On 2014-06-24 11:55, Bob MacCallum wrote:
> Hi Nicklas et al,
> Getting up to speed with BASE3 and NGS - so far all seems good - even
> upgrading our own API code has gone smoother than I expected.  Thanks!

Great to hear that it is going well.

> A possible feature request for general discussion:
> Would it be possible to have "placeholder" files in the BASE file system
> which weren't on disk but had an FTP location stored in the DB?   It
> would be a bit like the current "offline" option but for our use case
> (fastq and BAM files stored elsewhere and never processed by BASE3 or
> plugins) we would never even upload the files in the first place (I
> can't find a way to create a file that is offline from the start).
> The debate for other users/devs would be: should BASE automatically
> retrieve the files when needed?  I say no need for that - treat them
> like offline files are currently (if I understand correctly how offline
> files work).

There is already the *external files* feature. It can accessed with "New 
URL" in the BASE file manager. It's not the same as an *offline* file 
since by default BASE will try to check if it exists and download some 
metadata (such as size and modification date). And BASE will also 
retrieve the file if is requested by a plug-in or a user tries to 
download or view it.

The external files feature is "pluggable" and the BASE core only provide 
support for files that can be accessed with http or https. In theory it 
is possible to register unsupported URLs (eg. ftp://...) but I guess 
error messages will popup here and there.

As it happens, we discussed a similar problem last week. Up until now, 
our approach has been to simply store the file path as an annotation on 
bioassay items. In the future we'll need to provide access for external 
researchers to our data, but we really don't want to have them on our 
internal file servers so the idea is to let BASE act as a proxy.

So, I am currently working on an extension that add support for 
accessing external files via FTP, FTPS and SFTP (see 
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles). I might be 
able to release a first version later this week if you want to try it.

If you prefer the *offline* files feature there is unfortunately no 
support in the GUI for creating offline files without first uploading 
them. A possible solution would be to modify the "New URL" dialog to 
make the "URL" field optional, and use this to decide between 
offline/external file.

If you have any other ideas please let me know...


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