Re: [galaxy-dev] migration error
On Wed, May 8, 2013 at 10:19 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Robert, I assume this is sqlite? And, when you say you ran this without any existing database -- was this was a completely new clone of galaxy, or did you update a prior installation and delete database/universe.sqlite manually before running? -Dannon Hi guys, I've just hit this bug too, using SQLite on a working development machine which was running with schema 114 until I grabbed the latest galaxy-central just now, revision 80ab774559f8405a46082286c6cf35db420db002 $ sh manage_db.sh upgrade 114 - 115... Altering password column failed Traceback (most recent call last): File lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py, line 15, in upgrade user.c.password.alter(type=String(255)) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py, line 491, in alter return alter_column(self, *p, **k) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py, line 136, in alter_column engine._run_visitor(visitorcallable, delta) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 2302, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1972, in _run_visitor **kwargs).traverse_single(element) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py, line 53, in traverse_single ret = super(AlterTableVisitor, self).traverse_single(elem) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/visitors.py, line 106, in traverse_single return meth(obj, **kw) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py, line 53, in visit_column self.recreate_table(table,column,delta) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py, line 36, in recreate_table self.execute() File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py, line 42, in execute return self.connection.execute(self.buffer.getvalue()) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1449, in execute params) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1628, in _execute_text statement, parameters File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1698, in _execute_context context) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1691, in _execute_context context) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py, line 331, in do_execute cursor.execute(statement, parameters) OperationalError: (OperationalError) there is already another table or index with this name: migration_tmp 'ALTER TABLE galaxy_user RENAME TO migration_tmp' () done Presumably one of the previous migration scripts has left an old migration_tmp table in place? Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] migration error
On Thu, May 9, 2013 at 11:03 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, May 8, 2013 at 10:19 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Robert, I assume this is sqlite? And, when you say you ran this without any existing database -- was this was a completely new clone of galaxy, or did you update a prior installation and delete database/universe.sqlite manually before running? -Dannon Hi guys, I've just hit this bug too, using SQLite on a working development machine which was running with schema 114 until I grabbed the latest galaxy-central just now, revision 80ab774559f8405a46082286c6cf35db420db002 $ sh manage_db.sh upgrade 114 - 115... Altering password column failed Traceback (most recent call last): File lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py, line 15, in upgrade user.c.password.alter(type=String(255)) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py, line 491, in alter return alter_column(self, *p, **k) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py, line 136, in alter_column engine._run_visitor(visitorcallable, delta) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 2302, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1972, in _run_visitor **kwargs).traverse_single(element) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py, line 53, in traverse_single ret = super(AlterTableVisitor, self).traverse_single(elem) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/visitors.py, line 106, in traverse_single return meth(obj, **kw) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py, line 53, in visit_column self.recreate_table(table,column,delta) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py, line 36, in recreate_table self.execute() File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py, line 42, in execute return self.connection.execute(self.buffer.getvalue()) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1449, in execute params) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1628, in _execute_text statement, parameters File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1698, in _execute_context context) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1691, in _execute_context context) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py, line 331, in do_execute cursor.execute(statement, parameters) OperationalError: (OperationalError) there is already another table or index with this name: migration_tmp 'ALTER TABLE galaxy_user RENAME TO migration_tmp' () done Presumably one of the previous migration scripts has left an old migration_tmp table in place? Note that attempting to re-run the migration appeared to do nothing: $ sh manage_db.sh upgrade $ sh run.sh ... This isn't a big issue for my development machine, but it would seem that this migration step aborted halfway (having marked the schema as being updated to version 115), and did not roll back the database to the previous state labelled as version 114. If that happens just on SQLite that's tolerable, but if there is no transaction integrity used on MySQL or PostgreSQL the migration framework seems very fragile. Regards, Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] migration error
