Hi,
I have come across a problem with how import configurations are
autodetected, and wanted to check with the list whether this is an issue
with my code or a genuine bug in the API.
I am trying to autodetect in my code plugin configs that are suitable
for importing raw data from a given file. I supply a reference to the
file I want to import, open a stream from it, and then call
RawDataFlatFileImporter.isImportable():
//this is the importer plugin
RawDataFlatFileImporter importer =
plugin.newInstance(RawDataFlatFileImporter.class,null, sc, config,
null);
//get a stream from the file
InputStream in = file.getDownloadStream(0);
//check for importability
if (importer.isImportable(in))
{
configs.add(config);
}
Now that returns import configs that definitely do not (and should not)
work. This could be a problem with how I have coded this of course but
more likely I think it is a problem with API since I seem to be getting
the same problem when I try to manually import data into a raw bioassay
and I get a choice of several configs, some of which do not work. The
BASE source uses similar code in this context (I have, in fact, ripped
it off from there.... :-) and it makes me think there is a problem with
the isImportable method.
Please let me know if you think this is a proper bug and I'll file in
the bug tracker system. I am using BASE 2.3.0.
thanks
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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