[galaxy-commits] commit/galaxy-central: carlfeberhard: Visualizations Registry: small fixes

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bf7251133a03/ Changeset: bf7251133a03 User: carlfeberhard Date: 2014-01-30 19:10:34 Summary: Visualizations Registry: small fixes Affected #: 4 files diff -r d9f6f3f2467195397828d452664c68e5e4c104ef -r bf7251133a037cda8ca7025a15af4ab9efb326ba lib/galaxy/datatypes/dataproviders/decorators.py --- a/lib/galaxy/datatypes/dataproviders/decorators.py +++ b/lib/galaxy/datatypes/dataproviders/decorators.py @@ -18,6 +18,7 @@ from functools import wraps #from types import MethodType +import urllib2 import copy import logging @@ -143,8 +144,9 @@ 'int' : int, 'float' : float, 'bool' : bool, - 'list:str' : lambda s: list_from_query_string( s ), - 'list:int' : lambda s: [ int( i ) for i in list_from_query_string( s ) ], + 'list:str' : lambda s: list_from_query_string( s ), + 'list:escaped' : lambda s: [ urllib2.unquote( e ) for e in list_from_query_string( s ) ], + 'list:int' : lambda s: [ int( i ) for i in list_from_query_string( s ) ], } settings = settings or {} # yay! yet another set of query string parsers! <-- sarcasm diff -r d9f6f3f2467195397828d452664c68e5e4c104ef -r bf7251133a037cda8ca7025a15af4ab9efb326ba lib/galaxy/datatypes/dataproviders/line.py --- a/lib/galaxy/datatypes/dataproviders/line.py +++ b/lib/galaxy/datatypes/dataproviders/line.py @@ -78,7 +78,7 @@ line = line.strip( '\n' ) if not self.provide_blank and line == '': return None - elif line.startswith( self.comment_char ): + elif self.comment_char and line.startswith( self.comment_char ): return None return super( FilteredLineDataProvider, self ).filter( line ) @@ -94,7 +94,7 @@ the line it is considered valid and will be provided). """ settings = { - 'regex_list' : 'list:str', + 'regex_list' : 'list:escaped', 'invert' : 'bool', } diff -r d9f6f3f2467195397828d452664c68e5e4c104ef -r bf7251133a037cda8ca7025a15af4ab9efb326ba lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -41,23 +41,18 @@ NOTE: also searches dictionaries """ - #print '\n\t getattr_recursive:', item, attr_key using_default = len( args ) >= 1 default = args[0] if using_default else None - #print '\t defaults:', using_default, default for attr_key in attr_key.split( '.' ): try: - #print '\t\t attr:', attr_key, 'item:', item if isinstance( item, dict ): item = item.__getitem__( attr_key ) else: item = getattr( item, attr_key ) except ( KeyError, AttributeError ), err: - #print '\t\t error:', err if using_default: - #print '\t\t\t default:', default return default raise @@ -77,7 +72,6 @@ attr_key = last_key try: - #print '\t\t attr:', attr_key, 'item:', item if isinstance( item, dict ): return item.__contains__( attr_key ) else: @@ -88,6 +82,7 @@ return True + # ------------------------------------------------------------------- the registry class VisualizationsRegistry( pluginframework.PageServingPluginManager ): """ @@ -118,7 +113,7 @@ super( VisualizationsRegistry, self ).__init__( app, 'visualizations', **kwargs ) # what to use to parse query strings into resources/vars for the template self.resource_parser = ResourceParser() - log.debug( '%s loaded', str( self ) ) + #log.debug( '%s loaded', str( self ) ) def is_plugin( self, plugin_path ): """ @@ -265,8 +260,6 @@ #precondition: the target_object should be usable by the visualization (accrd. to data_sources) # convert params using vis.data_source.to_params params = self.get_url_params( trans, target_object, param_data ) - #for param in params: - # print param # we want existing visualizations to work as normal but still be part of the registry (without mod'ing) # so generate their urls differently @@ -294,12 +287,8 @@ # assign takes precedence (goes last, overwrites)? #NOTE this is only one level - #print 'target_object:', target_object - #print 'target_attr:', target_attr - if target_attr and hasattr_recursive( target_object, target_attr ): params[ to_param_name ] = getattr_recursive( target_object, target_attr ) - #print 'params[ %s ]:' %( to_param_name ), params[ to_param_name ] if assign: params[ to_param_name ] = assign @@ -394,7 +383,6 @@ returned[ 'name' ] = xml_tree.attrib.get( 'name', None ) if not