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/
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