On Wed, Mar 16, 2011 at 2:06 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> Peter Cock wrote:
>> On Tue, Mar 15, 2011 at 3:18 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>>
>> Hi Nate,
>>
>> The workaround failed for me,
>>
>> $ python -ES ./scripts/manage_db.py upgrade
>> Traceback (most recent call last):
>>   File "./scripts/manage_db.py", line 12, in <module>
>>     from migrate.versioning.shell import main
>>   File 
>> "/Users/pjcock/repositories/galaxy-central-stuck-db-75/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
>> line 7, in <module>
>>     from migrate.versioning.base import *
>>   File 
>> "/Users/pjcock/repositories/galaxy-central-stuck-db-75/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/base/__init__.py",
>> line 5, in <module>
>>     from const import databases,operations
>>   File 
>> "/Users/pjcock/repositories/galaxy-central-stuck-db-75/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/base/const.py",
>> line 7, in <module>
>>     from sqlalchemy.util import OrderedDict
>> ImportError: No module named sqlalchemy.util
>>
>> There's probably some PYTHONPATH or something solution to this... I
>> don't use eggs enough to see it immediately though.
>
> Hmm, okay.  Try the following:
>
>  python -ES ./scripts/fetch_eggs.py
>
> And then again:
>
>  python -ES ./scripts/manage_db.py upgrade
>
>> Is there a bug open for the upgrade issue?
>
> No, I think this is isolated to something going on in your specific
> python environment.  If I can reproduce it then I can work on a fix.
>
> --nate


$ python -ES ./scripts/fetch_eggs.py
Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.2.5-py2.6.egg
Fetched 
http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-macosx-10.6-universal-ucs2.egg
Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg
Fetched 
http://eggs.g2.bx.psu.edu/Cheetah/Cheetah-2.2.2-py2.6-macosx-10.6-universal-ucs2.egg
Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg
Warning: decorator (a dependent egg of sqlalchemy-migrate) cannot be fetched
Fetched 
http://eggs.g2.bx.psu.edu/bx_python/bx_python-0.7.0_14b6a6c95da6-py2.6-macosx-10.6-universal-ucs2.egg
Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
Fetched 
http://eggs.g2.bx.psu.edu/numpy/numpy-1.3.0-py2.6-macosx-10.6-universal-ucs2.egg
Fetched 
http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.6-macosx-10.6-universal-ucs2.egg
Fetched http://eggs.g2.bx.psu.edu/Beaker/Beaker-1.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/SVGFig/SVGFig-1.1.6-py2.6.egg
Fetched 
http://eggs.g2.bx.psu.edu/SQLAlchemy/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg
Fetched 
http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.6-macosx-10.6-universal-ucs2.egg
Fetched http://eggs.g2.bx.psu.edu/NoseTestDiff/NoseTestDiff-0.1-py2.6.egg
Fetched 
http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.6-macosx-10.6-universal-ucs2.egg
Fetched http://eggs.g2.bx.psu.edu/wchartype/wchartype-0.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/twill/twill-0.9-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/Routes/Routes-1.12.3-py2.6.egg
Fetched 
http://eggs.g2.bx.psu.edu/elementtree/elementtree-1.2.6_20050316-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/decorator/decorator-3.1.2-py2.6.egg
Fetched 
http://eggs.g2.bx.psu.edu/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.6.egg
Fetched 
http://eggs.g2.bx.psu.edu/pycrypto/pycrypto-2.0.1-py2.6-macosx-10.6-universal-ucs2.egg
Fetched http://eggs.g2.bx.psu.edu/WebError/WebError-0.8a-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/Paste/Paste-1.6-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/wsgiref/wsgiref-0.1.2-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/python_daemon/python_daemon-1.5.5-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/nose/nose-0.11.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/WebOb/WebOb-0.8.5-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/PasteScript/PasteScript-1.7.3-py2.6.egg

$ python -ES ./scripts/manage_db.py upgrade
75 -> 76...

This migration script fixes the data corruption caused in the form_values
table (content json field) by migrate script 65.

No corrupted rows found.
done


Job done - thanks! This also worked on the old install I had stuck on DB
version 73. Does this help explain what the root cause of the problem is?

Peter

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