Re: [galaxy-dev] [galaxy-user] Cleanup script error - guess_dialect_for_url
Hello,
I finally managed to solve this issue. To restore the
cleanup scripts I had to 'update' my universe_wsgi.ini
file. In the old one the use of the database_connection
field was disabled in presence of the standard sqlite
database and there was a database_file field pointing to
database/universe.sqlite. In the new universe_wsgi.ini
the database_file field is no longer present and
database_connection points to
'sqlite:///./database/universe.sqlite'. The new
cleanup scripts (probably?) identify the database in use
by looking at the database_connection field, using the
split(':', 1) function to retrieve the name of the
database. In absence of the database_connection field the
split function fails.
Thanks for pointing me in the right direction!
Regards,
Rocco
On Wed, 28 Mar 2012 09:07:55 -0400
Emil Bouvier wrote:
Rocco,
Are you running delete_datasets.sh from the base galaxy
directory or scripts/cleanup_datasets?
From what I can tell, it's not finding your database
configuration details in universe_wsgi.ini, which it
looks for in the current directory.
Dave B.
On 3/27/12 3:34 AM, rocco.piazza wrote:
Hello Jennifer,
thank you for your support.
The galaxy-dist I'm running is the March 2012 one. 'hg
incoming' doesn't
give any further update. Python is 2.6.5.
Please, note that I can still delete datasets from the
UI (if I click on
the x button the dataset disappears and if I set
Options->Show Deleted
Datasets it reappears as a deleted dataset, as expected)
however, if I
try to purge (Options->Purge Deleted Datasets) it
reports a '0 datasets
have been deleted permanently' message with the deleted
dataset happily
sitting in my history (still labeled as 'deleted').
Any help would be appreciated!
Regards,
Rocco
On Mon, 26 Mar 2012 14:25:43 -0700
Jennifer Jackson wrote:
Hi Rocco,
To help us get oriented, which galaxy-dist pull did you
start from and
which did you update to? If you have the release date/hg
pull numbers,
that would be great. If you need to reference, these are
the prior
distributions:
http://wiki.g2.bx.psu.edu/DevNewsBriefs
Ideally, you would be current through the March 12, 2012
distribution,
which included some bugs fixes for python 2.5 support.
Support for
python 2.4 ended with the Nov 18, 2011 distribution.
If there is anything else customized about your system
that you feel
would be relevant (other odd behavior?), that would be
good to send
back. For example, can you delete and purge datasets
through the UI?
Histories?
I am going to move your question over the
galaxy-...@bx.psu.edu
mailing list, which is the best place to reach the
development
community. The galaxy-user list is intended for
data/tool usage
questions, with a focus on Galaxy main.
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
Please leave the galaxy-dev list in the "cc" for your
return email,
Thanks!
Jen
Galaxy team
On 3/26/12 1:57 AM, rocco.piazza wrote:
Hello,
I'm working on a local instance of Galaxy-dist and I
just
updated it. Right after the update I tried to run the
cleanup scripts. Unfortunately what I'm getting is the
following error:
# sh delete_datasets.sh -d 0 -r
Traceback (most recent call last):
File
"./scripts/cleanup_datasets/cleanup_datasets.py",
line 524, in
if __name__ == "__main__": main()
File
"./scripts/cleanup_datasets/cleanup_datasets.py",
line 101, in main
app = CleanupDatasetsApplication( config )
File
"./scripts/cleanup_datasets/cleanup_datasets.py",
line 512, in __init__
self.model = galaxy.model.mapping.init(
config.file_path, config.database_connection,
engine_options={}, create_tables=False,
object_store=self.object_store )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1818, in init
load_egg_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1798, in load_egg_for_url
dialect = guess_dialect_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1794, in guess_dialect_for_url
return (url.split(':', 1))[0]
AttributeError: 'bool' object has no attribute 'split'
The same error occurs if I try to run other cleanup
scripts, such as the delete_datasets or purge_datasets.
Any idea to solve this issue?
