Hi,
>public class ZipFileImporter extends AbstractPlugin implements
InteractivePlugin, AutoDetectingImporter {
> private static final Set<GuiContext> guiContexts =
> Collections.singleton(new GuiContext(Item.EXPERIMENT,
GuiContext.Type.ITEM));
>
>....then I'll get an import tab created in the Experiment list view which
will let me import the zip file using >my plugin?
That code is correct but to see an import tab you will have to specify that
the plugin is an import plugin .For instance:
public MainType getMainType()
{
return Plugin.MainType.IMPORT;
}
Please, see the plugin examples in base2 source code for more information on
this.
>We're planning to make the Excel plugin available for everyone too BTW,
once it's finished.
Cool, this will be good for the community.
Dominic
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Micha Bayer
Sent: 30 November 2006 09:52
To: BASE ML
Subject: Re: [base] Offline files
That sounds like a hell of a lot more work than what I have done so far....
:-)
My first shot at this has been quite basic and it only creates new
RawBioAssays and a single Experiment that these belong to. It could of
course be extended to do more stuff, but my time allowance for this is
limited and I don't think I'll be able to spend a lot more time on this than
I already have.
I think the upshot of all this discussion has been:
1. people need a batch importer (desperately, in fact), and 2. a plugin is
much better and will (hopefully) be possible
With that in mind, I'll go away and look into turning my stuff into a plugin
now, and when I have got the basic version of that working (i.e. file
upload, RawBioAssay and Experiment creation only, as above) I'll make the
code available to the community somehow and someone else can pick it up from
there if they want to make it fancier. I hope that's okay -- even with no
extra effort from someone else it'll still mean that a hell of a lot of
effort can be saved.
Perhaps the dev team can point me in the right direction initially. My
colleague Iain here is just working on a file importer plugin that handles
Excel files and his code starts off like this:
public class ExcelFileImporter extends AbstractPlugin implements
InteractivePlugin, AutoDetectingImporter {
private static final Set<GuiContext> guiContexts =
Collections.singleton(new GuiContext(Item.RAWBIOASSAY,
GuiContext.Type.ITEM));
So am I right in thinking that if I change this to the following...
public class ZipFileImporter extends AbstractPlugin implements
InteractivePlugin, AutoDetectingImporter {
private static final Set<GuiContext> guiContexts =
Collections.singleton(new GuiContext(Item.EXPERIMENT,
GuiContext.Type.ITEM));
....then I'll get an import tab created in the Experiment list view which
will let me import the zip file using my plugin?
We're planning to make the Excel plugin available for everyone too BTW, once
it's finished.
Cheers
Micha
==================================
Dr Micha M Bayer
Bioinformatics Specialist
Genetics Programme
The Scottish Crop Research Institute
Invergowrie
Dundee
DD2 5DA
Scotland, UK
Telephone +44(0)1382 562731 ext. 2309
Fax +44(0)1382 562426
http://www.scri.sari.ac.uk/MichaBayer.htm
=============================
> -----Original Message-----
> From: [EMAIL PROTECTED] [mailto:basedb-users-
> [EMAIL PROTECTED] On Behalf Of Bob MacCallum
> Sent: 29 November 2006 18:36
> To: BASE ML
> Subject: Re: [base] Offline files
>
>
> It looks like I let the cat out of the bag on this one...
>
> Some discussion among the community would be good to establish what we
> want from a bulk loader. For example, I would like all objects
> created and linked, from samples (with annotations) right up to raw
> bioassays (grouped into an experiment as Micha does, ideally).
> Obviously to do this you need to specify the relationships between all
> the samples, annotations, dyes, hybs, data files, but that could
> easily end up being as much work as manually loading the data ;-)
>
> Therefore you have to make compromises; the main one being that you
> treat every sample/extract/etc in exactly the same way (same
> protocols, same amounts, same labels, same array design). This would
> probably work for most people - but let's discuss it anyway...
>
> One issue with the bulk loader I wrote for BASE 1 is that if your
> experiment involves a dye swap for one biological replicate, the bulk
> loader will label each extract with both dyes for *all* replicates
> (leaving you with unused labelled extracts after linking to the hybs).
>
> One quite low cost way to define your experiment for a bulk loader is
> Tab2MAGE (soon to be MAGE-TAB, see
> http://www.biomedcentral.com/1471-2105/7/489/abstract ) - although it
> feels strange to say this because I have been *exporting* Tab2MAGE
> from BASE 1.2 rather than importing it. The input files for our bulk
> loader are specified
> here:
> http://wiki.vectorbase.org/vectorbase/index.php/MicroarrayExperiments
> (look for the example file links) but note that the BASE-specific
> parameters (protocols, raw file parsers, array designs, etc) are
> configured by the user in an interactive process before the upload.
> Our bulk loader is also 2-channel only...
>
> I have a feeling that the Tab2MAGE parser could be adapted into a BASE
> 2 bulk loader somehow, although I think all Tab2MAGE code is Perl.
>
> I think MAGE-TAB is something we could get the average bench scientist
> to provide (with a little help MGEDifying the annotations). So far
> every experiment I have loaded has come with some kind of spreadsheet
> (each one in a different format of course), so the leap to MAGE-TAB is
> not so great.
>
> Ok, enough from me...
>
>
>
>
> Micha Bayer writes:
> >
> >
> > > -----Original Message-----
> > > From: [EMAIL PROTECTED] [mailto:basedb-
> users-
> > > [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg > >
> Sent: 29 November 2006 14:40 > > To: BASE ML > > Subject: Re: [base]
> Offline files > > > > Jari Häkkinen wrote:
> > > > Hi all,
> > > >
> > > > Just a thought, I think the best choice to trigger a large
> import like > > > this is to create a plug-in instead of adding extra
> tabs to the file > > > browser. The plug-in should start by
> requesting the zip file/directory > > > to import. If the zip file is
> not already uploaded the user will have an > > > opportunity to
> upload it. After choosing the zip file/directory the > > > plug-in
> could start its import and creation of necessary items.
> > > >
> > > > The above is fairly straightforward already today and the new
> code would > > > start at import/creation of necessary items.
> > > >
> > > > This will yield very little (or no) changes to the core and the
> plug-in > > > should probably be started from the experiment listing
> page. This will > > > of course change the experiment list jsp (a
> import tab is needed).
> > >
> > > No change is needed to the jsp. The new plugin will be detected
> and an > > "Import" button will appear.
> > >
> > > /Nicklas
> >
> > So what interface would I have to implement for this to happen, if
> I were to turn my code into a plugin?
> >
> > If it's not too much work I might consider doing this, that would
> be much better.
> >
> > Cheers
> >
> > Micha
> >
> > ==================================
> > Dr Micha M Bayer
> > Bioinformatics Specialist
> > Genetics Programme
> > The Scottish Crop Research Institute > Invergowrie > Dundee >
> DD2 5DA > Scotland, UK > Telephone +44(0)1382 562731 ext. 2309 >
> Fax +44(0)1382 562426 > http://www.scri.sari.ac.uk/MichaBayer.htm
> > =============================
> >
> >
> >
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> --
> Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
> Division of Cell and Molecular Biology | Imperial College London |
> Phone +442075941945 | Email [EMAIL PROTECTED]
>
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