Re: [galaxy-dev] migration error
On Thu, May 9, 2013 at 12:56 PM, Dannon Baker 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/
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 wrote: > On Thu, May 9, 2013 at 11:03 AM, Peter Cock > wrote: > > On Wed, May 8, 2013 at 10:19 PM, Dannon Baker > 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 th
Re: [galaxy-dev] migration error
On Thu, May 9, 2013 at 11:03 AM, Peter Cock wrote: > On Wed, May 8, 2013 at 10:19 PM, Dannon Baker 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
On Wed, May 8, 2013 at 10:19 PM, Dannon Baker 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
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 wrote: > 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/
___
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in your mail client. T
