Hi Nate,
Sorry I had an empty database set the first time (which was giving me the
revision error):
Part of my problem has been trying to convert the db from sqlite to mysql --
the closest I got using scripts was 40 tables in the database:
datasetdataset_permissionsdefault_history_permissions
default_user_permissionseventform_definition_currentgalaxy_group
galaxy_sessiongalaxy_session_to_historygalaxy_usergroup_role_association
historyhistory_dataset_associationhistory_user_share_association
implicitly_converted_dataset_associationjobjob_external_output_metadata
job_parameterjob_to_input_datasetjob_to_output_datasetlibrarylibrary_dataset
library_dataset_dataset_association
library_dataset_dataset_association_permissionslibrary_dataset_permissions
library_folderlibrary_folder_permissionslibrary_permissionsmetadata_file
migrate_versionrolestored_workflowstored_workflow_menu_entry
stored_workflow_user_share_connectionuser_group_association
user_role_associationvalidation_errorworkflowworkflow_step
workflow_step_connection
When I try to run it linked to the above database I get the following error:
galaxy.model.migrate.check DEBUG 2010-02-19 13:42:18,987 MySQL_python egg
successfully loaded for mysql dialect
Traceback (most recent call last):
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py",
line 61, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py",
line 28, in __init__
create_or_verify_database( db_url, self.config.database_engine_options )
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py",
line 102, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest ) )
Exception: Your database has version '22' but this code expects version
'39'. Please backup your database and then migrate the schema by running
'sh manage_db.sh upgrade'.
So when I try to run the manage_db.sh I get:
22 -> 23...
Migration script to add columns for tracking whether pages are deleted and
publicly accessible.
Traceback (most recent call last):
File "./scripts/manage_db.py", line 45, in <module>
main( repository='lib/galaxy/model/migrate', url=db_url )
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/shell.py",
line 150, in main
ret = command_func(**kwargs)
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py",
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py",
line 349, in _migrate
schema.runchange(ver, change, changeset.step)
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py",
line 184, in runchange
change.run(self.engine, step)
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/script/py.py",
line 101, in run
func()
File
"lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py",
line 20, in upgrade
Page_table = Table( "page", metadata, autoload=True )
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py",
line 108, in __call__
return type.__call__(self, name, metadata, *args, **kwargs)
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py",
line 236, in __init__
_bind_or_error(metadata).reflecttable(self,
include_columns=include_columns)
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py",
line 1265, in reflecttable
self.dialect.reflecttable(conn, table, include_columns)
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py",
line 1664, in reflecttable
sql = self._show_create_table(connection, table, charset)
File
"/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py",
line 1835, in _show_create_table
raise exc.NoSuchTableError(full_name)
sqlalchemy.exc.NoSuchTableError: page
I guess my problem all along is not having the full table schema for use in
mySQL.
Rgds,
Roy Weckiewicz
On Fri, Feb 19, 2010 at 1:33 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
> Roy Weckiewicz wrote:
>
>> Thanks again Nate,
>>
>> I just tried the one you sent me - it seems I just have a database
>> revision issue:
>>
>> Traceback (most recent call last):
>> File
>> "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py",
>> line 61, in app_factory
>> app = UniverseApplication( global_conf = global_conf, **kwargs )
>> File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py",
>> line 28, in __init__
>> create_or_verify_database( db_url, self.config.database_engine_options
>> )
>> File
>> "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py",
>> line 72, in create_or_verify_database
>> raise Exception( "Your database is older than hg revision
>> 1464:c7acaa1bb88f and will need to be updated manually" )
>> Exception: Your database is older than hg revision 1464:c7acaa1bb88f and
>> will need to be updated manually
>>
>
> Hi Roy,
>
> Is this the database you converted from sqlite? Does it include the
> 'migrate_version' table? Could you paste the output of 'SHOW TABLES;'?
>
> Thanks,
>
>
>>
>> Rgds,
>>
>>
>> Roy Weckiewicz
>>
>>
>> On Fri, Feb 19, 2010 at 1:28 PM, Nate Coraor <nate(a)bx.psu.edu <mailto:
>> nate(a)bx.psu.edu>> wrote:
>>
>> Roy Weckiewicz wrote:
>>
>> What's strange is that eventhough the file name on the egg is
>> MySQL*fat-ucs2.egg the error still reports the file in question
>> as MySQL*fat.egg -- I've tried renaming the egg to match the
>> original file, but it didn't seem to make a difference.
>> Furthermore, when I run.sh, the program will create a directory
>> in home called .python-eggs/ containing the _MySQL.so file,
>> among other things - Will I have to add a different URL to the
>> eggs.ini to keep it from re-downloading the old file?