This isn't an issue with postgresql or mysql; they don't use a temporary table for table alterations. Can you open up the sqlite database if you still have it and see what the contents of the migrate_tmp table were? They'll be a copy of a prior migrated table, I'm just curious what from -- it should have been cleaned up previously in the event of successful migrations. My hunch is that previously various scripts threw a lot of errors for mysql and so this table wasn't automatically cleaned up after after the execution of one of those migration scripts, but the old version of sqlalchemy-migrate didn't care if it existed or not and would overwrite it, while the new version is more reticent to delete the table (which is probably more reasonable, should you need to recover data after an unsuccessful migration). In any event, to fix it, you'll want to make sure that the contents of that migrate_tmp table aren't something you want and drop it, downgrade to 114, then upgrade to 115 again. If I can recreate this I'll work on a more reasonable solution. Dannon On Thu, May 9, 2013 at 6:12 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Thu, May 9, 2013 at 11:03 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, May 8, 2013 at 10:19 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Robert, I assume this is sqlite? And, when you say you ran this without any existing database -- was this was a completely new clone of galaxy, or did you update a prior installation and delete database/universe.sqlite manually before running? -Dannon Hi guys, I've just hit this bug too, using SQLite on a working development machine which was running with schema 114 until I grabbed the latest galaxy-central just now, revision 80ab774559f8405a46082286c6cf35db420db002 $ sh manage_db.sh upgrade 114 - 115... Altering password column failed Traceback (most recent call last): File lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py, line 15, in upgrade user.c.password.alter(type=String(255)) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py, line 491, in alter return alter_column(self, *p, **k) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py, line 136, in alter_column engine._run_visitor(visitorcallable, delta) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 2302, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1972, in _run_visitor **kwargs).traverse_single(element) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py, line 53, in traverse_single ret = super(AlterTableVisitor, self).traverse_single(elem) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/visitors.py, line 106, in traverse_single return meth(obj, **kw) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py, line 53, in visit_column self.recreate_table(table,column,delta) File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py, line 36, in recreate_table self.execute() File /mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py, line 42, in execute return self.connection.execute(self.buffer.getvalue()) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1449, in execute params) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1628, in _execute_text statement, parameters File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1698, in _execute_context context) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1691, in _execute_context context) File /mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py, line 331, in do_execute cursor.execute(statement, parameters) OperationalError: (OperationalError) there is already another table or index with this name: migration_tmp 'ALTER TABLE galaxy_user RENAME TO migration_tmp' () done Presumably one of the previous migration scripts has left an old migration_tmp table in place? Note that attempting to re-run the migration appeared to do nothing: $ sh manage_db.sh upgrade $ sh run.sh ... This isn't a big issue for
Re: [galaxy-dev] migration error
On Thu, May 9, 2013 at 12:56 PM, Dannon Baker dannon.ba...@gmail.com wrote: This isn't an issue with postgresql or mysql; they don't use a temporary table for table alterations. Oh good :) Can you open up the sqlite database if you still have it and see what the contents of the migrate_tmp table were? They'll be a copy of a prior migrated table, I'm just curious what from -- it should have been cleaned up previously in the event of successful migrations. It looks like whatever was there has been lost (which doesn't really worry me on this machine - it is a test setup only): $ sqlite3 database/universe.sqlite SQLite version 3.6.20 Enter .help for instructions Enter SQL statements terminated with a ; sqlite select * from migrate_tmp; Error: no such table: migrate_tmp My hunch is that previously various scripts threw a lot of errors for mysql and so this table wasn't automatically cleaned up after after the execution of one of those migration scripts, but the old version of sqlalchemy-migrate didn't care if it existed or not and would overwrite it, while the new version is more reticent to delete the table (which is probably more reasonable, should you need to recover data after an unsuccessful migration). That makes sense. In any event, to fix it, you'll want to make sure that the contents of that migrate_tmp table aren't something you want and drop it, downgrade to 114, then upgrade to 115 again. If I can recreate this I'll work on a more reasonable solution. One idea might be to name the migration_tmp tables using the schema revision to avoid clashes, e.g. migration_115_tmp in this case? Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] migration error