returned[ 'name' ]: raise ParsingException( 'visualization needs a name attribute' ) - print returned[ 'name' ] # a (for now) text description of what the visualization does description = xml_tree.find( 'description' ) @@ -532,7 +520,7 @@ raise ParsingException( 'data_source entry requires a model_class' ) if xml_tree.text not in self.ALLOWED_MODEL_CLASSES: - log.debug( 'available data_source model_classes: %s' %( str( self.ALLOWED_MODEL_CLASSES ) ) ) + #log.debug( 'available data_source model_classes: %s' %( str( self.ALLOWED_MODEL_CLASSES ) ) ) raise ParsingException( 'Invalid data_source model_class: %s' %( xml_tree.text ) ) # look up the model from the model module returning an empty data_source if not found @@ -760,6 +748,7 @@ If param is required and not present, raises a `KeyError`. """ + #log.debug( 'parse_parameter_dictionary, query_params:\n%s', query_params ) # first parse any params from any visualizations that were passed query_params = self.get_params_from_visualization_param( trans, controller, param_config_dict, query_params ) @@ -842,8 +831,8 @@ return self.parse_parameter( trans, param_config, default ) def get_params_from_visualization_param( self, trans, controller, param_config_dict, query_params ): - log.debug( 'parse_visualization_params: %s', param_config_dict ) - log.debug( ' : %s', query_params ) + #log.debug( 'parse_visualization_params: %s', param_config_dict ) + #log.debug( ' : %s', query_params ) # first, find the visualization in the parameters if any visualization = None @@ -854,25 +843,25 @@ if query_val is None: continue - log.debug( 'found visualization param: %s, %s', param_name, query_val ) + #log.debug( 'found visualization param: %s, %s', param_name, query_val ) visualization = self.parse_parameter( trans, controller, param_config, query_val ) if visualization: break # if no vis is found, can't get any new params from it: return the original query_params if not visualization: - log.debug( 'visualization not found' ) + #log.debug( 'visualization not found' ) return query_params - log.debug( 'found visualization: %s', visualization ) + #log.debug( 'found visualization: %s', visualization ) # next, attempt to copy any params from the visualizations config visualization_config = visualization.latest_revision.config - log.debug( '\t config: %s', visualization_config ) + #log.debug( '\t config: %s', visualization_config ) params_from_visualization = {} for param_name, param_config in param_config_dict.items(): if param_name in visualization_config: params_from_visualization[ param_name ] = visualization_config[ param_name ] - log.debug( 'params_from_visualization: %s', params_from_visualization ) + #log.debug( 'params_from_visualization: %s', params_from_visualization ) # layer the query_params over the params from the visualization, returning the combined params_from_visualization.update( query_params ) @@ -926,7 +915,7 @@ #TODO: subclass here? elif param_type == 'visualization': encoded_visualization_id = query_param - log.debug( 'visualization param, id : %s', encoded_visualization_id ) + #log.debug( 'visualization param, id : %s', encoded_visualization_id ) #TODO:?? some fallback if there's no get_X in controller that's passed? parsed_param = controller.get_visualization( trans, encoded_visualization_id, check_ownership=False, check_accessible=True ) @@ -948,5 +937,4 @@ dbkey = query_param parsed_param = galaxy.util.sanitize_html.sanitize_html( dbkey, 'utf-8' ) - #print ( '%s, %s -> %s, %s' %( param_type, query_param, str( type( parsed_param ) ), parsed_param ) ) return parsed_param diff -r d9f6f3f2467195397828d452664c68e5e4c104ef -r bf7251133a037cda8ca7025a15af4ab9efb326ba lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -62,7 +62,7 @@ :param skip_bad_plugins: whether to skip plugins that cause exceptions when loaded or to raise that exception """ - log.debug( 'PluginManager.init: %s, %s', directories_setting, kwargs ) + #log.debug( 'PluginManager.init: %s, %s', directories_setting, kwargs ) self.directories = [] self.skip_bad_plugins = skip_bad_plugins self.plugins = odict.odict() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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