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Fixes for Data source async controller.

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This commit is contained in:
Daniel Blankenberg
2011-11-14 11:37:02 -05:00
parent 73f68f226a
commit 03097a32c6
2 changed files with 13 additions and 13 deletions
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lib/galaxy/jobs/__init__.py
+1 -1
View File
@@ -591,7 +591,7 @@ class JobWrapper( object ):
dataset.blurb = 'done'
dataset.peek = 'no peek'
dataset.info = context['stdout'] + context['stderr']
dataset.info = ( dataset.info or '' ) + context['stdout'] + context['stderr']
dataset.tool_version = self.version_string
dataset.set_size()
if context['stderr']:
lib/galaxy/web/controllers/async.py
+12 -12
View File
@@ -67,7 +67,7 @@ class ASync( BaseUIController ):
trans.log_event( 'Async executing tool %s' % tool.id, tool_id=tool.id )
galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key )
galaxy_url = params.get("GALAXY_URL",galaxy_url)
params = dict( url=URL, GALAXY_URL=galaxy_url )
params = dict( URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext )
# Assume there is exactly one output file possible
params[tool.outputs.keys()[0]] = data.id
tool.execute( trans, incoming=params )
@@ -80,20 +80,20 @@ class ASync( BaseUIController ):
trans.sa_session.flush()
return "Data %s with status %s received. OK" % (data_id, STATUS)
#
# no data_id must be parameter submission
#
if not data_id and len(params)>3:
if params.galaxyFileFormat == 'wig':
else:
#
# no data_id must be parameter submission
#
if params.data_type:
GALAXY_TYPE = params.data_type
elif params.galaxyFileFormat == 'wig': #this is an undocumented legacy special case
GALAXY_TYPE = 'wig'
else:
GALAXY_TYPE = params.GALAXY_TYPE or 'interval'
GALAXY_TYPE = params.GALAXY_TYPE or tool.outputs.values()[0].format
GALAXY_NAME = params.GALAXY_NAME or '%s query' % tool.name
GALAXY_INFO = params.GALAXY_INFO or params.galaxyDescription or ''
GALAXY_BUILD = params.GALAXY_BUILD or params.galaxyFreeze or 'hg17'
GALAXY_NAME = params.name or params.GALAXY_NAME or '%s query' % tool.name
GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or ''
GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or '?'
#data = datatypes.factory(ext=GALAXY_TYPE)()
#data.ext = GALAXY_TYPE