Re: [base] Files with FTP locations only

[Bob M. <r.m...@im...>]

Thanks Nicklas,
Sorry I hadn't seen the existing functionality - we will check it all out
and get back to you soon!



On Tue, Jun 24, 2014 at 12:42 PM, Nicklas Nordborg <
nic...@me...> wrote:

> 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...
>
> /Nicklas
>
>
>
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