details: http://www.bx.psu.edu/hg/galaxy/rev/70747a610c28 changeset: 3775:70747a610c28 user: Greg Von Kuster greg@bx.psu.edu date: Wed May 12 14:50:25 2010 -0400 description: Force modENCODE worm dbkey to be ce6 and modENCODE fly dbkey to be dm2.

diffstat:

lib/galaxy/tools/__init__.py | 6 ++++++ tools/data_source/fly_modencode.xml | 2 +- tools/data_source/worm_modencode.xml | 2 +- 3 files changed, 8 insertions(+), 2 deletions(-)

diffs (40 lines):

diff -r 58500dfab084 -r 70747a610c28 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed May 12 14:37:00 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Wed May 12 14:50:25 2010 -0400 @@ -1646,6 +1646,12 @@ 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 58500dfab084 -r 70747a610c28 tools/data_source/fly_modencode.xml --- a/tools/data_source/fly_modencode.xml Wed May 12 14:37:00 2010 -0400 +++ b/tools/data_source/fly_modencode.xml Wed May 12 14:50:25 2010 -0400 @@ -10,7 +10,7 @@ <request_param galaxy_name="URL" remote_name="URL" missing=""> <append_param separator="&amp;" first_separator="?" join="="> <value name="d" missing="" /> - <value name="dbkey" missing="" /> + <value name="dbkey" missing="dm2" /> <value name="q" missing="" /> <value name="s" missing="" /> <value name="t" missing="" /> diff -r 58500dfab084 -r 70747a610c28 tools/data_source/worm_modencode.xml --- a/tools/data_source/worm_modencode.xml Wed May 12 14:37:00 2010 -0400 +++ b/tools/data_source/worm_modencode.xml Wed May 12 14:50:25 2010 -0400 @@ -10,7 +10,7 @@ <request_param galaxy_name="URL" remote_name="URL" missing=""> <append_param separator="&amp;" first_separator="?" join="="> <value name="d" missing="" /> - <value name="dbkey" missing="" /> + <value name="dbkey" missing="ce6" /> <value name="q" missing="" /> <value name="s" missing="" /> <value name="t" missing="" />