database upgrade crashes after upgrade to the June 3, 2013 Galaxy release

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database upgrade crashes after upgrade to the June 3, 2013 Galaxy release

Christophe Antoniewski-2
Hi,
Sorry to bother again, but we have now a problem with the last release of galaxy-dist

The lack of a python module asked by a python eggs seems to interrupt our postgresql database upgrade from version '114' to '115'


sh manage_db.sh upgrade
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 13, in <module>
    from migrate.versioning.shell import main
  File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 12, in <module>
    from migrate.versioning import api
  File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 33, in <module>
    from migrate.versioning import (repository, schema, version,
  File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py", line 13, in <module>
    from migrate.versioning import version, pathed, cfgparse
  File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py", line 10, in <module>
    from migrate.versioning import pathed, script
  File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py", line 11, in <module>
    from migrate.versioning.util import KeyedInstance
  File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 7, in <module>
    from decorator import decorator
ImportError: No module named decorator

Any idea ?

Thanks

Chris
--

Christophe Antoniewski


Drosophila Genetics and Epigenetics
Laboratoire de Biolologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50

http://drosophile.org


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Re: database upgrade crashes after upgrade to the June 3, 2013 Galaxy release

Björn Grüning
Hi Christophe,

can you try to update to the latest revision?

It is fixed here:
https://bitbucket.org/galaxy/galaxy-central/commits/47b86d6a9077facb54804576be49ca545d18bd4e

Cheers,
Bjoern

> Hi,
> Sorry to bother again, but we have now a problem with the last release
> of galaxy-dist
>
>
> The lack of a python module asked by a python eggs seems to interrupt
> our postgresql database upgrade from version '114' to '115'
>
>
>
>
> sh manage_db.sh upgrade
> Traceback (most recent call last):
>   File "./scripts/manage_db.py", line 13, in <module>
>     from migrate.versioning.shell import main
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 12, in <module>
>     from migrate.versioning import api
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 33, in <module>
>     from migrate.versioning import (repository, schema, version,
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py", line 13, in <module>
>     from migrate.versioning import version, pathed, cfgparse
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py", line 10, in <module>
>     from migrate.versioning import pathed, script
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py", line 11, in <module>
>     from migrate.versioning.util import KeyedInstance
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 7, in <module>
>     from decorator import decorator
> ImportError: No module named decorator
>
>
> Any idea ?
>
>
> Thanks
>
>
> Chris
> --
> Christophe Antoniewski
>
>
> Drosophila Genetics and Epigenetics
> Laboratoire de Biolologie du Développement
> 9, Quai St Bernard, Boîte courrier 24
> 75252 Paris Cedex 05
>
> Tel +33 1 44 27 34 39
> Fax +33 1 44 27 34 45
> Mobile +33 6 68 60 51 50
>
> http://drosophile.org
>
>
> ___________________________________________________________
> 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:
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Re: database upgrade crashes after upgrade to the June 3, 2013 Galaxy release

Christophe Antoniewski-2
Thank you so much Björn,

I made the change of the file directly by hand (not sure to be able to cleanly switch to default from stable with the new mercurial mode) and it worked.

Chris


2013/6/12 Björn Grüning <[hidden email]>
Hi Christophe,

can you try to update to the latest revision?

It is fixed here:
https://bitbucket.org/galaxy/galaxy-central/commits/47b86d6a9077facb54804576be49ca545d18bd4e

Cheers,
Bjoern

> Hi,
> Sorry to bother again, but we have now a problem with the last release
> of galaxy-dist
>
>
> The lack of a python module asked by a python eggs seems to interrupt
> our postgresql database upgrade from version '114' to '115'
>
>
>
>
> sh manage_db.sh upgrade
> Traceback (most recent call last):
>   File "./scripts/manage_db.py", line 13, in <module>
>     from migrate.versioning.shell import main
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 12, in <module>
>     from migrate.versioning import api
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 33, in <module>
>     from migrate.versioning import (repository, schema, version,
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py", line 13, in <module>
>     from migrate.versioning import version, pathed, cfgparse
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py", line 10, in <module>
>     from migrate.versioning import pathed, script
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py", line 11, in <module>
>     from migrate.versioning.util import KeyedInstance
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 7, in <module>
>     from decorator import decorator
> ImportError: No module named decorator
>
>
> Any idea ?
>
>
> Thanks
>
>
> Chris
> --
> Christophe Antoniewski
>
>
> Drosophila Genetics and Epigenetics
> Laboratoire de Biolologie du Développement
> 9, Quai St Bernard, Boîte courrier 24
> 75252 Paris Cedex 05
>
> Tel +33 1 44 27 34 39
> Fax +33 1 44 27 34 45
> Mobile +33 6 68 60 51 50
>
> http://drosophile.org
>
>
> ___________________________________________________________
> 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/







--

Christophe Antoniewski


Drosophila Genetics and Epigenetics
Laboratoire de Biolologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50

http://drosophile.org


___________________________________________________________
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/
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Re: database upgrade crashes after upgrade to the June 3, 2013 Galaxy release

Dannon Baker-2
Christophe,

Glad it's working.  The updates should merge seamlessly so you shouldn't need to do anything else when you update again.  That said, for future use, you can swap branches like: 'hg update stable' to swap to the stable branch.  If you're on galaxy-dist, you can still pull (and update) from the stable branch in galaxy-central using 'hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central'.

-Dannon


On Wed, Jun 12, 2013 at 5:33 PM, Christophe Antoniewski <[hidden email]> wrote:
Thank you so much Björn,

I made the change of the file directly by hand (not sure to be able to cleanly switch to default from stable with the new mercurial mode) and it worked.

Chris


2013/6/12 Björn Grüning <[hidden email]>
Hi Christophe,

can you try to update to the latest revision?

It is fixed here:
https://bitbucket.org/galaxy/galaxy-central/commits/47b86d6a9077facb54804576be49ca545d18bd4e

Cheers,
Bjoern

> Hi,
> Sorry to bother again, but we have now a problem with the last release
> of galaxy-dist
>
>
> The lack of a python module asked by a python eggs seems to interrupt
> our postgresql database upgrade from version '114' to '115'
>
>
>
>
> sh manage_db.sh upgrade
> Traceback (most recent call last):
>   File "./scripts/manage_db.py", line 13, in <module>
>     from migrate.versioning.shell import main
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 12, in <module>
>     from migrate.versioning import api
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 33, in <module>
>     from migrate.versioning import (repository, schema, version,
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py", line 13, in <module>
>     from migrate.versioning import version, pathed, cfgparse
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py", line 10, in <module>
>     from migrate.versioning import pathed, script
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py", line 11, in <module>
>     from migrate.versioning.util import KeyedInstance
>   File
> "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 7, in <module>
>     from decorator import decorator
> ImportError: No module named decorator
>
>
> Any idea ?
>
>
> Thanks
>
>
> Chris
> --
> Christophe Antoniewski
>
>
> Drosophila Genetics and Epigenetics
> Laboratoire de Biolologie du Développement
> 9, Quai St Bernard, Boîte courrier 24
> 75252 Paris Cedex 05
>
> Tel +33 1 44 27 34 39
> Fax +33 1 44 27 34 45
> Mobile +33 6 68 60 51 50
>
> http://drosophile.org
>
>
> ___________________________________________________________
> 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/







--

Christophe Antoniewski


Drosophila Genetics and Epigenetics
Laboratoire de Biolologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50

http://drosophile.org


___________________________________________________________
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/