I think this most likely is a problem with too unspecific regular
expression in the file format configurations. The isImportable() method
will only scan the file until it finds a line which matches the "Data
header" regular expression. The rest of the file is not checked.
/Nicklas
Micha Bayer wrote:
> 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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