Migrating 14.02 to 15.05 : KeyError: 'tool_test' after migrate_tools/0012

Question: Migrating 14.02 to 15.05 : KeyError: 'tool_test' after migrate_tools/0012_tools.sh

3.5 years ago by

France

jpvillemin • 10 wrote:

I'm trying to make an update ... I' have done the following commands.

hg pull
hg update -C latest_15.05
./run.sh
"Exception: Your database has version '118' but this code expects version '129'.  Please backup your database and then migrate the schema by running 'sh manage_db.sh -c ./universe_wsgi.ini upgrade'."
sh manage_db.sh -c ./universe_wsgi.ini upgrade

sh ./scripts/migrate_tools/0012_tools.sh -c universe_wsgi.ini install_dependencies

I have the following error and i don't know what it means :

No handlers could be found for logger "galaxy.tools.data"
Traceback (most recent call last):
  File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
    app = MigrateToolsApplication( sys.argv[ 1 ] )
  File "/Users/galaxy_dev_user/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py", line 41, in __init__
    self._configure_toolbox()
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/config.py", line 748, in _configure_toolbox
    self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/__init__.py", line 106, in __init__
    app=app,
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 78, in __init__
    self._load_tool_panel()
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 312, in _load_tool_panel
    self.__add_tool_to_tool_panel( val, self._tool_panel, section=False )
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 251, in __add_tool_to_tool_panel
    tool = self._tools_by_id[ tool_id ]
KeyError: 'tool_test'

Thanlks

error update install • 1.1k views

ADD COMMENT • link •

modified 3.5 years ago • written 3.5 years ago by jpvillemin • 10

No one has a little idea what's going on ? :-/

ADD REPLY • link written 3.5 years ago by jpvillemin • 10

Hold tight, we are working out who is the best person to help troubleshoot from our team. And the community may still jump in. It is now getting later on the East Coast, US, so a reply may come in the morning. Thanks for patience! Jen, Galaxy team

ADD REPLY • link modified 3.5 years ago • written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k

Ohh ok sorry, thanks :)

If i comment this script section in tool_conf.xml, the command seems to work well :

sh ./scripts/migrate_tools/0012_tools.sh -c universe_wsgi.ini install_dependencies

 <!--
  <section id="tool_test" name="tool_test">
    <tool file="test/python_version.xml" />
  </section>-->

Then the run.sh method worked too...

Initialy, the run.sh was modified for use of an virtual env for python....

# added 2014/02/25  launches python virtualenv with python 2.6
. ~/galaxy_env/bin/activate

python --version

Now i'will try to modify the new run.sh for using the python env 2.6

ADD REPLY • link modified 3.5 years ago • written 3.5 years ago by jpvillemin • 10

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