There is a possibility to get access to the subversion repository and
trac environment just for this kind of stuff. Check out
http://baseplugins.thep.lu.se Trac environment allows for discussions
about the importer through the ticketing system.
Jari
Micha Bayer wrote:
> 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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--
Jari Häkkinen, PhD
Complex Systems Division mailto:[EMAIL PROTECTED]
Department of Theoretical Physics phone: +46 (0)46 2229347
Lund University fax: +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se
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