Re: [galaxy-dev] liftOver functional tests failed
Hi John,
Many thanks for coming back to me on this issue. Unfortunately adding the full
path into the test did not solve the issue for me, e.g.
param name=to_dbkey
value=/data/galaxy/genomes/hg18/liftOver/hg18ToPanTro2.over.chain /
So for the time being I will comment these out. Many thanks again.
Kind regards,
Anne.
On 24 Feb 2015, at 04:02, John Chilton jmchil...@gmail.com wrote:
Yes, indeed liftOver's tests are broken :(. Thanks for the bug report.
The way liftOver's loc file is being handled is problematic - it uses full
paths as parameter values. Fixing that
(https://github.com/jmchilton/galaxy/commit/b27e79133a6b2e467b17f502b05faf5af11127f5)
fixes the test cases and would make liftOver more robust - a seeming
win-win. Unfortunately I don't think I can fix liftOver in -dist because it
would break everyone's tool re-runs and workflows (but if I were running my
own new Galaxy I would definitely apply that commit now).
Back to the functional test - the testing framework can no longer handle this
case for some fairly technical and uninteresting reasons. I could fix it but
it would be a substantial amount of work and the corner case is sufficiently
corner-y that I imagine only liftOver is affected by the bug - so I would
prefer to just say the test framework cannot do this anymore and comment out
the liftOver tests until we bite the bullet on the loc file structure.
If you want the tests and you want them to pass without the above commit -
you can replace the test values that look like:
param name=to_dbkey value=panTro2 /
with full paths to the .over.chain file, e.g.
param name=to_dbkey value=/path/to/hg18ToPanTro2.over.chain /
I would expect to see these tests all just commented out in the next release
though :(.
Hope this helps and thanks again for the bug report,
-John
On Mon, Feb 16, 2015 at 1:34 PM, Anne Pajon anne.pa...@cruk.cam.ac.uk wrote:
Dear All,
I am still trying to migrate my production server to new hardware and would
like to have all functional tests pass before turning off my old server.
I am facing an issue with liftOver functional tests, they failed when running
'sh run_tests.sh -id liftOver1' on the command line with these errors:
==
ERROR: test_tool_00 (functional.test_toolbox.TestForTool_liftOver1)
Convert genome coordinates ( liftOver1 ) Test-1
--
Traceback (most recent call last):
File /mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py,
line 122, in test_tool
self.do_it( td )
File /mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py,
line 37, in do_it
data_list, jobs = galaxy_interactor.run_tool( testdef, test_history )
File /mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py, line 218,
in run_tool
raise Exception( datasets_object[ 'message' ] )
Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was
selected, please verify'}}
begin captured logging
==
ERROR: test_tool_01 (functional.test_toolbox.TestForTool_liftOver1)
Convert genome coordinates ( liftOver1 ) Test-2
--
Traceback (most recent call last):
File /mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py,
line 122, in test_tool
self.do_it( td )
File /mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py,
line 37, in do_it
data_list, jobs = galaxy_interactor.run_tool( testdef, test_history )
File /mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py, line 218,
in run_tool
raise Exception( datasets_object[ 'message' ] )
Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was
selected, please verify'}}
begin captured logging
==
ERROR: test_tool_02 (functional.test_toolbox.TestForTool_liftOver1)
Convert genome coordinates ( liftOver1 ) Test-3
--
Traceback (most recent call last):
File /mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py,
line 122, in test_tool
self.do_it( td )
File /mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py,
line 37, in do_it
data_list, jobs = galaxy_interactor.run_tool( testdef, test_history )
File /mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py, line 218,
in run_tool
raise Exception( datasets_object[ 'message' ] )
Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was
selected, please verify'}}
begin captured logging
Re: [galaxy-dev] tool shed updates broken on my local server
Hi Martin,
Many thanks for your answer, and sorry for this late reply I've been off sick.
In order to ease my migration, I am looking into reducing the number of tools
installed that are not in used. We do run a cut down version of galaxy with
much fewer tools that currently in Galaxy Main, but the tool migration scripts
have installed lots of tools within my system that are not needed as I see them
in 'Installed tool shed repositories' . I wish I could find a way to
automatically remove installed tools that are not in use. Any ideas if such a
script already exists? Or should I write it myself? Any guidance on where to
start would be great. Many thanks in advance for your help.
Cheers,
Anne.
On 30 Jan 2015, at 15:46, Martin Čech mar...@bx.psu.edu wrote:
Hi Anne,
moving the whole Galaxy installation is a tough job and we do not really have
a good process for it. Your problem is most probably caused by the
inconsistency in the DB. The path to the shed_tool_conf.xml is stored there
and the changes you made to the location of the installation did not
propagate there.
Please have a look at the following script that Dave B. made:
https://gist.github.com/InitHello/d208cd056baf088aca1f
This script will soon be part of the distribution (in /scripts) and should
help you solving your issues.
Thank you for using Galaxy.
Martin, Galaxy Team
On Thu Jan 29 2015 at 11:47:19 AM Anne Pajon anne.pa...@cruk.cam.ac.uk
wrote:
Hi there,
I am currently trying to migrate our Galaxy production server onto new
hardware and I am facing many challenges. Recently I've been unable to update
tools from the tool shed. During the migration I've moved across the files,
the data, the tools and their dependencies as well as the database. But I am
getting this error while trying to update any tools that are marked 'Updates
are available in the Tool Shed for this revision' from the GUI: Admin
Manage installed tool shed repositories fasta_formatter menu Get updates:
Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
The error has been logged to our team.
Here is the log from paster.log:
10.20.13.16 - - [29/Jan/2015:16:43:45 +0100] GET
/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/name=fasta_formatterowner=devteamchangeset_revision=8f0ae92440b8latest_changeset_revision=1dbb5181c327latest_ctx_rev=1
HTTP/1.1 500 -
http://bioinf-gal001:8080/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falseadvanced_search=falsef-deleted=Falsef-free-text-search=fasta_formatter;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:35.0) Gecko/20100101
Firefox/35.0
Error - type 'exceptions.AttributeError': 'NoneType' object has no
attribute 'get'
URL:
http://bioinf-gal001:8080/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/name=fasta_formatterowner=devteamchangeset_revision=8f0ae92440b8latest_changeset_revision=1dbb5181c327latest_ctx_rev=1
File
'/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/mnt/nfs/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/mnt/nfs/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 132 in __call__
return self.handle_request( environ, start_response )
File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 190 in handle_request
body = method( trans, **kwargs )
File
'/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py',
line 87 in decorator
return func( self, trans, *args, **kwargs )
File
'/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 1953 in update_to_changeset_revision
persist=True )
File
'/mnt/nfs/data/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py',
line 31 in __init__
metadata_dict=metadata_dict, user=None )
File
'/mnt/nfs/data/galaxy/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py',
line 60 in __init__
self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get(
'config_filename', None ) }
AttributeError: 'NoneType' object has no attribute 'get'
CGI Variables
-
CONTENT_LENGTH: '0'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_ENCODING: 'gzip, deflate
[galaxy-dev] Data manager for liftOver
Dear All, Could someone let me know if there is already a data manager tool for getting liftOver reference data within Galaxy or should I write one? Please let me know. Kind regards, Anne. -- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cruk.cam.ac.uk | +44 (0)1223 769 631 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