Best regards,
Rocco
___
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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
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Please keep all replie
Re: [galaxy-dev] [galaxy-user] Cleanup script error - guess_dialect_for_url
Rocco,
Are you running delete_datasets.sh from the base galaxy directory or
scripts/cleanup_datasets?
From what I can tell, it's not finding your database configuration
details in universe_wsgi.ini, which it looks for in the current directory.
Dave B.
On 3/27/12 3:34 AM, rocco.piazza wrote:
Hello Jennifer,
thank you for your support.
The galaxy-dist I'm running is the March 2012 one. 'hg incoming' doesn't
give any further update. Python is 2.6.5.
Please, note that I can still delete datasets from the UI (if I click on
the x button the dataset disappears and if I set Options->Show Deleted
Datasets it reappears as a deleted dataset, as expected) however, if I
try to purge (Options->Purge Deleted Datasets) it reports a '0 datasets
have been deleted permanently' message with the deleted dataset happily
sitting in my history (still labeled as 'deleted').
Any help would be appreciated!
Regards,
Rocco
On Mon, 26 Mar 2012 14:25:43 -0700
Jennifer Jackson wrote:
Hi Rocco,
To help us get oriented, which galaxy-dist pull did you start from and
which did you update to? If you have the release date/hg pull numbers,
that would be great. If you need to reference, these are the prior
distributions:
http://wiki.g2.bx.psu.edu/DevNewsBriefs
Ideally, you would be current through the March 12, 2012 distribution,
which included some bugs fixes for python 2.5 support. Support for
python 2.4 ended with the Nov 18, 2011 distribution.
If there is anything else customized about your system that you feel
would be relevant (other odd behavior?), that would be good to send
back. For example, can you delete and purge datasets through the UI?
Histories?
I am going to move your question over the galaxy-...@bx.psu.edu
mailing list, which is the best place to reach the development
community. The galaxy-user list is intended for data/tool usage
questions, with a focus on Galaxy main.
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
Please leave the galaxy-dev list in the "cc" for your return email,
Thanks!
Jen
Galaxy team
On 3/26/12 1:57 AM, rocco.piazza wrote:
Hello,
I'm working on a local instance of Galaxy-dist and I just
updated it. Right after the update I tried to run the
cleanup scripts. Unfortunately what I'm getting is the
following error:
# sh delete_datasets.sh -d 0 -r
Traceback (most recent call last):
File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 524, in
if __name__ == "__main__": main()
File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 101, in main
app = CleanupDatasetsApplication( config )
File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 512, in __init__
self.model = galaxy.model.mapping.init(
config.file_path, config.database_connection,
engine_options={}, create_tables=False,
object_store=self.object_store )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1818, in init
load_egg_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1798, in load_egg_for_url
dialect = guess_dialect_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1794, in guess_dialect_for_url
return (url.split(':', 1))[0]
AttributeError: 'bool' object has no attribute 'split'
The same error occurs if I try to run other cleanup
scripts, such as the delete_datasets or purge_datasets.
Any idea to solve this issue?
Best regards,
Rocco
___
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/
___
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/
Re: [galaxy-dev] [galaxy-user] Cleanup script error - guess_dialect_for_url
Hello Jennifer,
thank you for your support.
The galaxy-dist I'm running is the March 2012 one. 'hg
incoming' doesn't give any further update. Python is
2.6.5.
Please, note that I can still delete datasets from the UI
(if I click on the x button the dataset disappears and if
I set Options->Show Deleted Datasets it reappears as a
deleted dataset, as expected) however, if I try to purge
(Options->Purge Deleted Datasets) it reports a '0 datasets
have been deleted permanently' message with the deleted
dataset happily sitting in my history (still labeled as
'deleted').
Any help would be appreciated!
