Actually, the example in my previous letter wasn't correct - I have tried
to run run.sh and manage_db.sh scripts several times after creation of
novel db, and the copy-paste is the result of the last attempt. So, indeed,
the db galaxy was created in the first running, while warning messages from
the last running. But now I drop the db again, and the issue is reproduced
right after creation of the fresh db:
[galaxy@cluster galaxy-dist]$ sh run.sh
<~! several messages are omitted !~>
migrate.versioning.script.base DEBUG 2013-09-11 18:33:49,426 Loading script
lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py...
migrate.versioning.script.base DEBUG 2013-09-11 18:33:49,426 Script
lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded
successfully
migrate.versioning.script.base DEBUG 2013-09-11 18:33:49,426 Loading script
lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py...
migrate.versioning.script.base DEBUG 2013-09-11 18:33:49,426 Script
lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
loaded successfully
migrate.versioning.script.base DEBUG 2013-09-11 18:33:49,426 Loading script
lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py...
migrate.versioning.script.base DEBUG 2013-09-11 18:33:49,426 Script
lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded
successfully
migrate.versioning.repository DEBUG 2013-09-11 18:33:49,427 Repository
lib/galaxy/model/migrate loaded successfully
migrate.versioning.repository DEBUG 2013-09-11 18:33:49,427 Config:
OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'),
('repository_id', 'Galaxy'), ('version_table', 'migrate_version'),
('required_dbs', '[]')]))])
galaxy.model.migrate.check DEBUG 2013-09-11 18:33:49,433 psycopg2 egg
successfully loaded for postgres dialect
/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/url.py:105:
SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed
from 'postgres' to 'postgresql'. The new URL format is
postgresql[+driver]://<user>:<pass>@<host>/<dbname>
galaxy.model.migrate.check INFO 2013-09-11 18:33:49,447 No database,
initializing
galaxy.model.migrate.check INFO 2013-09-11 18:33:49,477 Migrating 0 -> 1...
galaxy.model.migrate.check INFO 2013-09-11 18:33:49,712
galaxy.model.migrate.check INFO 2013-09-11 18:33:49,712 Migrating 1 -> 2...
galaxy.model.migrate.check INFO 2013-09-11 18:33:50,013
galaxy.model.migrate.check INFO 2013-09-11 18:33:50,014 Migrating 2 -> 3...
galaxy.model.migrate.check INFO 2013-09-11 18:33:50,803
galaxy.model.migrate.check INFO 2013-09-11 18:33:50,803 Migrating 3 -> 4...
galaxy.model.migrate.check INFO 2013-09-11 18:33:51,502
galaxy.model.migrate.check INFO 2013-09-11 18:33:51,502 Migrating 4 -> 5...
galaxy.model.custom_types DEBUG 2013-09-11 18:33:51,556 Fixing a
discrepancy concerning deleted shared history items.
galaxy.model.custom_types DEBUG 2013-09-11 18:33:51,583 0 items affected,
and restored.
galaxy.model.custom_types DEBUG 2013-09-11 18:33:51,583 Time elapsed:
0.0264229774475
galaxy.model.custom_types DEBUG 2013-09-11 18:33:51,583 Fixing a
discrepancy concerning cleaning up deleted history items shared before HDAs.
galaxy.model.custom_types DEBUG 2013-09-11 18:33:51,586 0 items affected,
and restored.
galaxy.model.custom_types DEBUG 2013-09-11 18:33:51,586 Time elapsed:
0.00265407562256
galaxy.model.migrate.check INFO 2013-09-11 18:33:51,589
galaxy.model.migrate.check INFO 2013-09-11 18:33:51,589 Migrating 5 -> 6...
galaxy.model.migrate.check INFO 2013-09-11 18:33:52,334
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:52,334 This migration
script changes certain values in the history_dataset_association.extension
galaxy.model.migrate.check INFO 2013-09-11 18:33:52,334 column,
specifically 'qual' is chaged to be 'qual454'.
galaxy.model.migrate.check INFO 2013-09-11 18:33:52,334
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:52,334
galaxy.model.migrate.check INFO 2013-09-11 18:33:52,335 Migrating 6 -> 7...
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,053
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,053 This migration
script creates the new history_user_share_association table, and adds
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,053 a new boolean type
column to the history table. This provides support for sharing
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,053 histories in the
same way that workflows are shared.
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,053
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,053
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,054 Migrating 7 -> 8...
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,969
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,970 This migration
script adds the following new tables for supporting Galaxy forms:
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,970 1)
form_definition_current
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,970 2) form_definition
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,970 3) form_values
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,970 4) request_type
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,970 5) request
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,970 6) sample
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,970 7) sample_state
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,971 8) sample_event
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,971
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,971
galaxy.model.migrate.check INFO 2013-09-11 18:33:53,971 Migrating 8 -> 9...
galaxy.model.migrate.check INFO 2013-09-11 18:33:54,784
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:54,784 This migration
script adds a new column to 2 tables:
galaxy.model.migrate.check INFO 2013-09-11 18:33:54,785 1) a new boolean
type column named 'submitted' to the 'request' table
galaxy.model.migrate.check INFO 2013-09-11 18:33:54,785 2) a new string
type column named 'bar_code' to the 'sample' table
galaxy.model.migrate.check INFO 2013-09-11 18:33:54,785
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:54,785
galaxy.model.migrate.check INFO 2013-09-11 18:33:54,785 Migrating 9 ->
10...
