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Merge pull request #245 from blankenberg/tool-data-table-enhancements

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[15.05] Allow a tool data table to declare that duplicate entries are not allowed.
This commit is contained in:
Dannon Baker
2015-05-08 11:34:41 -04:00
parent 95d7108b1b 7483b043f6
commit 9d4099ac36
1 changed files with 23 additions and 1 deletions
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lib/galaxy/tools/data/__init__.py
+23 -1
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@@ -185,6 +185,7 @@ class ToolDataTable( object ):
self.comment_char = config_element.get( 'comment_char' )
self.empty_field_value = config_element.get( 'empty_field_value', '' )
self.empty_field_values = {}
self.allow_duplicate_entries = util.asbool( config_element.get( 'allow_duplicate_entries', True ) )
self.here = filename and os.path.dirname(filename)
self.filenames = odict()
self.tool_data_path = tool_data_path
@@ -354,6 +355,11 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
self.filenames[ filename ] = info
#save info about table
self._merged_load_info.append( ( other_table.__class__, other_table._load_info ) )
# If we are merging in a data table that does not allow duplicates, enforce that upon the data table
if self.allow_duplicate_entries and not other_table.allow_duplicate_entries:
log.debug( 'While attempting to merge tool data table "%s", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries.', self.name )
self.allow_duplicate_entries = False
self._deduplicate_data()
#add data entries and return current data table version
return self.add_entries( other_table.data, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd )
@@ -426,6 +432,8 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
def extend_data_with( self, filename, errors=None ):
here = os.path.dirname(os.path.abspath(filename))
self.data.extend( self.parse_file_fields( open( filename ), errors=errors, here=here ) )
if not self.allow_duplicate_entries:
self._deduplicate_data()
def parse_file_fields( self, reader, errors=None, here="__HERE__" ):
"""
@@ -536,7 +544,7 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
is_error = False
if self.largest_index < len( fields ):
fields = self._replace_field_separators( fields )
if fields not in self.get_fields() or allow_duplicates:
if fields not in self.get_fields() or ( allow_duplicates and self.allow_duplicate_entries ):
self.data.append( fields )
else:
log.debug( "Attempted to add fields (%s) to data table '%s', but this entry already exists and allow_duplicates is False.", fields, self.name )
@@ -624,6 +632,20 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
replace = " "
return map( lambda x: x.replace( separator, replace ), fields )
def _deduplicate_data( self ):
# Remove duplicate entries, without recreating self.data object
dup_lines = []
hash_list = []
for i, fields in enumerate( self.data ):
fields_hash = hash( self.separator.join( fields ) )
if fields_hash in hash_list:
dup_lines.append( i )
log.debug( 'Found duplicate entry in tool data table "%s", but duplicates are not allowed, removing additional entry for: "%s"', self.name, fields )
else:
hash_list.append( fields_hash )
for i in reversed( dup_lines ):
self.data.pop( i )
@property
def xml_string( self ):
return util.xml_to_string( self.config_element )