Sanka, Ravi wrote:
> Hi Nate,
>
> Thanks for the response. I have been testing out our installation to see what
> happens when the datasets get cleaned-out of the storage location. One thing
> I noticed is that the dataset disappears from the user's history. He is no
> longer able to view or use the dataset. That would circumvent any error that
> you mentioned, since the user can't find the dataset in the first place.
>
> This would be fine for us, since we don't intend for the datasets to be kept
> indefinitely. That would lead to space issues.
>
> However, the dataset is still referred to in the database in all relevant
> tables. Is there an existing script or tool in the installation that clears
> the database tables of such rows? If so, it would help keep the users'
> histories in sync with the database.
The cleanup script will mark the row as deleted, although not actually
remove them (which is most likely better anyway):
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
--nate
>
> -----------------------------------------------
> Ravi Sanka
> ICS - Bioinformatics Engineer
> J. Craig Venter Institute
> 301-795-7743
> -----------------------------------------------
>
> -----Original Message-----
> From: Nate Coraor [mailto:n...@bx.psu.edu]
> Sent: Wednesday, August 17, 2011 12:52 PM
> To: Sanka, Ravi
> Cc: galaxy-dev@lists.bx.psu.edu; Zhang, Haiyan; Singh, Indresh
> Subject: Re: [galaxy-dev] Galaxy: self-cleaning on file_path
>
> Sanka, Ravi wrote:
> > Hello,
> >
> > We have recently put a local installation of Galaxy on our network and
> > connected it to a MYSQL database. In order to have more space available for
> > uploaded and created files, we also changed the values of file_path and
> > new_file_path in the config file. The file_path field was changed to a
> > larger, communal location. The new_file_path was changed to a directory
> > called "tmp" in that same communal location.
> >
> > This location, however, undergoes self-cleaning; deleting any files that
> > reach 7 days old (and any directories that have no files less than 7 days
> > old). This would include any datasets uploaded or created by Galaxy.
> >
> > Can the Galaxy framework and schema handle this occurrence? Or will it
> > cause errors to occur?
>
> Hi Ravi,
>
> Galaxy won't know that the file has been removed until it tries to access it,
> and when that happens, it will fail whatever operation you are trying to
> perform (view, download, use the dataset as a tool input).
>
> --nate
>
> >
> > -----------------------------------------------
> > Ravi Sanka
> > ICS - Bioinformatics Engineer
> > J. Craig Venter Institute
> > 301-795-7743
> > -----------------------------------------------
> >
>
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>
>
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