Re: [base] file storage system question

2006-11-08 Thread Nicklas Nordborg
Keith Ching wrote: > it seems you can make a String annotation type and attach it to raw > bioassay and fill it with > > > src="/base2/images/download.gif"> > > which will produce a link to the specified raw file. Wow, that's a bug, HTML tags should be escaped. Besides, it won't work anyway,

Re: [base] file storage system question

2006-11-08 Thread Keith Ching
it seems you can make a String annotation type and attach it to raw bioassay and fill it with which will produce a link to the specified raw file. Keith Ching wrote: > is there a way to link the original source file to the raw bioassay into > which it was imported? say i have an experiment

Re: [base] how to import reporters ?

2006-11-08 Thread Jari Häkkinen
The reporter import button does appear because there is no plug-in configured for import of reporters. You need to create a configuration for the "Reporter importer" plug-in. We have compiled a getting started document that outlines the first steps with BASE 2, http://base.thep.lu.se/chrome/sit

Re: [base] how to import reporters ?

2006-11-08 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: >> As I wrote in the previous mail: >>The columns are numbered from 0 so the >>file we have been testing on the "Rgn R²" column should be column >>number 32 and the mapping to use \32\. >> >> I counted twice, but of course you should check that it is correct. >

[base] how to import reporters ?

2006-11-08 Thread Emmanuel Courcelle
> As I wrote in the previous mail: >The columns are numbered from 0 so the >file we have been testing on the "Rgn R²" column should be column >number 32 and the mapping to use \32\. > > I counted twice, but of course you should check that it is correct. > > Sorry, you're right > You

Re: [base] BASE 2 API: creating subdirectories in users' home directories

2006-11-08 Thread Nicklas Nordborg
Micha Bayer wrote: > Directory subDir = Directory.getNew(dc,dataDir); > String fileName = uploadedFile.getFilename(); > String fileNameNoExt = fileName.substring(0, fileName.indexOf(".")); > subDir.setName(fileNameNoExt); > subDir.checkPermission(Permission.CREATE); Remove t

[base] BASE 2 API: creating subdirectories in users' home directories

2006-11-08 Thread Micha Bayer
Hi again, Sorry for the barrage of messages from me recently but it's obviously early days for BASE 2 and whenever I have got stuck recently there hasn't been any existing messages to fall back on. I guess this will improve over time I am trying to write some code to do a combined zip file up

[base] comment on ticket 334 Project default items

2006-11-08 Thread Keith Ching
when entering in a lot of arrays performed on some date in the past, you have to change the creation date of the sample, extract, labeled extract, hybridization, etc.. for each one from the default creation date. i could enter them faster if i could set the default date once somewhere. thanks,

[base] file storage system question

2006-11-08 Thread Keith Ching
is there a way to link the original source file to the raw bioassay into which it was imported? say i have an experiment which contains 20 raw bioassays. what would be the best way to be able to list / retrieve the original data files that were used to create the raw bioassays? on another note,

Re: [base] Plugin configuration (still some pb)

2006-11-08 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: > >> file we have been testing on the "Rgn R²" column should be column number >> 32 and the mapping to use \32\. >> > hum... rather 33, I think (it was 33 in Base 1.2). > Does the column numbers start at 0 or at 1 ? As I wrote in the previous mail: The columns a

[base] Plugin configuration (still some pb)

2006-11-08 Thread Emmanuel Courcelle
file we have been testing on the "Rgn R²" column should be column number 32 and the mapping to use \32\. hum... rather 33, I think (it was 33 in Base 1.2). Does the column numbers start at 0 or at 1 ? If they start at 1 it is 33 Sorry to bother you, but  I still have a problem (not