galaxy-commits August 2010

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galaxy-dist commit 231738037345: Automated merge with https://bitbucket.org/galaxy/galaxy-central/
by commits-noreply＠bitbucket.org 20 Aug '10

20 Aug '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User James Taylor <james(a)jamestaylor.org> # Date 1280944899 14400 # Node ID 23173803734597fe8cce4215d18d8d52c061c303 # Parent 77575a5f348d7d10c1df423c5faa71abaefd5f8a # Parent c164c2fb3a6516f8a086956a118145ae4aa1093f Automated merge with https://bitbucket.org/galaxy/galaxy-central/ --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -46,9 +46,9 @@ class StaticValueFilter( Filter ): Filter.__init__( self, d_option, elem ) self.value = elem.get( "value", None ) assert self.value is not None, "Required 'value' attribute missing from filter" - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter, when loading from file" - self.column = int ( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter, when loading from file" + self.column = d_option.column_spec_to_index( column ) self.keep = string_as_bool( elem.get( "keep", 'True' ) ) def filter_options( self, options, trans, other_values ): rval = [] @@ -81,11 +81,11 @@ class DataMetaFilter( Filter ): d_option.has_dataset_dependencies = True self.key = elem.get( "key", None ) assert self.key is not None, "Required 'key' attribute missing from filter" - self.column = elem.get( "column", None ) - if self.column is None: + column = elem.get( "column", None ) + if column is None: assert self.dynamic_option.file_fields is None and self.dynamic_option.dataset_ref_name is None, "Required 'column' attribute missing from filter, when loading from file" else: - self.column = int ( self.column ) + self.column = d_option.column_spec_to_index( column ) self.multiple = string_as_bool( elem.get( "multiple", "False" ) ) self.separator = elem.get( "separator", "," ) def get_dependency_name( self ): @@ -142,9 +142,9 @@ class ParamValueFilter( Filter ): Filter.__init__( self, d_option, elem ) self.ref_name = elem.get( "ref", None ) assert self.ref_name is not None, "Required 'ref' attribute missing from filter" - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter" - self.column = int ( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter" + self.column = d_option.column_spec_to_index( column ) self.keep = string_as_bool( elem.get( "keep", 'True' ) ) self.ref_attribute = elem.get( "ref_attribute", None ) if self.ref_attribute: @@ -177,9 +177,9 @@ class UniqueValueFilter( Filter ): """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter" - self.column = int ( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter" + self.column = d_option.column_spec_to_index( column ) def get_dependency_name( self ): return self.dynamic_option.dataset_ref_name def filter_options( self, options, trans, other_values ): @@ -205,9 +205,9 @@ class MultipleSplitterFilter( Filter ): def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) self.separator = elem.get( "separator", "," ) - self.columns = elem.get( "column", None ) - assert self.columns is not None, "Required 'columns' attribute missing from filter" - self.columns = [ int ( column ) for column in self.columns.split( "," ) ] + columns = elem.get( "column", None ) + assert columns is not None, "Required 'columns' attribute missing from filter" + self.columns = [ d_option.column_spec_to_index( column ) for column in columns.split( "," ) ] def filter_options( self, options, trans, other_values ): rval = [] for fields in options: @@ -345,9 +345,9 @@ class SortByColumnFilter( Filter ): """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter" - self.column = int( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter" + self.column = d_option.column_spec_to_index( column ) def filter_options( self, options, trans, other_values ): rval = [] for i, fields in enumerate( options ): @@ -398,20 +398,25 @@ class DynamicOptions( object ): data_file = elem.get( 'from_file', None ) dataset_file = elem.get( 'from_dataset', None ) from_parameter = elem.get( 'from_parameter', None ) - if data_file is not None or dataset_file is not None or from_parameter is not None: - for column_elem in elem.findall( 'column' ): - name = column_elem.get( 'name', None ) - assert name is not None, "Required 'name' attribute missing from column def" - index = column_elem.get( 'index', None ) - assert index is not None, "Required 'index' attribute missing from column def" - index = int( index ) - self.columns[name] = index - if index > self.largest_index: - self.largest_index = index - assert 'value' in self.columns, "Required 'value' column missing from column def" - if 'name' not in self.columns: - self.columns['name'] = self.columns['value'] + tool_data_table_name = elem.get( 'from_data_table', None ) + + # Options are defined from a data table loaded by the app + self.tool_data_table = None + if tool_data_table_name: + app = tool_param.tool.app + assert tool_data_table_name in app.tool_data_tables, \ + "Data table named '%s' is required by tool but not configured" % tool_data_table_name + self.tool_data_table = app.tool_data_tables[ tool_data_table_name ] + # Column definitions are optional, but if provided override those from the table + if elem.find( "column" ) is not None: + self.parse_column_definitions( elem ) + else: + self.columns = self.tool_data_table.columns + # Options are defined by parsing tabular text data from an data file + # on disk, a dataset, or the value of another parameter + elif data_file is not None or dataset_file is not None or from_parameter is not None: + self.parse_column_definitions( elem ) if data_file is not None: data_file = data_file.strip() if not os.path.isabs( data_file ): @@ -432,6 +437,20 @@ class DynamicOptions( object ): # Load Validators for validator in elem.findall( 'validator' ): self.validators.append( validation.Validator.from_element( self.tool_param, validator ) ) + + def parse_column_definitions( self, elem ): + for column_elem in elem.findall( 'column' ): + name = column_elem.get( 'name', None ) + assert name is not None, "Required 'name' attribute missing from column def" + index = column_elem.get( 'index', None ) + assert index is not None, "Required 'index' attribute missing from column def" + index = int( index ) + self.columns[name] = index + if index > self.largest_index: + self.largest_index = index + assert 'value' in self.columns, "Required 'value' column missing from column def" + if 'name' not in self.columns: + self.columns['name'] = self.columns['value'] def parse_file_fields( self, reader ): rval = [] @@ -465,6 +484,8 @@ class DynamicOptions( object ): assert dataset is not None, "Required dataset '%s' missing from input" % self.dataset_ref_name if not dataset: return [] #no valid dataset in history options = self.parse_file_fields( open( dataset.file_name ) ) + elif self.tool_data_table: + options = self.tool_data_table.get_fields() else: options = list( self.file_fields ) for filter in self.filters: @@ -473,7 +494,7 @@ class DynamicOptions( object ): def get_options( self, trans, other_values ): rval = [] - if self.file_fields is not None or self.dataset_ref_name is not None: + if self.file_fields is not None or self.tool_data_table is not None or self.dataset_ref_name is not None: options = self.get_fields( trans, other_values ) for fields in options: rval.append( ( fields[self.columns['name']], fields[self.columns['value']], False ) ) @@ -481,3 +502,15 @@ class DynamicOptions( object ): for filter in self.filters: rval = filter.filter_options( rval, trans, other_values ) return rval + + def column_spec_to_index( self, column_spec ): + """ + Convert a column specification (as read from the config file), to an + index. A column specification can just be a number, a column name, or + a column alias. + """ + # Name? + if column_spec in self.columns: + return self.columns[column_spec] + # Int? + return int( column_spec ) --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -48,6 +48,7 @@ class Configuration( object ): self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.tool_config = resolve_path( kwargs.get( 'tool_config_file', 'tool_conf.xml' ), self.root ) + self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) )

