[2] | 1 | """ |
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| 2 | Manage tool data tables, which store (at the application level) data that is |
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| 3 | used by tools, for example in the generation of dynamic options. Tables are |
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| 4 | loaded and stored by names which tools use to refer to them. This allows |
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| 5 | users to configure data tables for a local Galaxy instance without needing |
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| 6 | to modify the tool configurations. |
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| 7 | """ |
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| 8 | |
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| 9 | import logging, sys, os.path |
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| 10 | from galaxy import util |
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| 11 | |
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| 12 | log = logging.getLogger( __name__ ) |
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| 13 | |
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| 14 | class ToolDataTableManager( object ): |
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| 15 | """ |
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| 16 | Manages a collection of tool data tables |
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| 17 | """ |
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| 18 | |
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| 19 | def __init__( self, config_filename=None ): |
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| 20 | self.data_tables = {} |
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| 21 | if config_filename: |
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| 22 | self.add_from_config_file( config_filename ) |
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| 23 | |
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| 24 | def __getitem__( self, key ): |
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| 25 | return self.data_tables.__getitem__( key ) |
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| 26 | |
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| 27 | def __contains__( self, key ): |
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| 28 | return self.data_tables.__contains__( key ) |
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| 29 | |
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| 30 | def add_from_config_file( self, config_filename ): |
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| 31 | tree = util.parse_xml( config_filename ) |
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| 32 | root = tree.getroot() |
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| 33 | for table_elem in root.findall( 'table' ): |
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| 34 | type = table_elem.get( 'type', 'tabular' ) |
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| 35 | assert type in tool_data_table_types, "Unknown data table type '%s'" % type |
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| 36 | table = tool_data_table_types[ type ]( table_elem ) |
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| 37 | self.data_tables[ table.name ] = table |
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| 38 | log.debug( "Loaded tool data table '%s", table.name ) |
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| 39 | |
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| 40 | class ToolDataTable( object ): |
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| 41 | def __init__( self, config_element ): |
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| 42 | self.name = config_element.get( 'name' ) |
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| 43 | |
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| 44 | class TabularToolDataTable( ToolDataTable ): |
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| 45 | """ |
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| 46 | Data stored in a tabular / separated value format on disk, allows multiple |
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| 47 | files to be merged but all must have the same column definitions. |
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| 48 | |
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| 49 | <table type="tabular" name="test"> |
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| 50 | <column name='...' index = '...' /> |
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| 51 | <file path="..." /> |
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| 52 | <file path="..." /> |
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| 53 | </table> |
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| 54 | """ |
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| 55 | |
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| 56 | type_key = 'tabular' |
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| 57 | |
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| 58 | def __init__( self, config_element ): |
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| 59 | super( TabularToolDataTable, self ).__init__( config_element ) |
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| 60 | self.configure_and_load( config_element ) |
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| 61 | |
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| 62 | def configure_and_load( self, config_element ): |
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| 63 | """ |
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| 64 | Configure and load table from an XML element. |
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| 65 | """ |
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| 66 | self.separator = config_element.get( 'separator', '\t' ) |
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| 67 | self.comment_char = config_element.get( 'comment_char', '#' ) |
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| 68 | # Configure columns |
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| 69 | self.parse_column_spec( config_element ) |
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| 70 | # Read every file |
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| 71 | all_rows = [] |
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| 72 | for file_element in config_element.findall( 'file' ): |
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| 73 | filename = file_element.get( 'path' ) |
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| 74 | if not os.path.exists( filename ): |
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| 75 | log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) |
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| 76 | else: |
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| 77 | all_rows.extend( self.parse_file_fields( open( filename ) ) ) |
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| 78 | self.data = all_rows |
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| 79 | |
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| 80 | def get_fields( self ): |
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| 81 | return self.data |
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| 82 | |
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| 83 | def parse_column_spec( self, config_element ): |
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| 84 | """ |
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| 85 | Parse column definitions, which can either be a set of 'column' elements |
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| 86 | with a name and index (as in dynamic options config), or a shorthand |
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| 87 | comma separated list of names in order as the text of a 'column_names' |
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| 88 | element. |
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| 89 | |
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| 90 | A column named 'value' is required. |
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| 91 | """ |
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| 92 | self.columns = {} |
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| 93 | if config_element.find( 'columns' ) is not None: |
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| 94 | column_names = util.xml_text( config_element.find( 'columns' ) ) |
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| 95 | column_names = [ n.strip() for n in column_names.split( ',' ) ] |
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| 96 | for index, name in enumerate( column_names ): |
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| 97 | self.columns[ name ] = index |
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| 98 | self.largest_index = index |
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| 99 | else: |
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| 100 | for column_elem in config_element.findall( 'column' ): |
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| 101 | name = column_elem.get( 'name', None ) |
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| 102 | assert name is not None, "Required 'name' attribute missing from column def" |
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| 103 | index = column_elem.get( 'index', None ) |
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| 104 | assert index is not None, "Required 'index' attribute missing from column def" |
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| 105 | index = int( index ) |
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| 106 | self.columns[name] = index |
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| 107 | if index > self.largest_index: |
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| 108 | self.largest_index = index |
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| 109 | assert 'value' in self.columns, "Required 'value' column missing from column def" |
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| 110 | if 'name' not in self.columns: |
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| 111 | self.columns['name'] = self.columns['value'] |
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| 112 | |
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| 113 | def parse_file_fields( self, reader ): |
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| 114 | """ |
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| 115 | Parse separated lines from file and return a list of tuples. |
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| 116 | |
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| 117 | TODO: Allow named access to fields using the column names. |
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| 118 | """ |
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| 119 | rval = [] |
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| 120 | for line in reader: |
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| 121 | if line.lstrip().startswith( self.comment_char ): |
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| 122 | continue |
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| 123 | line = line.rstrip( "\n\r" ) |
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| 124 | if line: |
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| 125 | fields = line.split( self.separator ) |
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| 126 | if self.largest_index < len( fields ): |
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| 127 | rval.append( fields ) |
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| 128 | return rval |
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| 129 | |
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| 130 | # Registry of tool data types by type_key |
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| 131 | tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) |
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