Hi Nicklas, That's excellent -- well spotted. That has sorted the problem. If I specify the entire header row it no longer picks up unsuitable configs.
What had happened was that I did try initially to specify whole header rows but the file parse test kept on failing so I just went on to specify something short like Block\tRow\tColumn.* (as suggested by the interface, and that worked. What I should have done is kept trying, but I am rubbish at regular expressions (and a lazy git). I have done that now and I have worked out that what stopped the whole header from working was that I didn't escape characters like "+", "(" and ")". These are pretty commonplace in e.g. Genepix file formats. I am copying this to the users list because this is of concern not just for the developers -- apologies for the cross-post. 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-devel- > [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg > Sent: 13 August 2007 07:19 > To: BASE dev > Subject: Re: [basedb-devel] problem with auto detection of raw data import > configurations > > 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 > > ============================= > > > > > > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ _ > > > > SCRI, Invergowrie, Dundee, DD2 5DA. > > The Scottish Crop Research Institute is a charitable company limited by > guarantee. > > Registered in Scotland No: SC 29367. > > Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. > > > > > > DISCLAIMER: > > > > This email is from the Scottish Crop Research Institute, but the views > > expressed by the sender are not necessarily the views of SCRI and its > > subsidiaries. This email and any files transmitted with it are > confidential > > to the intended recipient at the e-mail address to which it has been > > addressed. It may not be disclosed or used by any other than that > addressee. > > If you are not the intended recipient you are requested to preserve this > > confidentiality and you must not use, disclose, copy, print or rely on > this > > e-mail in any way. Please notify [EMAIL PROTECTED] quoting the > > name of the sender and delete the email from your system. > > > > Although SCRI has taken reasonable precautions to ensure no viruses are > > present in this email, neither the Institute nor the sender accepts any > > responsibility for any viruses, and it is your responsibility to scan > the email > > and the attachments (if any). > > > > > > ------------------------------------------------------------------------ > - > > This SF.net email is sponsored by: Splunk Inc. > > Still grepping through log files to find problems? Stop. > > Now Search log events and configuration files using AJAX and a browser. > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > _______________________________________________ > > basedb-devel mailing list > > [EMAIL PROTECTED] > > https://lists.sourceforge.net/lists/listinfo/basedb-devel > > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > basedb-devel mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/basedb-devel ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]