at the top of 
OME/Install/CoreDatabaseTablesTask.pm to include your module.
Don't worry about running the installer again - it will not wipe out 
your database.  You have to dropdb yourself if you want a clean 
install.  If it finds an OME DB, it will simply update it.  Once you've 
run through the installer successfully, subsequent runnings are 
trouble-free.

Yes, the files are presented to the importers as objects of the 
OME::Image::Server::File class.  For whatever reason (I really have no 
idea why), the path part of the file is not preserved.  This is a 
relatively straight forward fix with few side-effects (I think), and I 
can look into it for you.

Since in your case, it appears that directory structure is actually 
used to store information about your files, you will need to have 
access to the file path to fully reconstruct all the info.  Is the 
information you need really only stored in the directory structure?  We 
just haven't run into this before, hence the "bug" in our File class 
wasn't fixed.  Can you please register a bug in Bugzilla so you and I 
can keep track?

If you can provide a brief explanation of what the directory structure 
actually is, that would help too.
Thanks
Ilya



On Sep 23, 2005, at 8:55 AM, Bernd Jagla wrote:

> Hello again,
>
> I just found out that the files that the method getGroups receives are 
> of
> type Ome::image::server::file. Unfortunately I couldn't find any 
> information
> on the path. Also, if I select a path as an import file neither the 
> path
> itself nor the files underneath are being used.
>
> Is there any way to get the path of an input file and the paths within 
> that
> directory plus the files in a directory underneath?
>
> Thanks,
>
> Bernd
>
> |-----Original Message-----
> |From: ome-devel-bounces at lists.openmicroscopy.org.uk [mailto:ome-devel-
> |bounces at lists.openmicroscopy.org.uk] On Behalf Of Bernd Jagla
> |Sent: Thursday, September 22, 2005 2:12 PM
> |To: ome-devel at lists.openmicroscopy.org.uk
> |Subject: RE: [ome-devel] new file formats
> |
> |Hello,
> |
> |I found one answer:
> |In the tests directory there is the ForkedImageImport.pl program with 
> which
> |I can test my import functions.
> |
> |And I want to reformulate one other question, which I guess is more a 
> Perl
> |than an OME question:
> |I need to get all the directories in the directory of the ".run" file 
> that
> |I
> |am reading in. For this, I thought to find first the path to the run 
> file,
> |and then list all directories underneath. Unfortunately I don't know 
> how to
> |do this. Any help is very much appreciated...
> |
> |Do I have to insert a line to CoreDatabaseTablesTask.pm for my new 
> module
> |in
> |order to register? And is this all, or do I have to reinstall after???
> |
> |I know this information is somewhere but I am having a hard time 
> finding
> |all
> |the bits and peaces....
> |
> |Thanks again for your kind understanding and help
> |
> |Bernd
> |
> ||-----Original Message-----
> ||From: ome-devel-bounces at lists.openmicroscopy.org.uk 
> [mailto:ome-devel-
> ||bounces at lists.openmicroscopy.org.uk] On Behalf Of Bernd Jagla
> ||Sent: Thursday, September 22, 2005 11:52 AM
> ||To: ome-devel at lists.openmicroscopy.org.uk
> ||Subject: [ome-devel] new file formats
> ||
> ||Hello,
> ||
> ||Sorry for posting this twice, but I guess it is better to put it in 
> the
> |dev
> ||list...
> ||
> ||And I have one more question:
> ||The ImportEngine is using a variable $filenames, that I believe is a
> ||IO:File
> ||object ???, but I don't understand why in the MetamorphHTDFormat.pm 
> (line
> ||100) a method getFilename can be called, since I can't find this 
> method
> ||anywhere in IO:File or any inherited package (IO:Handle, IOSeekable).
> ||
> ||Thanks, and here is my e-mail from yesterday...
> ||
> |||Hello again,
> |||
> |||Long time no hear, but I haven't forgotten about my little project 
> of
> |||importing INCell files into OME, it's just that it is hard find the 
> time
> ||to
> |||work on it...
> |||
> |||Anyway, I think by now I understood a little bit the
> |MetamorphHTDFormat.pm
> |||module and wanted to program my own version for the .run and .frm
> |files...
> |||How would I go about this?
> |||	I want to test the module not through the web-page but rather
> |||through the command line. But I don't know how I could do it! Can 
> you
> ||please
> |||give me an example?
> |||
> |||	How do I register the module in OME without reinstalling?
> |||
> |||Thanks a lot for your kind help.
> |||
> |||Best
> |||
> |||Bernd
> |||
> ||
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