Question: Problems Upgrading To Mercurial
0
Assaf Gordon • 320 wrote:
Hello,
I'm trying to upgrade an existing galaxy installation to use
mercurial,
and experiencing some problems.
In one directory (called "galaxy_devel_old") I've got the old galaxy
code base, updated to SVN revision r2771.
On another directory (called "galaxy_devel") I've got the new galaxy
code base, which was created using:
$ hg clone http://www.bx.psu.edu/hg/galaxy galaxy_devel
Both installations use the same configuration files, the same postgres
database, and the same 'database/files' directory.
The old galaxy works fine.
With the new galaxy, I get the following SQL error (at the bottom of
the
text log):
URL: http://tango:8081/root/history
File
'build/bdist.solaris-2.11-i86pc/egg/weberror/evalexception/middleware.
py',
line 364 in respond
File 'build/bdist.solaris-2.11-i86pc/egg/paste/debug/prints.py', line
98
in __call__
File 'build/bdist.solaris-2.11-i86pc/egg/paste/wsgilib.py', line 539
in
intercept_output
File 'build/bdist.solaris-2.11-i86pc/egg/beaker/session.py', line 103
in
__call__
File 'build/bdist.solaris-2.11-i86pc/egg/paste/recursive.py', line 80
in
__call__
File 'build/bdist.solaris-2.11-i86pc/egg/paste/httpexceptions.py',
line
632 in __call__
File
'/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/framework/base.py',
line 125 in __call__
body = method( trans, **kwargs )
File
'/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/controllers/root.py',
line 66 in history
return trans.fill_template( "root/history.mako", history=history )
File
'/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/framework/__init__.py'
,
line 497 in fill_template
return self.fill_template_mako( filename, **kwargs )
File
'/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/framework/__init__.py'
,
line 507 in fill_template_mako
return template.render( **data )
File 'build/bdist.solaris-2.11-i86pc/egg/mako/template.py', line 114
in
render
File 'build/bdist.solaris-2.11-i86pc/egg/mako/runtime.py', line 287 in
_render
File 'build/bdist.solaris-2.11-i86pc/egg/mako/runtime.py', line 304 in
_render_context
File 'build/bdist.solaris-2.11-i86pc/egg/mako/runtime.py', line 337 in
_exec_template
File
'/media/sdb1/galaxy/galaxy_devel/database/compiled_templates/root/hist
ory.mako.py',
line 35 in render_body
if bool( [ data for data in history.active_datasets if data.state
in
['running', 'queued', '', None ] ] ):
File
'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/orm/attributes.py',
line 53 in __get__
File
'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/orm/attributes.py',
line 208 in get
File
'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/orm/strategies.py',
line 226 in lazyload
File 'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/orm/query.py',
line
359 in select_whereclause
File 'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/orm/query.py',
line
1078 in _select_statement
File 'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/orm/query.py',
line
977 in execute
File 'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/orm/session.py',
line 195 in execute
File 'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/engine/base.py',
line 517 in execute
File 'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/engine/base.py',
line 557 in execute_clauseelement
File 'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/engine/base.py',
line 568 in execute_compiled
File 'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/engine/base.py',
line 581 in _execute_raw
File 'build/bdist.solaris-2.11-i86pc/egg/sqlalchemy/engine/base.py',
line 599 in _execute
SQLError: (ProgrammingError) column
history_dataset_association.copied_from_history_dataset_association_id
does not exist
LINE 1: ...ation.blurb AS history_dataset_association_blurb,
history_da...
^
'SELECT history_dataset_association.designation AS
history_dataset_association_designation, anon_d37b.update_time AS
anon_d37b_update_time, anon_d37b.deleted AS anon_d37b_deleted,
anon_d37b._extra_files_path AS anon_d37b__extra_files_path,
anon_d37b.purged AS anon_d37b_purged, anon_d37b.purgable AS
anon_d37b_purgable, anon_d37b.state AS anon_d37b_state,
anon_d37b.create_time AS anon_d37b_create_time, anon_d37b.file_size AS
anon_d37b_file_size, anon_d37b.id AS anon_d37b_id,
anon_d37b.external_filename AS anon_d37b_external_filename,
history_dataset_association.visible AS
history_dataset_association_visible,
history_dataset_association.create_time AS
history_dataset_association_create_time,
history_dataset_association.dataset_id AS
history_dataset_association_dataset_id, history_dataset_association.id
AS history_dataset_association_id,
history_dataset_association.parent_id
AS history_dataset_association_parent_id,
history_dataset_association.metadata AS
history_dataset_association_metadata,
history_dataset_association.blurb
AS history_dataset_association_blurb,
history_dataset_association.copied_from_history_dataset_association_id
AS history_dataset_association_copied_from_history_dataset_a_1,
history_dataset_association.peek AS history_dataset_association_peek,
history_dataset_association.update_time AS
history_dataset_association_update_time,
history_dataset_association.deleted AS
history_dataset_association_deleted,
history_dataset_association.history_id AS
history_dataset_association_history_id,
history_dataset_association.hid
AS history_dataset_association_hid, history_dataset_association.info
AS
history_dataset_association_info, history_dataset_association.name AS
history_dataset_association_name,
history_dataset_association.extension
AS history_dataset_association_extension \nFROM
history_dataset_association LEFT OUTER JOIN dataset AS anon_d37b ON
anon_d37b.id = history_dataset_association.dataset_id \nWHERE
history_dataset_association.history_id = %(lazy_245d)s AND NOT
history_dataset_association.deleted ORDER BY
history_dataset_association.hid ASC, anon_d37b.id' {'lazy_245d': 37L}
I guess I didn't perform some required database alteration, I just
don't
know which one...
Please advise.
Thanks for your help,
Gordon.