James Taylor
0ac85dac80
Commenting out another biomart test, they just hang forever.
2007-03-08 18:35:05 +00:00
James Taylor
a70768b255
Buildbot functional test script updates.
2007-03-08 18:27:00 +00:00
James Taylor
95698117eb
Unit test fix.
2007-03-08 18:25:01 +00:00
James Taylor
cf5405b244
Bugfix.
2007-03-08 18:23:50 +00:00
James Taylor
ea9a819235
Working on getting tests going again. Modified the history.xml template to
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only return active datasets so deletes should test correctly again.
2007-03-08 18:14:50 +00:00
James Taylor
9370ea6a48
Don't echo database queries.
2007-03-08 18:11:51 +00:00
James Taylor
165cfdaf63
Remove psycopg dependency.
2007-03-08 17:58:16 +00:00
James Taylor
113bff99bc
Use an association object for the relationship between parent and child
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datasets.
THIS REQUIRES DATABASE CHANGES!
Also, test parse errors should now cause errors.
2007-03-08 17:52:29 +00:00
James Taylor
e20cf00c91
"User" relation interface: normalizing form styles and such to be consistent
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with the rest of the application.
2007-03-08 17:31:28 +00:00
James Taylor
4ac180091e
Cheetah changes: upgrade to Cheetah 2.0 (release candidate 7, looking very
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stable at this point). This gives us big improvements to template compilation
and caching, and thus a nice little speed boost.
2007-03-08 17:29:58 +00:00
Daniel Blankenberg
d389d70b5b
Add sequence to tablebrowser direct connection. Custom track can be added after an actual datatype is created.
2007-03-08 16:42:48 +00:00
Daniel Blankenberg
1ebbc0c583
Fix for hyperlinks for UCSC table browser direct connection.
2007-03-08 16:35:58 +00:00
David C. King
078389e8f0
aggregate_binned_scores now invokes the up-to-date tool
2007-03-07 22:49:54 +00:00
James Taylor
553b2d4c7b
Made the conversion to HTML much prettier.
2007-03-05 22:39:06 +00:00
James Taylor
72260d2887
New profile middleware.
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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 the
page.
- Profile output can be viewed inline or in a popup window.
- Doesn't require a lock, should be thread safe (but let me know if you see
anything odd).
To use, just add 'use_profile = True' in the config file. Not for production
use, will slow things down, but no nearly as much as hotshot was.
2007-03-05 20:34:43 +00:00
Daniel Blankenberg
6e951364f8
Fix some broken logging.
2007-03-01 16:23:06 +00:00
Daniel Blankenberg
84e2dc5ed5
Fix for UCSC direct connection for unknown datatypes.
2007-03-01 16:22:29 +00:00
Daniel Blankenberg
e013dc254e
Make BED default datatype for UCSC direct connection.
2007-03-01 15:53:03 +00:00
Ian Schenck
bdb37ba8ce
Another change to ops to hopefully kill the never-ending strand problem. This makes anything that isn't a +/- into a +.
2007-02-28 21:59:38 +00:00
Ian Schenck
f4f9e1d7b2
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 parsers in bx for mafs, fasta, axt's, etc do not have any kind of validation built.
2007-02-28 21:46:54 +00:00
Daniel Blankenberg
412b9a9677
Add UCSC Table Browser direct connection tool.
2007-02-28 20:46:06 +00:00
Greg Von Kuster
0dfd869918
Enhanced column_maker.py to gracefully handle invalid data in input file and to display more meaningful info to user.
2007-02-28 16:10:31 +00:00
Greg Von Kuster
7ab5369033
Corrected the way these tools read input datasets to keep them from entering infinite loops if the dataset is empty.
2007-02-27 16:32:05 +00:00
Anton Nekrutenko
8c09569e13
Unsequenced genome for March form Dulles airport
2007-02-27 02:34:21 +00:00
Greg Von Kuster
0191564e9b
Added another example since I noticed several jobs where the user was confused about the "==" requirement.
2007-02-26 20:43:31 +00:00
Greg Von Kuster
97e5cb8f9d
Enhanced event logging for session activity reports.
