details: http://www.bx.psu.edu/hg/galaxy/rev/997d55c65f49 changeset: 3776:997d55c65f49 user: Greg Von Kuster greg@bx.psu.edu date: Wed May 12 15:18:40 2010 -0400 description: Remove the hack I just committed for changing modENCODE fly and worm dbkeys, and translate the values in the tool configs.

diffstat:

lib/galaxy/tools/__init__.py | 6 ------ tools/data_source/fly_modencode.xml | 5 +++++ tools/data_source/worm_modencode.xml | 5 +++++ 3 files changed, 10 insertions(+), 6 deletions(-)

diffs (46 lines):

diff -r 70747a610c28 -r 997d55c65f49 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed May 12 14:50:25 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Wed May 12 15:18:40 2010 -0400 @@ -1646,12 +1646,6 @@ data.name = param_dict.get( 'name', data.name ) data.info = param_dict.get( 'info', data.name ) data.dbkey = param_dict.get( 'dbkey', data.dbkey ) - # HACK to map modENCODEfly dbkey, which is always "fly" to be dm2 - # and modENCODEworm dbkey, which is always "worm" to be ce6 - if data.dbkey == 'fly': - data.dbkey = 'dm2' - elif data.dbkey == 'worm': - data.dbkey = 'ce6' data.extension = param_dict.get( 'data_type', data.extension ) #TODO: these should be possible as part of data_source.py and external set_meta, see the upload tool: if data.extension in [ 'txt', 'tabular' ]: diff -r 70747a610c28 -r 997d55c65f49 tools/data_source/fly_modencode.xml --- a/tools/data_source/fly_modencode.xml Wed May 12 14:50:25 2010 -0400 +++ b/tools/data_source/fly_modencode.xml Wed May 12 15:18:40 2010 -0400 @@ -7,6 +7,11 @@ <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEfly" /> </inputs> <request_param_translation> + <request_param galaxy_name="dbkey" remote_name="dbkey" missing="dm2" > + <value_translation> + <value galaxy_value="dm2" remote_value="fly" /> + </value_translation> + </request_param> <request_param galaxy_name="URL" remote_name="URL" missing=""> <append_param separator="&amp;" first_separator="?" join="="> <value name="d" missing="" /> diff -r 70747a610c28 -r 997d55c65f49 tools/data_source/worm_modencode.xml --- a/tools/data_source/worm_modencode.xml Wed May 12 14:50:25 2010 -0400 +++ b/tools/data_source/worm_modencode.xml Wed May 12 15:18:40 2010 -0400 @@ -7,6 +7,11 @@ <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEworm" /> </inputs> <request_param_translation> + <request_param galaxy_name="dbkey" remote_name="dbkey" missing="ce6" > + <value_translation> + <value galaxy_value="ce6" remote_value="worm" /> + </value_translation> + </request_param> <request_param galaxy_name="URL" remote_name="URL" missing=""> <append_param separator="&amp;" first_separator="?" join="="> <value name="d" missing="" />