def phyloviz(self, trans, id=None, dataset_id=None, tree_index=0, **kwargs):
config = None
data = None
# if id, then this is a saved visualization; get its config and the dataset_id from there
if id:
visualization = self.get_visualization(trans, id)
config = self.get_visualization_config(trans, visualization)
dataset_id = config.get('dataset_id', None)
# get the hda if we can, then its data using the phyloviz parsers
if dataset_id:
decoded_id = self.decode_id(dataset_id)
hda = self.hda_manager.get_accessible(decoded_id, trans.user)
hda = self.hda_manager.error_if_uploading(hda)
else:
return trans.show_message("Phyloviz couldn't find a dataset_id")
pd = PhylovizDataProvider(original_dataset=hda)
data = pd.get_data(tree_index=tree_index)
# ensure at least a default configuration (gen. an new/unsaved visualization)
if not config:
config = {
'dataset_id': dataset_id,
'title' : hda.display_name(),
'ext' : hda.datatype.file_ext,
'treeIndex' : tree_index,
'saved_visualization' : False
}
return trans.fill_template_mako("visualization/phyloviz.mako", data=data, config=config)
def phyloviz( self, trans, id=None, dataset_id=None, tree_index=0, **kwargs ):
config = None
data = None
# if id, then this is a saved visualization; get its config and the dataset_id from there
if id:
visualization = self.get_visualization( trans, id )
config = self.get_visualization_config( trans, visualization )
dataset_id = config.get( 'dataset_id', None )
# get the hda if we can, then its data using the phyloviz parsers
if dataset_id:
hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True )
else:
return trans.show_message( "Phyloviz couldn't find a dataset_id" )
pd = PhylovizDataProvider( original_dataset=hda )
data = pd.get_data( tree_index=tree_index )
# ensure at least a default configuration (gen. an new/unsaved visualization)
if not config:
config = {
'dataset_id': dataset_id,
'title' : hda.display_name(),
'ext' : hda.datatype.file_ext,
'treeIndex' : tree_index,
'saved_visualization' : False
}
return trans.fill_template_mako( "visualization/phyloviz.mako", data=data, config=config )
def phyloviz( self, trans, dataset_id, tree_index=0, **kwargs ):
# Get HDA.
hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True )
# Get data.
pd = PhylovizDataProvider( original_dataset=hda )
config = pd.get_data( tree_index=tree_index )
config["title"] = hda.display_name()
config["ext"] = hda.datatype.file_ext
config["dataset_id"] = dataset_id
config["treeIndex"] = tree_index
config["saved_visualization"] = False
# Return viz.
return trans.fill_template_mako( "visualization/phyloviz.mako", data = config[ "data" ], config=config )