Nate Coraor dfdbef9d36 Reintroduce roles. Unfinished stuff: setting default user and history ...

permissions, user-side permissions settings on datasets, viewing
associated datasets under the role page in the admin controler (is this
even necessary?), filtering out roles by type.  I haven't addressed
tests, so the security-related functional tests will fail.  I haven't
looked at history sharing yet either.  Cleanup to remove unused methods
is needed in the admin controller.  And the admin templates are a
bit messy.

2008-10-09 17:05:57 -04:00

..

annotation_profiler

Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values.

2008-09-30 16:17:12 -04:00

data_destination

merging conflicts

2008-10-06 13:45:45 -04:00

data_source

Reintroduce roles. Unfinished stuff: setting default user and history

2008-10-09 17:05:57 -04:00

emboss_5

Forgot to eliminate the emboss path...

2008-04-25 19:07:26 +00:00

encode

Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.

2008-07-23 15:27:39 -04:00

extract

Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values.

2008-09-30 16:17:12 -04:00

fasta_tools

Bug fix for Concatenate FASTA alignment by species tool.

2008-07-29 11:24:28 -04:00

filters

Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values.

2008-09-30 16:17:12 -04:00

hyphy

Revert 2715.

2008-06-04 13:02:15 +00:00

maf

Reintroduce roles. Unfinished stuff: setting default user and history

2008-10-09 17:05:57 -04:00

metag_tools

add error msg for shrimp_wrapper when memory error and zero hits.

2008-09-30 16:40:42 -04:00

new_operations

More fixes for twill 0.9, the annotation profiler tests do not yet pass, but all else should work now, more tests coming soon.

2008-09-05 16:36:51 -04:00

plotting

Fix for scatterplot.py: Handling an uncaught exception.

2008-09-08 14:36:37 -04:00

regVariation

Modified help message for indel rate tool.

2008-10-06 09:33:52 -04:00

sr_mapping

Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values.

2008-09-30 16:17:12 -04:00

stats

Fix for histogram tool when input dataset is empty

2008-10-01 10:19:20 -04:00

taxonomy

typo

2008-07-07 15:17:32 +00:00

validation

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

visualization

Update GMAJ tool interface.

2008-09-19 12:27:20 -04:00