4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0d61e421e06c/ Changeset: 0d61e421e06c Branch: stable User: dan Date: 2015-02-11 17:33:49+00:00 Summary: Fix for Data Tables persisting when .loc file doesn't exist. Affected #: 1 file diff -r 0b9127ab708d7d8497e80169a3b8636aea1e37c6 -r 0d61e421e06c25f7658b8405574a2aafa63d04f0 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -495,7 +495,7 @@ try: data_table_fh = open( filename, 'r+b' ) except IOError, e: - log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e ) + log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e ) data_table_fh = open( filename, 'wb' ) if os.stat( filename )[6] != 0: # ensure last existing line ends with new line https://bitbucket.org/galaxy/galaxy-central/commits/7df1519a9fbe/ Changeset: 7df1519a9fbe Branch: stable User: dan Date: 2015-02-11 17:37:59+00:00 Summary: Fix for TabularToolDataTable.get_named_fields_list() when a data line has extra columns. Affected #: 1 file diff -r 0d61e421e06c25f7658b8405574a2aafa63d04f0 -r 7df1519a9fbecfc8c07e0dde3bf9845714c9a2ac lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -335,11 +335,13 @@ def get_named_fields_list( self ): rval = [] - named_colums = self.get_column_name_list() + named_columns = self.get_column_name_list() for fields in self.get_fields(): field_dict = {} for i, field in enumerate( fields ): - field_name = named_colums[i] + if i == len( named_columns ): + break + field_name = named_columns[i] if field_name is None: field_name = i #check that this is supposed to be 0 based. field_dict[ field_name ] = field https://bitbucket.org/galaxy/galaxy-central/commits/ca653e8d044d/ Changeset: ca653e8d044d Branch: stable User: dan Date: 2015-02-11 17:40:33+00:00 Summary: Fix for parsing Tool Data Table columns that are defined as individual xml elements. Affected #: 1 file diff -r 7df1519a9fbecfc8c07e0dde3bf9845714c9a2ac -r ca653e8d044d29e15d4ff3266e333aa75c09e5d7 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -368,6 +368,7 @@ self.columns[ name ] = index self.largest_index = index else: + self.largest_index = 0 for column_elem in config_element.findall( 'column' ): name = column_elem.get( 'name', None ) assert name is not None, "Required 'name' attribute missing from column def" https://bitbucket.org/galaxy/galaxy-central/commits/577b270034b4/ Changeset: 577b270034b4 Branch: stable User: jmchilton Date: 2015-02-11 17:54:36+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #666) [STABLE] Several Fixes for Tool Data Tables Affected #: 1 file diff -r 32e4527bab2d79f0797c28500a379b6b6c7a3900 -r 577b270034b48d90e58ffbea296e700d229545c9 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -335,11 +335,13 @@ def get_named_fields_list( self ): rval = [] - named_colums = self.get_column_name_list() + named_columns = self.get_column_name_list() for fields in self.get_fields(): field_dict = {} for i, field in enumerate( fields ): - field_name = named_colums[i] + if i == len( named_columns ): + break + field_name = named_columns[i] if field_name is None: field_name = i #check that this is supposed to be 0 based. field_dict[ field_name ] = field @@ -366,6 +368,7 @@ self.columns[ name ] = index self.largest_index = index else: + self.largest_index = 0 for column_elem in config_element.findall( 'column' ): name = column_elem.get( 'name', None ) assert name is not None, "Required 'name' attribute missing from column def" @@ -495,7 +498,7 @@ try: data_table_fh = open( filename, 'r+b' ) except IOError, e: - log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e ) + log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e ) data_table_fh = open( filename, 'wb' ) if os.stat( filename )[6] != 0: # ensure last existing line ends with new line 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.