galaxy.model.migrate.check DEBUG 2010-02-19 12:48:02,077 MySQL_python egg successfully loaded for mysql dialect
Traceback (most recent call last):
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py", line 61, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py", line 28, in __init__
create_or_verify_database( db_url, self.config.database_engine_options )
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py", line 50, in create_or_verify_database
engine = create_engine( url, **engine_options )
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/__init__.py", line 223, in create_engine
return strategy.create(*args, **kwargs)
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/strategies.py", line 62, in create
dbapi = dialect_cls.dbapi(**dbapi_args)
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py", line 1456, in dbapi
import MySQLdb as mysql
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-macosx-10.3-fat-ucs2/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg/MySQLdb/__init__.py", line 19, in <module>
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-macosx-10.3-fat-ucs2/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg/_mysql.py", line 7, in <module>
File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-macosx-10.3-fat-ucs2/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg/_mysql.py", line 6, in __bootstrap__
Referenced from: /Users/rsw3284/.python-eggs/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg-tmp/_mysql.so
Reason: image not found
What's strange is that eventhough the file name on the egg is MySQL*fat-ucs2.egg the error still reports the file in question as MySQL*fat.egg -- I've tried renaming the egg to match the original file, but it didn't seem to make a difference. Furthermore, when I run.sh, the program will create a directory in home called .python-eggs/ containing the _MySQL.so file, among other things - Will I have to add a different URL to the eggs.ini to keep it from re-downloading the old file?
Rgds,
Roy Weckiewicz.
On Thu, Feb 18, 2010 at 8:34 PM, Nate Coraor
<nate@bx.psu.edu> wrote:
I was looking for someone to test it, try placing this in eggs/py2.4-macosx-10.3-fat-ucs2:
http://www.bx.psu.edu/~nate/galaxy/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat-ucs2.egg
--nate
Kanwei Li wrote:
Ah, I just tried it myself and it's because the mysql egg isn't being
loaded properly. I believe we're still working on creating a
statically linked mysql egg and it's not complete yet. I do suggest
using postgres, which is very good and used for our production
systems, and works on OS X. The connection strings look like:
mysql://user:pass@localhost/test
postgresql://user:pass@localhost/test
Kanwei
On Thu, Feb 18, 2010 at 7:25 PM, Roy Weckiewicz <roystefan@gmail.com> wrote:
Hi Kanwei,
Thank you for your response.
I've tried setting the database connection in the universe_wsgi.ini file
to: database_connection =
mysql:///galaxy?unix_socket=/private/tmp/mysql.sock (after a new download of
galaxy and first running setup.sh)
Is the format correct for a OSX system running OSX? -- When I try to 'sh
run.sh' with this line included, I get the following errors:
galaxy.model.migrate.check DEBUG 2010-02-18 18:15:06,092 MySQL_python egg
successfully loaded for mysql dialect
Traceback (most recent call last):
File "/Users/rsw3284/Downloads/galaxy-NEW/lib/galaxy/web/buildapp.py",
line 61, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/Users/rsw3284/Downloads/galaxy-NEW/lib/galaxy/app.py", line 28, in
__init__
create_or_verify_database( db_url, self.config.database_engine_options )
File
"/Users/rsw3284/Downloads/galaxy-NEW/lib/galaxy/model/migrate/check.py",
line 50, in create_or_verify_database
engine = create_engine( url, **engine_options )
File
"/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/__init__.py",
line 223, in create_engine
return strategy.create(*args, **kwargs)
File
"/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/strategies.py",
line 62, in create
dbapi = dialect_cls.dbapi(**dbapi_args)
File
"/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py",
line 1456, in dbapi
import MySQLdb as mysql
File
"/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-macosx-10.3-fat-ucs2/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg/MySQLdb/__init__.py",
line 19, in <module>
File
"/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-macosx-10.3-fat-ucs2/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg/_mysql.py",
line 7, in <module>
File
"/Users/rsw3284/Downloads/galaxy-NEW/eggs/py2.5-macosx-10.3-fat-ucs2/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg/_mysql.py",
line 6, in __bootstrap__
ImportError:
dlopen(/Users/rsw3284/.python-eggs/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg-tmp/_mysql.so,
2): Library not loaded:
/afs/bx.psu.edu/home/nate/work/galaxy_central/scripts/scramble/build/py2.4-macosx-10.3-fat-ucs2/MySQL_python/mysql/lib/mysql/libmysqlclient_r.15.dylib
Referenced from:
/Users/rsw3284/.python-eggs/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg-tmp/_mysql.so
Reason: image not found
The program fails here and no database file is ever created. If I run the
program with the previously mentioned line commented, the sqlite database
creation goes without a hitch, but once exported the syntax is much
different from what mysql will accept. Any ideas?
Rgds,
Roy Weckiewicz
On Thu, Feb 18, 2010 at 2:56 PM, Kanwei Li <kanwei@gmail.com> wrote:
Hi Roy,
What I would suggest is to dump the sqlite database to standard sql,
and then creating a new instance of galaxy that has mysql as the
configured database. When you run the setup and run script, you'll
have a freshly instantiated galaxy with empty mysql tables. Then you
can just import the standard sql file into the mysql database.
Hope this helps,
Kanwei
On Thu, Feb 18, 2010 at 1:27 PM, Roy Weckiewicz <roystefan@gmail.com>
wrote:
Hello,
I am trying to configure a local galaxy server using a MYSQL database
instead of the standard sqlite3. I'm using OSX and have been attempting
(unsuccessfully) to convert the sqlite database (universe.sql) to mysql
format. Basically, I am in need of the database table schema for mysql.
I
noticed on your web page that you host a mysql server
at: genome-mysql.cse.ucsc.edu
-- would it be possible to do some sort of mysqldump or mysqlhotcopy in
order to download the table schema, so that I could upload them into my
local mysql installation?
I've tried using Sqlite3 to dump the contents of universe.sql, but
there are numerous syntax differences that need to be addressed
before it will load successfully into my mysql database.
Do you have any suggestions on how to either migrate the database from
sqlite3 to MYSQL (via script or program),
or create the mysql database from scratch and just import the correct
table
schema?
Any help would be appreciated.
MYSQL: Ver 14.14 Distrib 5.1.37, for apple-darwin9.5.0 (i386) using
readline
5.1
Python 2.5.1
Rgds,
Roy Weckiewicz.
--
Roy Weckiewicz
Texas A&M University
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--
Roy Weckiewicz
Texas A&M University
--
Roy Weckiewicz
Texas A&M University