Thanks. Is there a script that will delete all files older than a certain date 
even if not marked as deleted by the user?

Thanks
Neil
________________________________________
From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Thursday, July 17, 2014 5:42 PM
To: Burdett, Neil (DP&S, Herston - RBWH); galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] cleanup_datasets.py not deleting files...

Hi Neil

The cleanup_datasets.py script only removes the files if older than the
time given (you did this, ie older than 20 days) AND if the dataset has
been marked as 'deleted' by the user - have you done that?

see also:
https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets


Hope this helps
Hans-Rudolf


On 07/17/2014 02:42 AM, neil.burd...@csiro.au wrote:
> Hi,
>      I'm trying to use the cleanup_datasets.py file to remove all files
> on my system older than 20 days. My crontab looks like this:
>
> # m h  dom mon dow   command
> 34 10 * * * cd /export/barium-data3/galaxy-suvr && python
> scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -1
>  > /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
> scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -2
> -r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
> scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -3
> -r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
> scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -5
> -r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
> scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -4
> -r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1 && python
> scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -6
> -r >> /home/galaxy/crontab_purge_milxcloud.log 2>&1
>
> The crontab executes and the contents of
> /home/galaxy/crontab_purge_milxcloud.log is:
>
> cat /home/galaxy/crontab_purge_milxcloud.log
> psycopg2 egg successfully loaded for postgres dialect
> ##########################################
>
> # 2014-07-17 10:34:02 - Handling stuff older than 20 days
> Datasets will NOT be removed from disk.
>
> Deleted 0 histories
> Elapsed time:  0.170083045959
> ##########################################
> psycopg2 egg successfully loaded for postgres dialect
> ##########################################
>
> # 2014-07-17 10:34:02 - Handling stuff older than 20 days
> Datasets will be removed from disk.
>
> Purged 0 histories.
> Elapsed time:  0.174137830734
> ##########################################
> psycopg2 egg successfully loaded for postgres dialect
> ##########################################
>
> # 2014-07-17 10:34:03 - Handling stuff older than 20 days
> Datasets will be removed from disk.
>
> Purged 0 datasets
> Freed disk space:  0
> Elapsed time:  0.168104887009
> ##########################################
> psycopg2 egg successfully loaded for postgres dialect
> ##########################################
>
> # 2014-07-17 10:34:04 - Handling stuff older than 20 days
> Datasets will be removed from disk.
>
> # Purged 0 folders.
> Elapsed time:  0.168635129929
> ##########################################
> psycopg2 egg successfully loaded for postgres dialect
> ##########################################
>
> # 2014-07-17 10:34:05 - Handling stuff older than 20 days
> Datasets will be removed from disk.
>
> # Purged 0 libraries .
> Elapsed time:  0.166506052017
> ##########################################
> psycopg2 egg successfully loaded for postgres dialect
> ##########################################
>
> # 2014-07-17 10:34:06 - Handling stuff older than 20 days
> Datasets will be removed from disk.
>
> Examined 0 datasets, marked 0 datasets and 0 dataset instances (HDA) as
> deleted
> Total elapsed time:  0.00744795799255
> ##########################################
>
> However, today is the 17th July and when I look into  the database
> directory i.e. ~/database/files/000 I still have files from the 18th
> June so older than 20 days i.e.:
>
> drwxr-xr-x 2 galaxy nogroup     4096 Jun 18 09:19 dataset_213_files
> -rw-r--r-- 1 galaxy nogroup     1061 Jun 18 09:19 dataset_213.dat
> drwxr-xr-x 2 galaxy nogroup     4096 Jun 18 09:19 dataset_215_files
> -rw-r--r-- 1 galaxy nogroup      270 Jun 18 09:19 dataset_215.dat
> drwxr-xr-x 2 galaxy nogroup     4096 Jun 18 09:19 dataset_221_files
> drwxr-xr-x 2 galaxy nogroup     4096 Jun 18 09:19 dataset_219_files
> drwxr-xr-x 2 galaxy nogroup     4096 Jun 18 09:19 dataset_220_files
> drwxr-xr-x 2 galaxy nogroup     4096 Jun 18 09:19 dataset_222_files
> drwxr-xr-x 2 galaxy nogroup     4096 Jun 18 09:19 dataset_218_files
> -rw-r--r-- 1 galaxy nogroup      994 Jun 18 09:19 dataset_216.dat
> -rw-r--r-- 1 galaxy nogroup      161 Jun 18 09:19 dataset_214.dat
>
> Am I doing something wrong? Using wrong arguments/file etc ?
>
> Thanks
> Neil
>
>
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