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galaxy-dist commit 6e19bc97f2b8: - Fix dbkey migrate script for downgrade and rare case when config is empty
by commits-noreply＠bitbucket.org 20 Aug '10

20 Aug '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1280868063 14400 # Node ID 6e19bc97f2b8ba816ab20fc53a88f3504c992e00 # Parent 0366c4a4765631188f1515fbd77fddbbf1532d4f - Fix dbkey migrate script for downgrade and rare case when config is empty - Fix grid sorting in "Visualize in Trackster" modal box - Refactor out sort_order in grids, fixing a bug with sort arrow not showing --- a/templates/tracks/add_to_viz.mako +++ b/templates/tracks/add_to_viz.mako @@ -6,8 +6,3 @@ ${render_grid_header( grid, False )} ${render_grid_table( grid, show_item_checkboxes=True )} -## Initialize the grid. -<script type="text/javascript"> - init_grid_elements(); - init_grid_controls(); -</script> --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -136,7 +136,6 @@ class Grid( object ): extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") # Process sort arguments. sort_key = None - sort_order = None if 'sort' in kwargs: sort_key = kwargs['sort'] elif base_sort_key: @@ -144,11 +143,9 @@ class Grid( object ): encoded_sort_key = sort_key if sort_key: if sort_key.startswith( "-" ): - sort_order = 'desc' # Can't use lower() on timestamp or integer objects, so func.lower() is not used here... query = query.order_by( self.model_class.table.c.get( sort_key[1:] ).desc() ) else: - sort_order = 'asc' # See reason for not using lower() to do case-insensitive search. query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) extra_url_args['sort'] = encoded_sort_key @@ -226,7 +223,6 @@ class Grid( object ): cur_filter_dict=cur_filter_dict, sort_key=sort_key, encoded_sort_key=encoded_sort_key, - sort_order=sort_order, current_item=current_item, ids = kwargs.get( 'id', [] ), url = url, --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -739,8 +739,8 @@ href = "" extra = "" if column.sortable: - if sort_key == column.key: - if sort_order == "asc": + if sort_key.endswith(column.key): + if not sort_key.startswith("-"): href = url( sort=( "-" + column.key ) ) extra = "↓" else: --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -205,7 +205,7 @@ class UsesVisualization( SharableItemSec # Set dbkey. try: - dbkey = latest_revision.config['dbkey'] + dbkey = latest_revision.dbkey except KeyError: dbkey = None --- a/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py +++ b/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py @@ -14,13 +14,13 @@ log = logging.getLogger( __name__ ) metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) -Visualization_table = Table( "visualization", metadata, autoload=True ) -Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True ) - def upgrade(): print __doc__ metadata.reflect() + + Visualization_table = Table( "visualization", metadata, autoload=True ) + Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True ) # Create dbkey columns. x = Column( "dbkey", TEXT, index=True ) @@ -47,12 +47,16 @@ def upgrade(): for viz in all_viz: viz_id = viz['viz_id'] viz_rev_id = viz['viz_rev_id'] - dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'") - db_session.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id)) - db_session.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id)) + if viz[Visualization_revision_table.c.config]: + dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'") + db_session.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id)) + db_session.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id)) def downgrade(): metadata.reflect() + + Visualization_table = Table( "visualization", metadata, autoload=True ) + Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True ) Visualization_table.c.dbkey.drop() Visualization_revision_table.c.dbkey.drop()

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galaxy-commits August 2010