[ome-devel] Import again...

[Curtis Rueden]

Hi Stefan,

Regarding the "semantic_type" bug, I reported it a while ago and Doug 
has already fixed it. There is currently another TestImport issue 
currently under investigation, which will hopefully be cleared up soon.

I am nearing completion of VisBio v3.00alpha3. The timing seems good 
because I'll probably end up releasing near the same time as OME v2.2.1. 
My hope is that these two releases will play nicely together again (with 
respect to client-side import).

As for doing command-line client-side imports, VisBio3's code is pretty 
clean for the most part, and writing a small command-line Java 
application to do client-side upload shouldn't be too hard. The file 
pattern detection logic is completely modular 
(loci.visbio.data.FilePattern), as is the data object infrastructure 
(loci.visbio.data.Dataset). The only thing that's not as of alpha2 is 
the actual OME upload code (loci.visbio.ome.OMEManager). But I'll clean 
it up for alpha3, providing an OME upload method for use with external 
applications (if I have time, I may even code a simple command-line 
client-side OME upload tool and include it with the alpha3 release).

The goal from the beginning has been for VisBio to function not only as 
an end-user application, but also as a Java visualization toolkit for 
multidimensional biological image data. Please let me know if you have 
any comments, questions or suggestions.

Cheers,
Curtis

Stefan Frank wrote:

> Hi folks,
>
> we're still struggling with the import of images and are pursuing 
> different paths for importing files - apart from hacking the 
> perl-import-scripts(glad to have put this on josh's list, not mine), I 
> went through the different approaches using the XML-RPC from java: As 
> far as I can see, we have several duplicate Codebases here that do 
> (part of) the Job: We have the TestImport from OME-JAVA, there is the 
> code in Visbio3 that started out with copying TestImport-Code and I 
> even remember to have seen first Steps towards an import from inside 
> Shoola.
>
> On the 
> docs-site(http://www.openmicroscopy.org/system-admin/import.html), 
> there is already a marriage between visbio and the Import-Module 
> announced - what is the state of this marriage? VisBio is pretty cool 
> on the import- side, with a clever way of determining the files that 
> belong together, however, we need a Command-Line-Interface, preferably 
> tweakable via parameters to set the z/time/channel-patterns. We'd like 
> to put this into a cron-job and upload files from a given directory 
> over night. Or is this already possible with Visbio3?!
>
> Is anybody already doing this?! I do not want to add another 
> code-base, but I think refactoring the TestImport.java from OME-JAVA, 
> adding cli to it,  and then taking this together with the 
> VisBio-Classes would do the trick - maybe we can come up with classes 
> that can be used inside Shoola for the import, too?!
>
> cheers
> stefan