1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/caade2c602d6/
Changeset: caade2c602d6
Branch: stable
User: natefoo
Date: 2014-12-04 14:20:19+00:00
Summary: Merged in dan/galaxy-central-prs/stable (pull request #584)
[STABLE] DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format).
Affected #: 1 file
diff -r cfdd5c45c63eee193cdefa7767e9b43217238e88 -r caade2c602d65a005d54997e95fcb1a9eab6ea17 lib/galaxy/tools/parameters/dataset_matcher.py
--- a/lib/galaxy/tools/parameters/dataset_matcher.py
+++ b/lib/galaxy/tools/parameters/dataset_matcher.py
@@ -39,26 +39,30 @@
return state_valid and ( not check_security or self.__can_access_dataset( dataset ) )
def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ):
- """ Return False of this parameter can not be matched to a the supplied
+ """ Return False of this parameter can not be matched to the supplied
HDA, otherwise return a description of the match (either a
HdaDirectMatch describing a direct match or a HdaImplicitMatch
describing an implicit conversion.)
"""
+ rval = False
+ formats = self.param.formats
+ if hda.datatype.matches_any( formats ):
+ rval = HdaDirectMatch( hda )
+ else:
+ if not check_implicit_conversions:
+ return False
+ target_ext, converted_dataset = hda.find_conversion_destination( formats )
+ if target_ext:
+ if converted_dataset:
+ hda = converted_dataset
+ if check_security and not self.__can_access_dataset( hda.dataset ):
+ return False
+ rval = HdaImplicitMatch( hda, target_ext )
+ else:
+ return False
if self.filter( hda ):
return False
- formats = self.param.formats
- if hda.datatype.matches_any( formats ):
- return HdaDirectMatch( hda )
- if not check_implicit_conversions:
- return False
- target_ext, converted_dataset = hda.find_conversion_destination( formats )
- if target_ext:
- if converted_dataset:
- hda = converted_dataset
- if check_security and not self.__can_access_dataset( hda.dataset ):
- return False
- return HdaImplicitMatch( hda, target_ext )
- return False
+ return rval
def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ):
""" If HDA is accessible, return information about whether it could
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f6914532d844/
Changeset: f6914532d844
Branch: stable
User: dan
Date: 2014-12-03 16:35:35+00:00
Summary: DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format).
Affected #: 1 file
diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r f6914532d8440041ee6741815355d36dac0c1b10 lib/galaxy/tools/parameters/dataset_matcher.py
--- a/lib/galaxy/tools/parameters/dataset_matcher.py
+++ b/lib/galaxy/tools/parameters/dataset_matcher.py
@@ -39,26 +39,30 @@
return state_valid and ( not check_security or self.__can_access_dataset( dataset ) )
def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ):
- """ Return False of this parameter can not be matched to a the supplied
+ """ Return False of this parameter can not be matched to the supplied
HDA, otherwise return a description of the match (either a
HdaDirectMatch describing a direct match or a HdaImplicitMatch
describing an implicit conversion.)
"""
+ rval = False
+ formats = self.param.formats
+ if hda.datatype.matches_any( formats ):
+ rval = HdaDirectMatch( hda )
+ else:
+ if not check_implicit_conversions:
+ return False
+ target_ext, converted_dataset = hda.find_conversion_destination( formats )
+ if target_ext:
+ if converted_dataset:
+ hda = converted_dataset
+ if check_security and not self.__can_access_dataset( hda.dataset ):
+ return False
+ rval = HdaImplicitMatch( hda, target_ext )
+ else:
+ return False
if self.filter( hda ):
return False
- formats = self.param.formats
- if hda.datatype.matches_any( formats ):
- return HdaDirectMatch( hda )
- if not check_implicit_conversions:
- return False
- target_ext, converted_dataset = hda.find_conversion_destination( formats )
- if target_ext:
- if converted_dataset:
- hda = converted_dataset
- if check_security and not self.__can_access_dataset( hda.dataset ):
- return False
- return HdaImplicitMatch( hda, target_ext )
- return False
+ return rval
def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ):
""" If HDA is accessible, return information about whether it could
https://bitbucket.org/galaxy/galaxy-central/commits/caade2c602d6/
Changeset: caade2c602d6
Branch: stable
User: natefoo
Date: 2014-12-04 14:20:19+00:00
Summary: Merged in dan/galaxy-central-prs/stable (pull request #584)
[STABLE] DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format).