2007-02-26 19:03:37 +00:00
Daniel Blankenberg
e830b83b9f
Removing import psyco_full from tools that throw warning (already imported).
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Also, I noticed that the 2 aggregate score tools had the same tool id, and are live on the test server, so i fixed the tool ids.
2007-02-23 14:33:03 +00:00
Greg Von Kuster
5a8135f56c
Minor correction to the message for the location of the first invalid line in a dataset, if there is in fact one.
2007-02-21 21:44:22 +00:00
James Taylor
7285237f5b
Hack for database monitoring job queue to wait until after forking to start
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monitor thread.
2007-02-21 20:16:35 +00:00
Greg Von Kuster
67e1bb8846
Enhanced the Filter tool to handle invalid data and to display more useful, informative messages to the user.
2007-02-21 18:41:58 +00:00
Daniel Blankenberg
573e8cd8a2
Parameter sanitizer can now be turned off by individual tools. Refresh behavior after tool execution can now be defined in
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the tool xml file.
To Do: Allow individual parameters to have sanitation control.
2007-02-21 18:01:07 +00:00
Guruprasad Anada
9903924f97
Name change: Gene BED to Exon BED changed to Gene BED to Exon/Intron BED
2007-02-19 21:14:03 +00:00
Guruprasad Anada
84912a92fa
Filename test_kaks.py changed to kaks_yn00.py
2007-02-19 19:34:26 +00:00
Guruprasad Anada
be8f660cd3
yn00 binary added
2007-02-19 19:21:38 +00:00
Guruprasad Anada
ac747b8d6f
Modified tool: Gene BED to Exon BED
2007-02-19 16:59:51 +00:00
Guruprasad Anada
0ac0ec4086
"new tool: gene bed to intron bed- test output filr"
2007-02-19 16:25:54 +00:00
Guruprasad Anada
112f94c176
new tool: gene bed to intron bed
2007-02-19 16:22:28 +00:00
Guruprasad Anada
fb3b9255f5
yn00 binary added: kaks tool
2007-02-16 21:37:34 +00:00
Guruprasad Anada
b37f332a35
new toold kaks added
2007-02-16 21:28:21 +00:00
Nate Coraor
092c23f41b
Made run.sh Bourne-friendly and added path fix for cluster nodes.
2007-02-16 21:21:24 +00:00
Daniel Blankenberg
bfe9c45db9
Modify maf_to_bed to use database/tmp for its temp directory for additional output files.
2007-02-15 20:09:33 +00:00
Anton Nekrutenko
e554fb4d79
added get_flanks plus two additional tools for a David Gilmore: srg2wig and aggTrack. These two are for demo only and should not go to main
2007-02-15 15:11:08 +00:00
James Taylor
f6274675db
Close connections after setting up the application (just is case the WSGI
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server wants to fork, otherwise processes then try to share connections,
yikes!!!)
2007-02-13 23:49:49 +00:00
James Taylor
48cdd842f7
Support for the job "queue" reading new jobs from the database rather than
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from a Queue.
Enable this when running the server in a forking environment. The job queue
threads will live in the parent process, while jobs will be added to the
database by the child processes. Lovely!
2007-02-13 21:00:18 +00:00
Nate Coraor
5c494af61a
try the post-job hook so it doesn't kill the queue if it fails.
2007-02-13 17:54:43 +00:00
James Taylor
5a4182c243
1) A 'prefork threaded' mixin hacked together from existing flup components
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2) An AJP server using that mixin (we could also do fastcgi or scgi, but AJP
is the best option).
2007-02-13 17:27:25 +00:00
Guruprasad Anada
02a60145bf
2007-02-13 17:01:13 +00:00
Guruprasad Anada
0ef3bdbba0
modified test_kaks tool
2007-02-13 16:21:07 +00:00
James Taylor
ed76bdaff2
The correct file for pre-fork server.
2007-02-13 05:17:32 +00:00
James Taylor
bd0ff71748
rollback...
2007-02-13 05:17:18 +00:00
James Taylor