How does the main Galaxy server deal with it? Users data can't remain on the "project's free server" forever can it? and if not then there must be some automated way of deleting data? is that correct?
Thanks Neil ________________________________________ From: Hans-Rudolf Hotz [hrh@fmi.ch] Sent: Thursday, July 17, 2014 9:23 PM To: Burdett, Neil (DP&S, Herston - RBWH); galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cleanup_datasets.py not deleting files...
On 07/17/2014 12:38 PM, Neil.Burdett@csiro.au wrote:
Thanks. Is there a script that will delete all files older than a certain date even if not marked as deleted by the user?
I am not aware of such a script
Hans-Rudolf
Thanks Neil ________________________________________ From: Hans-Rudolf Hotz [hrh@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%20...
Hope this helps Hans-Rudolf
On 07/17/2014 02:42 AM, Neil.Burdett@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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