cleanup_datasets.py not deleting files...

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cleanup_datasets.py not deleting files...

burdettn
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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Re: cleanup_datasets.py not deleting files...

Hans-Rudolf Hotz
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, [hidden email] 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
>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
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Re: cleanup_datasets.py not deleting files...

burdettn
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 [[hidden email]]
Sent: Thursday, July 17, 2014 5:42 PM
To: Burdett, Neil (DP&S, Herston - RBWH); [hidden email]
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, [hidden email] 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
>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: cleanup_datasets.py not deleting files...

Hans-Rudolf Hotz


On 07/17/2014 12:38 PM, [hidden email] 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 [[hidden email]]
> Sent: Thursday, July 17, 2014 5:42 PM
> To: Burdett, Neil (DP&S, Herston - RBWH); [hidden email]
> 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, [hidden email] 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
>>
>>
>> ___________________________________________________________
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>>     http://galaxyproject.org/search/mailinglists/
>>
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
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Re: cleanup_datasets.py not deleting files...

burdettn
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 [[hidden email]]
Sent: Thursday, July 17, 2014 9:23 PM
To: Burdett, Neil (DP&S, Herston - RBWH); [hidden email]
Subject: Re: [galaxy-dev] cleanup_datasets.py not deleting files...

On 07/17/2014 12:38 PM, [hidden email] 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 [[hidden email]]
> Sent: Thursday, July 17, 2014 5:42 PM
> To: Burdett, Neil (DP&S, Herston - RBWH); [hidden email]
> 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, [hidden email] 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
>>
>>
>> ___________________________________________________________
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>>     http://galaxyproject.org/search/mailinglists/
>>

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: cleanup_datasets.py not deleting files...

Eric Rasche
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Neil,

It'd be pretty easy to fix that yourself. In
scripts/cleanup_datasets/cleanup_datasets.py, there's a filter which
selects which datasets should be removed.

Check L350 of that script. You could simply remove the other values from
the _and query, and delete everything older than N days. Make sure your
users know ahead of time!


Cheers,
Eric

On 07/17/2014 02:55 PM, [hidden email] wrote:

> 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 [[hidden email]]
> Sent: Thursday, July 17, 2014 9:23 PM
> To: Burdett, Neil (DP&S, Herston - RBWH); [hidden email]
> Subject: Re: [galaxy-dev] cleanup_datasets.py not deleting files...
>
> On 07/17/2014 12:38 PM, [hidden email] 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 [[hidden email]]
>> Sent: Thursday, July 17, 2014 5:42 PM
>> To: Burdett, Neil (DP&S, Herston - RBWH); [hidden email]
>> 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, [hidden email] 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
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>     http://galaxyproject.org/search/mailinglists/
>>>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>

- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
[hidden email]
[hidden email]
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___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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Re: cleanup_datasets.py not deleting files...

burdettn
Thanks, but this doesn't work. As there are further checks in "_purge_datasets" which check if the data has been deleted first. Can you purge data without deleting it? If so I can remove those checks. Has anyone else needed to do this?

Thanks
neil

-----Original Message-----
From: Eric Rasche [mailto:[hidden email]]
Sent: Friday, 18 July 2014 6:08 AM
To: Burdett, Neil (DP&S, Herston - RBWH); [hidden email]
Subject: Re: [galaxy-dev] cleanup_datasets.py not deleting files...

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Neil,

It'd be pretty easy to fix that yourself. In scripts/cleanup_datasets/cleanup_datasets.py, there's a filter which selects which datasets should be removed.

Check L350 of that script. You could simply remove the other values from the _and query, and delete everything older than N days. Make sure your users know ahead of time!


Cheers,
Eric

On 07/17/2014 02:55 PM, [hidden email] wrote:

> 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 [[hidden email]]
> Sent: Thursday, July 17, 2014 9:23 PM
> To: Burdett, Neil (DP&S, Herston - RBWH); [hidden email]
> Subject: Re: [galaxy-dev] cleanup_datasets.py not deleting files...
>
> On 07/17/2014 12:38 PM, [hidden email] 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 [[hidden email]]
>> Sent: Thursday, July 17, 2014 5:42 PM
>> To: Burdett, Neil (DP&S, Herston - RBWH); [hidden email]
>> 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%20Histo
>> ries%20and%20Datasets
>>
>>
>> Hope this helps
>> Hans-Rudolf
>>
>>
>> On 07/17/2014 02:42 AM, [hidden email] 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
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>     http://galaxyproject.org/search/mailinglists/
>>>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>

- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
[hidden email]
[hidden email]
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___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/