[ome-devel] Questions and proposals

[Chris Allan]

On Thu, Nov 11, 2004 at 11:38:58AM +1100, Richard Beare wrote:
> >
> >Try:
> >ome help admin data delete MEX
> >It is likely to delete more than you thought it would, so be careful,  
> >and try the -n flag first.
> >Only available from CVS so far...
> 
> 
> Thanks,
> so what does MEX actually stand for? I assumed it related to matlab mex 
> files so hadn't checked into it.

MEX in this case is OME specific vocabulary. It shorthand for "module
execution." :)

> 
> >Right now, the only way to enter it is to read an OME format XML 
> >file.   It hasn't been a priority for a user interface because this 
> >kind of  information need only be entered once, and eventually be 
> >entered for  you by the manufacturer (lets hope!).  Subsequent files 
> >(images) will  simply refer to fields in this structure by reference.
> 
> Are there some examples anywhere?

A good place to start would be the "Sample.ome" file in CVS.

http://cvs.openmicroscopy.org.uk/horde/chora/cvs.php/OME-WEBSITE/TestImages/Sample.ome

You can download a copy here:

http://www.openmicroscopy.org/TestImages/

> 
> 
> >CVS has a more generalized mechanism for scanning this type of  
> >information from filenames.  If this information is in a  
> >manufacturer-specific file, you will need to modify one of the 
> >importer  scripts to read this information from this type of file.   
> >Alternatively, this can be done by reading OME XML.  The datatype  
> >(Semantic Type in OME parlance) to contain this information is 
> >defined,  but probably not in a finalized state.  I believe the DKFZ 
> >group is  working on this.
> 
> We are mostly writing imagePro scripts, so we can save this information 
> in any form we like. I'll look into the data type.
> 
> >
> >>Unfortunately the CVS version is in an interim state right now.  It  
> >>works well off with a 'fresh' database (its tested nightly by an  
> >>automated script), but we are in the middle of a transition in how 
> >>we  define categories (from dataset-granularity to 
> >>global-granularity), so  your mileage may vary depending on what day 
> >>you update from CVS.  We  anticipate this to be resolved in the next 
> >>week or so.  Please try a  "latest" version, because a few problems 
> >>like this were corrected  recently.  If they weren't we would like to 
> >>work with you to resolve  them so that they don't come back to bite 
> >>us when we finally do our  next release. 
> >
> 
> I tried to install from scratch but obviously didn't do enough. Is 
> dropping the database, removing the installation (/OME/) heirarchy and 
> the /etc/ome-store file enough to constitute a fresh install? What else 
> is necessary.

That's about all that's required. For a *totally* clean install you'd
have to remove the installed Perl modules as well. I believe you can
still do this potentially dangerous option as follows:

cd src/perl2
make uninstall

> 
> Alternatively, are there cvs tags or branches that allow me to retrieve 
> a "latest" version. I've only seen "stable" and "current" on the web 
> site. I've installed current (as a fresh install if the above is 
> sufficient), but seem to have problems with thumbnails and serving images.
> 

The easiest way to get what's in development (assuming you're
comfortable with CVS) is to checkout the "OME" module. Details on how to
do that are available here:

http://cvs.openmicroscopy.org.uk/

> 
> Thanks again.
> 

Ciao.

-Chris