3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/70f062a9e200/ Changeset: 70f062a9e200 User: dannon Date: 2014-05-19 23:44:25 Summary: Merge from next-stable. Affected #: 1 file diff -r 05302ebc73772d383ef55781e7c59d7365258e5b -r 70f062a9e200c1b8d6ef5dc43a6c99f41ea70083 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -55,9 +55,9 @@ chrom_info = db_dataset.file_name else: # -- Get chrom_info (len file) from either a custom or built-in build. -- - if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): + if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): # Custom build. - custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] + custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ dbkey ] # HACK: the attempt to get chrom_info below will trigger the # fasta-to-len converter if the dataset is not available or, # which will in turn create a recursive loop when https://bitbucket.org/galaxy/galaxy-central/commits/5c2c82003b8f/ Changeset: 5c2c82003b8f Branch: next-stable User: dannon Date: 2014-05-19 23:47:20 Summary: Fix get_chrom_info to take (and use) the tool in question. Affected #: 2 files diff -r d62fd7469c626064d8fe9792ea4584c57b5ed431 -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,7 +193,7 @@ # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} - ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info diff -r d62fd7469c626064d8fe9792ea4584c57b5ed431 -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -2,7 +2,7 @@ Functionality for dealing with dbkeys. """ #dbkeys read from disk using builds.txt -from galaxy.util import dbnames, galaxy_directory +from galaxy.util import dbnames from galaxy.util.json import from_json_string from galaxy.util.odict import odict import os.path @@ -44,7 +44,7 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval - def get_chrom_info( self, dbkey, trans=None ): + def get_chrom_info( self, dbkey, tool, trans=None ): chrom_info = None db_dataset = None # Collect chromInfo from custom builds https://bitbucket.org/galaxy/galaxy-central/commits/3100a0f55b14/ Changeset: 3100a0f55b14 User: dannon Date: 2014-05-19 23:47:36 Summary: Merge next-stable. Affected #: 2 files diff -r 70f062a9e200c1b8d6ef5dc43a6c99f41ea70083 -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,7 +193,7 @@ # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} - ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info diff -r 70f062a9e200c1b8d6ef5dc43a6c99f41ea70083 -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -2,7 +2,7 @@ Functionality for dealing with dbkeys. """ #dbkeys read from disk using builds.txt -from galaxy.util import dbnames, galaxy_directory +from galaxy.util import dbnames from galaxy.util.json import from_json_string from galaxy.util.odict import odict import os.path @@ -44,7 +44,7 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval - def get_chrom_info( self, dbkey, trans=None ): + def get_chrom_info( self, dbkey, tool, trans=None ): chrom_info = None db_dataset = None # Collect chromInfo from custom builds Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.