I upgraded to the latest galaxy-central and got an error when running migration script 115 which lengthens the password field from 40-255. It failed saying that the table migration_tmp already exists. I ran this without any existing database so I don't think it is anything on my end. Any pointers? .schema migration_tmp CREATE TABLE migration_tmp ( id INTEGER NOT NULL, create_time TIMESTAMP, update_time TIMESTAMP, tool_shed_repository_id INTEGER NOT NULL, name VARCHAR(255), version VARCHAR(40), type VARCHAR(40), uninstalled BOOLEAN, error_message TEXT, PRIMARY KEY (id), FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id) ); ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] migration error
Hey Robert, I assume this is sqlite? And, when you say you ran this without any existing database -- was this was a completely new clone of galaxy, or did you update a prior installation and delete database/universe.sqlite manually before running? -Dannon On Wed, May 8, 2013 at 2:07 PM, Robert Baertsch robert.baert...@gmail.comwrote: I upgraded to the latest galaxy-central and got an error when running migration script 115 which lengthens the password field from 40-255. It failed saying that the table migration_tmp already exists. I ran this without any existing database so I don't think it is anything on my end. Any pointers? .schema migration_tmp CREATE TABLE migration_tmp ( id INTEGER NOT NULL, create_time TIMESTAMP, update_time TIMESTAMP, tool_shed_repository_id INTEGER NOT NULL, name VARCHAR(255), version VARCHAR(40), type VARCHAR(40), uninstalled BOOLEAN, error_message TEXT, PRIMARY KEY (id), FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id) ); ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Migration error: fields in MySQL
John Eppley wrote: I had an error upgrading my galaxy instance. I got the following exception while migrating the db (during step 64-65): sqlalchemy.exc.ProgrammingError: (ProgrammingError) (1064, You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'fields FROM form_definition' at line 1) u'SELECT id, fields FROM form_definition' [] It seems my version (4.1.22-log) of MySQL did not like 'fields' as a column name. If I alias the formdefinition as f and us f.fields, the error goes away. I also had to modify migration 76 for the same reason. Hi John, Thanks for the patch, I've committed it as 5619:b6689fb6532e. --nate Here is my diff of the migrations dir: diff -r 50e249442c5a lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py --- a/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py Thu Apr 07 08:39:07 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py Fri Apr 15 11:09:26 2011 -0400 @@ -39,7 +39,7 @@ return '' # Go through the entire table and add a 'name' attribute for each field # in the list of fields for each form definition -cmd = SELECT id, fields FROM form_definition +cmd = SELECT f.id, f.fields FROM form_definition f result = db_session.execute( cmd ) for row in result: form_definition_id = row[0] @@ -53,7 +53,7 @@ field[ 'helptext' ] = field[ 'helptext' ].replace(', '').replace('', ) field[ 'label' ] = field[ 'label' ].replace(', '') fields_json = to_json_string( fields_list ) -cmd = UPDATE form_definition SET fields='%s' WHERE id=%i %( fields_json, form_definition_id ) +cmd = UPDATE form_definition f SET f.fields='%s' WHERE f.id=%i %( fields_json, form_definition_id ) db_session.execute( cmd ) # replace the values list in the content field of the form_values table with a name:value dict cmd = SELECT form_values.id, form_values.content, form_definition.fields \ @@ -112,7 +112,7 @@ cmd = UPDATE form_values SET content='%s' WHERE id=%i %( to_json_string( values_list ), form_values_id ) db_session.execute( cmd ) # remove name attribute from the field column of the form_definition table -cmd = SELECT id, fields FROM form_definition +cmd = SELECT f.id, f.fields FROM form_definition f result = db_session.execute( cmd ) for row in result: form_definition_id = row[0] @@ -124,5 +124,5 @@ for index, field in enumerate( fields_list ): if field.has_key( 'name' ): del field[ 'name' ] -cmd = UPDATE form_definition SET fields='%s' WHERE id=%i %( to_json_string( fields_list ), form_definition_id ) +cmd = UPDATE form_definition f SET f.fields='%s' WHERE id=%i %( to_json_string( fields_list ), form_definition_id ) db_session.execute( cmd ) diff -r 50e249442c5a lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py --- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Thu Apr 07 08:39:07 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Fri Apr 15 11:09:26 2011 -0400 @@ -32,7 +32,7 @@ def upgrade(): print __doc__ metadata.reflect() -cmd = SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fields \ +cmd = SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fdfields \ + FROM form_definition, form_values \ + WHERE form_values.form_definition_id=form_definition.id \ + ORDER BY form_values.id @@ -46,7 +46,7 @@ except Exception, e: corrupted_rows = corrupted_rows + 1 # content field is corrupted -fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fields'] ) ) ) +fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fdfields'] ) ) ) field_values_str = _sniffnfix_pg9_hex( str( row['field_values'] ) ) try: #Encoding errors? Just to be safe. -j ___ 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/