Question: Problems Upgrading To Mercurial
0
gravatar for Assaf Gordon
10.2 years ago by
Assaf Gordon320
United States
Assaf Gordon320 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.
galaxy • 950 views
ADD COMMENTlink written 10.2 years ago by Assaf Gordon320
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