Regards,
Rocco
On Mon, 26 Mar 2012 14:25:43 -0700
Jennifer Jackson wrote:
Hi Rocco,
To help us get oriented, which galaxy-dist pull did you
start from and which did you update to? If you have the
release date/hg pull numbers, that would be great. If you
need to reference, these are the prior distributions:
http://wiki.g2.bx.psu.edu/DevNewsBriefs
Ideally, you would be current through the March 12, 2012
distribution, which included some bugs fixes for python
2.5 support. Support for python 2.4 ended with the Nov
18, 2011 distribution.
If there is anything else customized about your system
that you feel would be relevant (other odd behavior?),
that would be good to send back. For example, can you
delete and purge datasets through the UI? Histories?
I am going to move your question over the
galaxy-...@bx.psu.edu mailing list, which is the best
place to reach the development community. The galaxy-user
list is intended for data/tool usage questions, with a
focus on Galaxy main.
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
Please leave the galaxy-dev list in the "cc" for your
return email,
Thanks!
Jen
Galaxy team
On 3/26/12 1:57 AM, rocco.piazza wrote:
Hello,
I'm working on a local instance of Galaxy-dist and I
just
updated it. Right after the update I tried to run the
cleanup scripts. Unfortunately what I'm getting is the
following error:
# sh delete_datasets.sh -d 0 -r
Traceback (most recent call last):
File
"./scripts/cleanup_datasets/cleanup_datasets.py",
line 524, in
if __name__ == "__main__": main()
File
"./scripts/cleanup_datasets/cleanup_datasets.py",
line 101, in main
app = CleanupDatasetsApplication( config )
File
"./scripts/cleanup_datasets/cleanup_datasets.py",
line 512, in __init__
self.model = galaxy.model.mapping.init(
config.file_path, config.database_connection,
engine_options={}, create_tables=False,
object_store=self.object_store )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1818, in init
load_egg_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1798, in load_egg_for_url
dialect = guess_dialect_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1794, in guess_dialect_for_url
return (url.split(':', 1))[0]
AttributeError: 'bool' object has no attribute 'split'
The same error occurs if I try to run other cleanup
scripts, such as the delete_datasets or purge_datasets.
Any idea to solve this issue?
Best regards,
Rocco
___
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/
Re: [galaxy-dev] [galaxy-user] Cleanup script error - guess_dialect_for_url
Hi Rocco,
To help us get oriented, which galaxy-dist pull did you start from and
which did you update to? If you have the release date/hg pull numbers,
that would be great. If you need to reference, these are the prior
distributions:
http://wiki.g2.bx.psu.edu/DevNewsBriefs
Ideally, you would be current through the March 12, 2012 distribution,
which included some bugs fixes for python 2.5 support. Support for
python 2.4 ended with the Nov 18, 2011 distribution.
If there is anything else customized about your system that you feel
would be relevant (other odd behavior?), that would be good to send
back. For example, can you delete and purge datasets through the UI?
Histories?
I am going to move your question over the galaxy-...@bx.psu.edu mailing
list, which is the best place to reach the development community. The
galaxy-user list is intended for data/tool usage questions, with a focus
on Galaxy main.
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
Please leave the galaxy-dev list in the "cc" for your return email,
Thanks!
Jen
Galaxy team
On 3/26/12 1:57 AM, rocco.piazza wrote:
Hello,
I'm working on a local instance of Galaxy-dist and I just
updated it. Right after the update I tried to run the
cleanup scripts. Unfortunately what I'm getting is the
following error:
# sh delete_datasets.sh -d 0 -r
Traceback (most recent call last):
File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 524, in
if __name__ == "__main__": main()
File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 101, in main
app = CleanupDatasetsApplication( config )
File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 512, in __init__
self.model = galaxy.model.mapping.init(
config.file_path, config.database_connection,
engine_options={}, create_tables=False,
object_store=self.object_store )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1818, in init
load_egg_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1798, in load_egg_for_url
dialect = guess_dialect_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1794, in guess_dialect_for_url
return (url.split(':', 1))[0]
AttributeError: 'bool' object has no attribute 'split'
The same error occurs if I try to run other cleanup
scripts, such as the delete_datasets or purge_datasets.
Any idea to solve this issue?
Best regards,
Rocco
___
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/
