Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-18 Thread Nate Coraor
Peter Cock wrote:

> > Were there really no eggs, or did you remove your eggs directory prior
> > to running this fetch?
> 
> I can't tell you if there were no eggs (I'm fairly sure there were
> some), but I hadn't removed any deliberately. Might that have
> happened via hg update clean?

I'm pretty sure hg update clean will only remove changes of tracked
files, not untracked ones like the eggs.

> > Depending on the answer to the above question, it means there is
> > probably (still) a bug in the egg conflict/resolve code somewhere.
> 
> I will be in touch if this happens again (and it probably will next
> time the database schema is updated), but if you want I could
> try and reproduce it by doing a clean checkout of an old revision,
> running galaxy, then try to update it to the current code.

If you know the exact revision to start with to reproduce it, that'd
certainly help.

Thanks,
--nate

> 
> Regards,
> 
> Peter
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Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-17 Thread Peter Cock
On Thu, Mar 17, 2011 at 7:47 PM, Nate Coraor  wrote:
> Peter Cock wrote:
>>
>> $ 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/PasteScript/PasteScript-1.7.3-py2.6.egg
>
> Were there really no eggs, or did you remove your eggs directory prior
> to running this fetch?

I can't tell you if there were no eggs (I'm fairly sure there were
some), but I hadn't removed any deliberately. Might that have
happened via hg update clean?

>>
>> $ 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?
>
> Depending on the answer to the above question, it means there is
> probably (still) a bug in the egg conflict/resolve code somewhere.

I will be in touch if this happens again (and it probably will next
time the database schema is updated), but if you want I could
try and reproduce it by doing a clean checkout of an old revision,
running galaxy, then try to update it to the current code.

Regards,

Peter
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Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-17 Thread Nate Coraor
Peter Cock wrote:
> 
> $ 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

Were there really no eggs, or did you remove your eggs directory prior
to running this fetch?

> 
> $ 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?

Depending on the answer to the above question, it means there is
probably (still) a bug in the egg conflict/resolve code somewhere.

--nate

> 
> Peter
> 
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Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-17 Thread Peter Cock
On Wed, Mar 16, 2011 at 2:06 PM, Nate Coraor  wrote:
> Peter Cock wrote:
>> On Tue, Mar 15, 2011 at 3:18 PM, Nate Coraor  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 
>>     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 
>>     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 
>>     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 
>>     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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Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-16 Thread Nate Coraor
Peter Cock wrote:
> On Tue, Mar 15, 2011 at 3:18 PM, Nate Coraor  wrote:
> > Peter Cock wrote:
> >
> >> $ sh manage_db.sh upgrade
> >> Traceback (most recent call last):
> >>   File "./scripts/manage_db.py", line 12, in 
> >>     from migrate.versioning.shell import main
> >> ImportError: No module named migrate.versioning.shell
> >
> > This is a bug, but as a workaround try the following:
> >
> > python -ES ./scripts/manage_db.py upgrade
> >
> 
> 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 
> 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 
> 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 
> 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 
> 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

> 
> Thanks,
> 
> Peter
> 
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Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-15 Thread Peter Cock
On Tue, Mar 15, 2011 at 3:18 PM, Nate Coraor  wrote:
> Peter Cock wrote:
>
>> $ sh manage_db.sh upgrade
>> Traceback (most recent call last):
>>   File "./scripts/manage_db.py", line 12, in 
>>     from migrate.versioning.shell import main
>> ImportError: No module named migrate.versioning.shell
>
> This is a bug, but as a workaround try the following:
>
> python -ES ./scripts/manage_db.py upgrade
>

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 
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 
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 
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 
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.

Is there a bug open for the upgrade issue?

Thanks,

Peter

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Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-15 Thread Nate Coraor
Peter Cock wrote:

> $ sh manage_db.sh upgrade
> Traceback (most recent call last):
>   File "./scripts/manage_db.py", line 12, in 
> from migrate.versioning.shell import main
> ImportError: No module named migrate.versioning.shell

This is a bug, but as a workaround try the following:

python -ES ./scripts/manage_db.py upgrade

> 
> 
> Peter
> ___
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Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-11 Thread Peter Cock
On Mon, Feb 21, 2011 at 3:41 PM, Peter Cock  wrote:
> Hi all,
>
> I've just updated my Mac development machine with the latest
> galaxy-central, and run.sh tells me the database needs to be updated
> from 73 to 75. Note this is running on SQLite. Running manage_db.sh
> upgrade gives an ImportError: No module named migrate.versioning.shell
>
> I just grabbed a fresh hg clone and it worked, but in case there is an
> obvious bug lurking here, the full output is below (and I'll keep the
> broken install on disk a bit longer in case there is anything else you
> need to know).
>
> Regards,
>
> Peter


I just got the same issue with 75 to 76 on this machine :(

$ ./run.sh
...
galaxy.model.migrate.check DEBUG 2011-03-11 11:09:40,719 pysqlite>=2
egg successfully loaded for sqlite dialect
Traceback (most recent call last):
  File "/Users/pjcock/repositories/galaxy-central/lib/galaxy/web/buildapp.py",
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/Users/pjcock/repositories/galaxy-central/lib/galaxy/app.py",
line 32, in __init__
create_or_verify_database( db_url, self.config.database_engine_options )
  File 
"/Users/pjcock/repositories/galaxy-central/lib/galaxy/model/migrate/check.py",
line 102, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest ) )
Exception: Your database has version '75' but this code expects
version '76'.  Please backup your database and then migrate the schema
by running 'sh manage_db.sh upgrade'.

then:

$ sh manage_db.sh upgrade
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 12, in 
from migrate.versioning.shell import main
ImportError: No module named migrate.versioning.shell


Peter
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[galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-02-21 Thread Peter Cock
Hi all,

I've just updated my Mac development machine with the latest
galaxy-central, and run.sh tells me the database needs to be updated
from 73 to 75. Note this is running on SQLite. Running manage_db.sh
upgrade gives an ImportError: No module named migrate.versioning.shell

I just grabbed a fresh hg clone and it worked, but in case there is an
obvious bug lurking here, the full output is below (and I'll keep the
broken install on disk a bit longer in case there is anything else you
need to know).

Regards,

Peter

--


$ ./run.sh
python path is:
/Users/pjcock/repositories/galaxy-central/eggs/numpy-1.3.0-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/Whoosh-0.3.18-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/pycrypto-2.0.1-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/bx_python-0.7.0_14b6a6c95da6-py2.5-macosx-10.3-fat-ucs2.egg,
/Users/pjcock/repositories/galaxy-central/eggs/amqplib-0.6.1-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/pexpect-2.4-py2.5.egg,
/Users/pjcock/repositories/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg,
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