Hi Micha,
i would love to see how you accomplished this. after having put in over
100 RawBioAssays plus affiliated
biosources, samples, extracts, labeled extracts, hybridizations, and
scans by hand.. i am strongly
motivated to program an automated solution.
-keith
Micha Bayer wrote:
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:basedb-users-
[EMAIL PROTECTED] On Behalf Of Bob MacCallum
Sent: 29 November 2006 10:15
To: BASE ML
Subject: Re: [base] Offline files
[...]
At some point, someone will come up with a bulk loader which will
batch/bulk/mass upload files *and* create/annotate/link the data
objects
(I'm
not volunteering, yet...)
I have just finished writing one. The user uploads a zip file, a new
directory is created in the user's raw data directory (with the same
name as the zip file) and the files are then unzipped in there. They are
then imported one by one as new RawBioAssay objects and at the end a new
Experiment is created that has all these hanging off it. At the moment
it only works for non-Affy data though.
To do this I had to hack the BASE source (plugin wasn't possible as far
as I can tell), and I am always reluctant to do that sort of thing
because of versioning/upgrade issues (i.e. having to repeat this every
time a new version is out). I have modified the JSP page that controls
the menus and inserted a new item there, and added a couple of JSP pages
myself that provide the UI for all this.
I did some more detailed testing yesterday and things worked fine but
it's all still pretty raw and probably full of bugs. I am happy to share
the code with others though, or even make it a full contribution to BASE
if people are happy with it (perhaps after it has been gone over by some
of the BASE team). I also think the exception handling needs more work
probably.
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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--
Keith Ching, Ph.D.
Bioinformatics, Laboratory of Gene Regulation
Ludwig Institute for Cancer Research
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