Commits

Author Commit Message Labels Comments Date
James Taylor
Unbreaking everything ;)
James Taylor
Support for viewing the full stderr/stdout text associated with "error" datasets and for sending email reports.
Daniel Blankenberg
Add test data for maf limit to species.
James Taylor
Fix HTML test output to escape HTML properly (the UCSC browser page diff was throwing everything off)
James Taylor
Commenting out another biomart test, they just hang forever.
James Taylor
Buildbot functional test script updates.
James Taylor
Unit test fix.
James Taylor
Bugfix.
James Taylor
Working on getting tests going again. Modified the history.xml template to only return active datasets so deletes should test correctly again.
James Taylor
Don't echo database queries.
James Taylor
Remove psycopg dependency.
James Taylor
Use an association object for the relationship between parent and child datasets. THIS REQUIRES DATABASE CHANGES! Also, test parse errors should now cause errors.
James Taylor
"User" relation interface: normalizing form styles and such to be consistent with the rest of the application.
James Taylor
Cheetah changes: upgrade to Cheetah 2.0 (release candidate 7, looking very stable at this point). This gives us big improvements to template compilation and caching, and thus a nice little speed boost.
Daniel Blankenberg
Add sequence to tablebrowser direct connection. Custom track can be added after an actual datatype is created.
Daniel Blankenberg
Fix for hyperlinks for UCSC table browser direct connection.
David C. King
aggregate_binned_scores now invokes the up-to-date tool
James Taylor
Made the conversion to HTML much prettier.
James Taylor
New profile middleware. This resolved a lot of the problems with the profile middleware from Paste. In particular: - Uses cProfile from Python 2.5, for Python 2.4 this is part of Armin Rigo's lsprof package (http://codespeak.net/svn/user/arigo/hack/misc/lsprof/) - Does not use redirect stdout, instead the Stats object is extended (in an unavoidably hacky way) to generate HTML output that gets embedded in th…
Daniel Blankenberg
Fix some broken logging.
Daniel Blankenberg
Fix for UCSC direct connection for unknown datatypes.
Daniel Blankenberg
Make BED default datatype for UCSC direct connection.
Ian Schenck
Another change to ops to hopefully kill the never-ending strand problem. This makes anything that isn't a +/- into a +.
Ian Schenck
Preliminary data validation comit, much more to come. There will be a new datatype for errors which will hold pickled exceptions and repr them for display. In addition, errors should probably be a reserved or somehow special child dataset, so that there can be only one. Finally, implementing a tool or interface to fix errors needs to be done (and is why the exceptions must be pickled). Also, only the validation for intervals is done, as the parse…
Daniel Blankenberg
Add UCSC Table Browser direct connection tool.
Greg Von Kuster
Enhanced column_maker.py to gracefully handle invalid data in input file and to display more meaningful info to user.
Greg Von Kuster
Corrected the way these tools read input datasets to keep them from entering infinite loops if the dataset is empty.
anton nekrutenko
Unsequenced genome for March form Dulles airport
Greg Von Kuster
Added another example since I noticed several jobs where the user was confused about the "==" requirement.
Greg Von Kuster
Enhanced event logging for session activity reports.
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