Hi,
thank you for answer.
I have tried to use the mentioned scripts but it seems that the order of
their using at first time was incorrect.. As a result, the metadata in
database tables are modified but the datasets files corresponded to deleted
datasets in history remains unremoved. So, the following calling of the
scripts in the right order (as indicated in wiki) also didn't delete the
unused dataset files. Is there any way to update the metadata in tables
according to the real state of files?
I think that the order of calling the scripts at first time was the
following:
cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r
cleanup_datasets.py universe_wsgi.ini -d 6 -1 -r
cleanup_datasets.py universe_wsgi.ini -d 2 -1 -r
cleanup_datasets.py universe_wsgi.ini -d 3 -1 -r
cleanup_datasets.py universe_wsgi.ini -d 4 -1 -r
cleanup_datasets.py universe_wsgi.ini -d 5 -1 -r
cleanup_datasets.py universe_wsgi.ini -d 1 -1 -r
cleanup_datasets.py universe_wsgi.ini -d 1 -2 -r
cleanup_datasets.py universe_wsgi.ini -d 1 -4 -r
cleanup_datasets.py universe_wsgi.ini -d 1 -5 -r
cleanup_datasets.py universe_wsgi.ini -d 1 -3 -r
cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r

Also there are some strange things (imho) in galaxy.dataset table: there a
lot of datasets id having or NULL total size:

mysql> select * from dataset where (id="148" or id="53" or id="86" or
id="146" or id="330");
+-----+---------------------+---------------------+-----------+---------+--------+----------+-------------------+-------------------+-----------+------------+
| id | create_time | update_time | state | deleted | purged | purgable |
external_filename | _extra_files_path | file_size | total_size |
+-----+---------------------+---------------------+-----------+---------+--------+----------+-------------------+-------------------+-----------+------------+
| 53 | 2011-03-29 16:21:58 | 2011-07-06 14:17:49 | error | 1 | 0 | 1 | NULL
| NULL | 0 | NULL |
| 86 | 2011-03-29 20:35:44 | 2011-07-06 14:17:52 | discarded | 1 | 0 | 1 |
NULL | NULL | NULL | NULL |
| 146 | 2011-05-26 01:38:14 | 2011-07-06 14:18:00 | error | 1 | 0 | 1 | NULL
| NULL | NULL | NULL |
| 148 | 2011-05-26 02:20:44 | 2011-07-06 14:18:00 | discarded | 1 | 0 | 1 |
NULL | NULL | NULL | NULL |
| 330 | 2011-07-05 00:44:44 | 2011-07-05 00:44:44 | NULL | 0 | 0 | 1 | NULL
| NULL | NULL | NULL |
+-----+---------------------+---------------------+-----------+---------+--------+----------+-------------------+-------------------+-----------+------------+

I don't know how these records looked like before calling of the cleanup
scripts, but is it possible that it is because of incorrect order of their
calling? Is "discarded" state mean that the corresponded file should be
deleted? But in my case all these files are still in database folder.
Please, let me know if you need any other of clarification of my questions.


2011/7/6 Hans-Rudolf Hotz <h...@fmi.ch>

> Hi Sergei
>
> This is a question better asked on 'galaxy-...@bx.psu.edu' since you refer
> to your local Galaxy installation.
>
>
> In order to remove the data from your file system, you need to run the
> 'cleanup scripts', as described on this wiki page:
>
>
>
> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDatasets
>
>
>
> Regards, Hans
>
>
>
> On 07/06/2011 03:33 PM, Sergei Ryazansky wrote:
>
>>
>>
>> -------- Исходное сообщение --------
>> Тема:   deleting datasets from history
>> Дата:   Tue, 5 Jul 2011 19:58:45 +0300
>> От:     Sergei Ryazansky <s.ryazan...@gmail.com>
>> Кому:   galaxy-user-requ...@lists.bx.psu.edu
>>
>>
>>
>> Hello all,
>>
>>
>> After the deleating datasets from the history panel in our Galaxy mirror
>> the indicator at the top right corner shows the same amount of used
>> space as before deleting. Also, the files corresponded to the datasets
>> remains in the Galaxy database/files/000 directory. It seems, that
>> deleting of datasets from history is only delete the launch to file but
>> not the file itself. How to configure the Galaxy mirror to delete not
>> only records in history panel but also the corresponed files?
>> Thank you in advance!
>>
>>
>>
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to