>>
>>
>> Ah, sorry, that egg relies on some uncommitted patches. I've
>> rebuilt it using a clean checkout, could you try this one instead?:
>>
>>
>> http://www.bx.psu.edu/~nate/galaxy/MySQL_python-1.2.2_5.0.67_static-py2.5-m…
>>
>> Thanks,
>> --nate
>>
>>
>>
>>
>> --
>> Roy Weckiewicz
>> Texas A&M University
>>
>
>
--
Roy Weckiewicz
Texas A&M University
Hi,
Attached is a tool to calculate frequencies/distribution of values in a column (similar to "histogram" tool, but without plotting the chart).
The tool allows finer control of the output, by setting min,max,bin-width or number-of-bins.
This allows calculating distribution of multiple datasets, then comparing them or plotting them all together with the plotting tool.
Also available for download here:
http://cancan.cshl.edu/labmembers/gordon/files/calculate_frequncies.tar.bz2
comments are welcomed,
-gordon
Hello all,
Need a logo that tells people what your web site, database or GMOD
component is about? If your resource needs a logo then the GMOD Logo
Program (http://gmod.org/wiki/GMOD_Logo_Program) can help.
I am pleased to announce the first call for participation in the GMOD
Logo Program. This program is for GMOD users and developers that would
like have a custom designed logo for their web site, database or GMOD
component. The program pairs GMOD community members with students in
advanced design classes at colleges and universities. This spring we
will be working with a class at Linn-Benton Community College.
Participants will meet several times (remotely) over a 3 week period,
with the end result being a new logo for your resource.
Participation is limited to non-profits, and costs US$75. If you are
interested, please see http://gmod.org/wiki/GMOD_Logo_Program for
additional details and requirements, and an application form. The
program is accepting applications until March 1.
Thanks,
Dave Clements
GMOD Help Desk
PS: This program was inspired by ZFIN's success with its logo (see
http://zfin.org). ZFIN's excellent logo was created by working with a
design class at the University of Oregon.
--
Please keep responses on the list!
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americashttp://gmod.org/wiki/GMOD_Logo_Programhttp://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
Hello,
First, thanks for fixing the boolean testing bug.
We're having strange exception thrown in some of our tools, when a tool has a <repeat> section, a selection-box parameter and an output label.
That might sound strange, but I've narrowed it down and it's (almost) definitely caused by the combination of those three.
I know you don't use the "label" option in the public Galaxy, but we use it in many of our tools, and for some it simply doesn't work.
Attached are three simple tools:
tool_without_label:
has a <repeat> parameter, a selection-box parameter, no 'label' in the <output>. works ok.
tool_without_select:
has a <repeat> parameter, a text parameter (instead of a selection box), and a label in the <output>. works ok.
tool_with_label:
has all three items: a <repeat>, a selection-box, and a label. Executing this tool throws an exception:
=======================
URL: http://localhost:8080/tool_runner/index
File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__
environ, self.app)
File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__
return self.application(environ, start_response)
File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__
return self.application(environ, start_response)
File '/home/gordon/temp/galaxy/lib/galaxy/web/framework/base.py', line 125 in __call__
body = method( trans, **kwargs )
File '/home/gordon/temp/galaxy/lib/galaxy/web/controllers/tool_runner.py', line 53 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/gordon/temp/galaxy/lib/galaxy/tools/__init__.py', line 792 in handle_input
out_data = self.execute( trans, incoming=params )
File '/home/gordon/temp/galaxy/lib/galaxy/tools/__init__.py', line 1064 in execute
return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid )
File '/home/gordon/temp/galaxy/lib/galaxy/tools/actions/__init__.py', line 297 in execute
for name, value in tool.params_to_strings( incoming, trans.app ).iteritems():
File '/home/gordon/temp/galaxy/lib/galaxy/tools/__init__.py', line 1067 in params_to_strings
return params_to_strings( self.inputs, params, app )
File '/home/gordon/temp/galaxy/lib/galaxy/tools/parameters/__init__.py', line 80 in params_to_strings
rval[ key ] = str( to_json_string( value ) )
File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/__init__.py', line 182 in dumps
File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 312 in encode
File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 262 in _iterencode
File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 170 in _iterencode_list
File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 265 in _iterencode
File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 235 in _iterencode_dict
File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 273 in _iterencode
File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 279 in _iterencode_default
File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 300 in default
TypeError: <galaxy.tools.SelectToolParameterWrapper object at 0x49a8d10> is not JSON serializable
=======================
Any help/fix would be greatly appreciated.
thanks!
-gordon