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,607
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,607 This migration
script adds the history_dataset_association_display_at_authorization table,
which
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,608 allows 'private'
datasets to be displayed at external sites without making them public.
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,608
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,608 If using mysql,
this script will display the following error, which is corrected in the
next migration
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,608 script:
history_dataset_association_display_at_authorization table failed:
(OperationalError)
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,608 (1059, 'Identifier
name 'ix_history_dataset_association_display_at_authorization_update_time'
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,608 is too long.
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,608
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,608
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,609 Migrating 10 ->
11...
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,617
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,617 This script fixes a
problem introduced in the previous migration script ( 9->10 ). MySQL
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,617 has a name length
limit and thus the index 'ix_hdadaa_history_dataset_association_id' has
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,618 to be manually
created.
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,618
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,618
galaxy.model.migrate.check INFO 2013-09-11 18:33:55,618 Migrating 11 ->
12...
galaxy.model.migrate.check INFO 2013-09-11 18:33:56,467
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:56,467 This script adds a
new user_address table that is currently only used with sample requests,
where
galaxy.model.migrate.check INFO 2013-09-11 18:33:56,467 a user can select
from a list of his addresses to associate with the request. This script
also
galaxy.model.migrate.check INFO 2013-09-11 18:33:56,467 drops the
request.submitted column which was boolean and replaces it with a
request.state column
galaxy.model.migrate.check INFO 2013-09-11 18:33:56,467 which is a string,
allowing for more flexibility with request states.
galaxy.model.migrate.check INFO 2013-09-11 18:33:56,467
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:56,467
galaxy.model.migrate.check INFO 2013-09-11 18:33:56,468 Migrating 12 ->
13...
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,362
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,362 This migration
script eliminates all of the tables that were used for the 1st version of
the
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,362 library templates
where template fields and contents were each stored as a separate table row
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,362 in various library
item tables. All of these tables are dropped in this script, eliminating
all
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,362 existing template
data. A total of 14 existing tables are dropped.
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,362
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,362 We're now basing
library templates on Galaxy forms, so field contents are stored as a
jsonified
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,362 list in the
form_values table. This script introduces the following 3 new association
tables:
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,363 1)
library_info_association
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,363 2)
library_folder_info_association
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,363 3)
library_dataset_dataset_info_association
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,363
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,363 If using mysql,
this script will throw an (OperationalError) exception due to a long index
name
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,363 on the
library_dataset_dataset_info_association table, which is OK because the
script creates
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,363 an index with a
shortened name.
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,363
========================================
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,364
galaxy.model.migrate.check INFO 2013-09-11 18:33:57,364 Migrating 13 ->
14...
galaxy.model.migrate.check INFO 2013-09-11 18:33:58,217
galaxy.model.migrate.check INFO 2013-09-11 18:33:58,217 Migration script to
add support for "Pages".
galaxy.model.migrate.check INFO 2013-09-11 18:33:58,217 1) Creates Page
and PageRevision tables
galaxy.model.migrate.check INFO 2013-09-11 18:33:58,217 2) Adds username
column to User table
galaxy.model.migrate.check INFO 2013-09-11 18:33:58,217
galaxy.model.migrate.check INFO 2013-09-11 18:33:58,217
Traceback (most recent call last):
File
"/export/apps/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
line 35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/export/apps/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in
__init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options, app=self )
File "/export/apps/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
line 66, in create_or_verify_database
migrate_to_current_version( engine, db_schema )
File "/export/apps/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
line 124, in migrate_to_current_version
schema.runchange( ver, change, changeset.step )
File
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py",
line 91, in runchange
change.run(self.engine, step)
File
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/script/py.py",
line 145, in run
script_func(engine)
File "lib/galaxy/model/migrate/versions/0014_pages.py", line 67, in
upgrade
col.create( User_table, index_name='ix_user_username',
unique_name='username' )
File
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/schema.py",
line 533, in create
engine.execute(stmt)
File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 2446, in execute
return connection.execute(statement, *multiparams, **params)
File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1449, in execute
params)
File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
context)
File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
context)
File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
cursor.execute(statement, parameters)
ProgrammingError: (ProgrammingError) column "username" is of type character
varying but expression is of type boolean
HINT: You will need to rewrite or cast the expression.
'UPDATE galaxy_user SET username=%(username)s' {'username': False}
2013/9/11 Nate Coraor <n...@bx.psu.edu>
> On Sep 11, 2013, at 9:16 AM, hogart wrote:
>
> > Hi Nate,
> > Yes, db schema is old, but the upgrading (manage_db.sh upgrade) to the
> current version resulted to the error, as mentioned above. I don't remember
> the release number of the previous version of Galaxy, but it was installed
> in the March this year. A didn't restored the dump yet, now I am playinig
> with the newly created database. In my newbie point of view, it seems like,
> that dropping of the old database (drop database galaxy; as superuser) was
> incomplete, - is it possible?
> > Thanks for letting me know, I will try to upgrade the PostgeSQL (the
> current version is default version of CentOS 5.6).
>
>
> Sorry, I missed the bit where you were starting with an empty database and
> not reloading your dump of the old one.
>
> It does seem possible that your database is not empty on startup, as the
> username column should not already exist at the time that this migration
> script runs. When you drop and then create the database, Galaxy should
> create all the necessary tables and run through all of the migration
> scripts the first time that you start it. Is it doing this? If it thinks
> that the database is already at revision 13, I suspect the database is not
> empty when it starts up. Check your database_connection string in
> universe_wsgi.ini and make sure it is pointed at the correct database.
>
> --nate
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