Affected #: 1 file
diff -r cfdd5c45c63eee193cdefa7767e9b43217238e88 -r caade2c602d65a005d54997e95fcb1a9eab6ea17 lib/galaxy/tools/parameters/dataset_matcher.py
--- a/lib/galaxy/tools/parameters/dataset_matcher.py
+++ b/lib/galaxy/tools/parameters/dataset_matcher.py
@@ -39,26 +39,30 @@
return state_valid and ( not check_security or self.__can_access_dataset( dataset ) )
def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ):
- """ Return False of this parameter can not be matched to a the supplied
+ """ Return False of this parameter can not be matched to the supplied
HDA, otherwise return a description of the match (either a
HdaDirectMatch describing a direct match or a HdaImplicitMatch
describing an implicit conversion.)
"""
+ rval = False
+ formats = self.param.formats
+ if hda.datatype.matches_any( formats ):
+ rval = HdaDirectMatch( hda )
+ else:
+ if not check_implicit_conversions:
+ return False
+ target_ext, converted_dataset = hda.find_conversion_destination( formats )
+ if target_ext:
+ if converted_dataset:
+ hda = converted_dataset
+ if check_security and not self.__can_access_dataset( hda.dataset ):
+ return False
+ rval = HdaImplicitMatch( hda, target_ext )
+ else:
+ return False
if self.filter( hda ):
return False
- formats = self.param.formats
- if hda.datatype.matches_any( formats ):
- return HdaDirectMatch( hda )
- if not check_implicit_conversions:
- return False
- target_ext, converted_dataset = hda.find_conversion_destination( formats )
- if target_ext:
- if converted_dataset:
- hda = converted_dataset
- if check_security and not self.__can_access_dataset( hda.dataset ):
- return False
- return HdaImplicitMatch( hda, target_ext )
- return False
+ return rval
def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ):
""" If HDA is accessible, return information about whether it could
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/cfdd5c45c63e/
Changeset: cfdd5c45c63e
Branch: stable
User: natefoo
Date: 2014-12-04 14:00:18+00:00
Summary: Update tag latest_2014.10.06 for changeset 0e663285c743
Affected #: 1 file
diff -r 0e663285c74326737d4ff3c637d4c8aba8847755 -r cfdd5c45c63eee193cdefa7767e9b43217238e88 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-546ff6ef27b4b83e26ae228c292fd981173ac550 latest_2014.10.06
+0e663285c74326737d4ff3c637d4c8aba8847755 latest_2014.10.06
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1deca66fc876/
Changeset: 1deca66fc876
User: jmchilton
Date: 2014-12-04 03:38:37+00:00
Summary: Re-attempt fix in 37cf9cd.
Affected #: 2 files
diff -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 -r 1deca66fc876e855e8f286b6f0cd610227276e48 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2222,10 +2222,6 @@
raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" )
if value in [None, "None"]:
return None
- # would really like to not need to handle lists in here but
- # doing it for uniformity with DataToolParameters for now.
- if isinstance( value, list ):
- value = value[ 0 ]
if isinstance( value, str ) and value.find( "," ) > 0:
value = [ int( value_part ) for value_part in value.split( "," ) ]
elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ):
diff -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 -r 1deca66fc876e855e8f286b6f0cd610227276e48 lib/galaxy/tools/parameters/meta.py
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -123,6 +123,10 @@
def __collection_multirun_parameter( value ):
+ is_batch = value.get( 'batch', False )
+ if not is_batch:
+ return False
+
batch_values = util.listify( value[ 'values' ] )
if len( batch_values ) == 1:
batch_over = batch_values[ 0 ]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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