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.
----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -----------------------------------------------
-----Original Message----- From: Nate Coraor [mailto:nate@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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