The main worry here is that substantial changes have been made to the
how the HTTP server / threadpool work so we should run this in test for a
while and hit it with the load tests.
Also, now using WebError for the interactive exception debugging, it has many
more features including much better formatting of errors in Mako templates.
Added some new eggs that Paste/WebError depend on: wsgiref, WebOb, and Tempita.
It won't work with the current logic in lib/galaxy/model/mapping.py fixed in this revision
(Note the wierd traceback below - looking in build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py on a linux box!?)
[rerla@hg rgalaxy_svn]$ sh run.sh
Architecture appears to be linux-x86_64 UCS4
python path: /home/rerla/rgalaxy_svn/lib:/home/rerla/rgalaxy_svn/eggs/UCS4:/home/rerla/rgalaxy_svn/eggs
python path is: /home/rerla/rgalaxy_svn/scripts, /usr/local/lib/python2.4/site-packages/setuptools-0.6c6-py2.4.egg, /home/rerla/rgalaxy_svn/lib,
/home/rerla/rgalaxy_svn/eggs/UCS4/Cheetah-1.0-py2.4-linux-x86_64.egg, /home/rerla/rgalaxy_svn/eggs/UCS4/bx_python-0.5.0_dev-py2.4-linux-x86_64.egg,
/home/rerla/rgalaxy_svn/eggs/UCS4/pysqlite-2.3.5_3.4.2_static-py2.4-linux-x86_64.egg,
/home/rerla/rgalaxy_svn/eggs/UCS4/psycopg2-2.0.6_8.2.4_static-py2.4-linux-x86_64.egg, /home/rerla/rgalaxy_svn/eggs/UCS4,
/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/Paste-1.0-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Routes-1.6.3-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/flup-0.5.dev_r2311-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/docutils-0.4-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/elementtree-1.2.6_20050316-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/WebHelpers-0.2-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/simplejson-1.4-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Mako-0.1.8-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Beaker-0.5-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/MyghtyUtils-0.52-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/SQLAlchemy-0.3.11-py2.4.egg, /home/rerla/rgalaxy_svn/eggs,
/usr/local/lib/python24.zip, /usr/local/lib/python2.4, /usr/local/lib/python2.4/plat-linux2, /usr/local/lib/python2.4/lib-tk,
/usr/local/lib/python2.4/lib-dynload, /usr/local/lib/python2.4/site-packages, /usr/local/lib/python2.4/site-packages/Numeric,
/usr/local/lib/python2.4/site-packages/PIL
Traceback (most recent call last):
File "./scripts/paster.py", line 7, in ?
command.run()
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 76, in run
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 115, in invoke
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 210, in run
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 184, in command
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 204, in loadapp
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 193, in loadapp
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 214, in loadobj
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 99, in invoke
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call
File "/home/rerla/rgalaxy_svn/lib/galaxy/web/buildapp.py", line 56, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/rerla/rgalaxy_svn/lib/galaxy/app.py", line 23, in __init__
create_tables = True )
File "/home/rerla/rgalaxy_svn/lib/galaxy/model/mapping.py", line 297, in init
metadata.create_all()
File "build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py", line 1238, in create_all
File "build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py", line 1274, in _get_engine
sqlalchemy.exceptions.InvalidRequestError: This SchemaItem is not connected to any Engine or Connection.
Cleaned up some bugs in Bed and Interval set_meta associated functions.
set_meta() will no longer be called prior to the edit form being displayed since doing this displayed attribute values that were not from the database (misleading the user).
be compatible with ALL databases (tested with sqlite and postgres, probably
also eliminates the need for the mysql workarounds we have in mapping.init)
the history options page for "Construct workflow" link. It allows you to
select which steps from the current history you want to convert.
This is currently not very robust to changes in tool configuration, so old
histories may cause errors. This will be fixable to some extent, but we'll
probably need to go back and look at the past changes to tool configs and
define some migration rules.
- Workflows have a simple database representation (StoredWorkflow)
- Workflow step parameters can be manipulated
- Workflows can be saved and loaded
- Many improvements to workflow editing interface
2) General interface cleanup
- Styles for the overall layout have been moved from the index page to
CSS files, colors for layout backgrounds and borders and such can now
be configured in the colors.ini file
- Styles and javascript code for dialogs and popupmenus (code is currently
in the workflow editor but will be moved out after more testing)
James Taylor