def trackster(self, trans, **kwargs):
"""
Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`.
"""
# define app configuration
app = {'jscript' : "viz/trackster"}
# get dataset to add
id = kwargs.get("id", None)
# get dataset to add
new_dataset_id = kwargs.get("dataset_id", None)
# set up new browser if no id provided
if not id:
# use dbkey from dataset to be added or from incoming parameter
dbkey = None
if new_dataset_id:
decoded_id = self.decode_id(new_dataset_id)
hda = self.hda_manager.get_owned(decoded_id, trans.user, current_history=trans.user)
dbkey = hda.dbkey
if dbkey == '?':
dbkey = kwargs.get("dbkey", None)
# save database key
app['default_dbkey'] = dbkey
else:
# load saved visualization
vis = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
app['viz_config'] = self.get_visualization_config(trans, vis)
# backup id
app['id'] = id
# add dataset id
app['add_dataset'] = new_dataset_id
# check for gene region
gene_region = GenomeRegion.from_str(kwargs.get("gene_region", ""))
# update gene region of saved visualization if user parses a new gene region in the url
if gene_region.chrom is not None:
app['gene_region'] = {
'chrom' : gene_region.chrom,
'start' : gene_region.start,
'end' : gene_region.end
}
# fill template
return trans.fill_template('galaxy.panels.mako', config={'right_panel': True, 'app': app})
def trackster(self, trans, **kwargs):
"""
Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`.
"""
# define app configuration
app = { 'jscript' : "viz/trackster" }
# get dataset to add
id = kwargs.get( "id", None )
# get dataset to add
new_dataset_id = kwargs.get( "dataset_id", None )
# set up new browser if no id provided
if not id:
# use dbkey from dataset to be added or from incoming parameter
dbkey = None
if new_dataset_id:
decoded_id = self.decode_id( new_dataset_id )
hda = self.hda_manager.get_owned( decoded_id, trans.user, current_history=trans.user )
dbkey = hda.dbkey
if dbkey == '?':
dbkey = kwargs.get( "dbkey", None )
# save database key
app['default_dbkey'] = dbkey
else:
# load saved visualization
vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
app['viz_config'] = self.get_visualization_config( trans, vis )
# backup id
app['id'] = id;
# add dataset id
app['add_dataset'] = new_dataset_id
# check for gene region
gene_region = GenomeRegion.from_str(kwargs.get("gene_region", ""))
# update gene region of saved visualization if user parses a new gene region in the url
if gene_region.chrom is not None:
app['gene_region'] = {
'chrom' : gene_region.chrom,
'start' : gene_region.start,
'end' : gene_region.end
}
# fill template
return trans.fill_template('galaxy.panels.mako', config = {'right_panel' : True, 'app' : app})
def trackster(self, trans, id=None, **kwargs):
"""
Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`.
"""
# Get dataset to add.
new_dataset_id = kwargs.get( "dataset_id", None )
# Check for gene region
gene_region = GenomeRegion.from_str(kwargs.get("gene_region", ""))
# Set up new browser if no id provided.
if not id:
# Use dbkey from dataset to be added or from incoming parameter.
dbkey = None
if new_dataset_id:
dbkey = self.get_dataset( trans, new_dataset_id ).dbkey
if dbkey == '?':
dbkey = kwargs.get( "dbkey", None )
# fill template
return trans.fill_template( "tracks/browser.mako", viewport_config=gene_region.__dict__, add_dataset=new_dataset_id, default_dbkey=dbkey )
# Display saved visualization.
vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
viz_config = self.get_visualization_config( trans, vis )
# Update gene region of saved visualization if user parses a new gene region in the url
if gene_region.chrom is not None:
viz_config['viewport']['chrom'] = gene_region.chrom
viz_config['viewport']['start'] = gene_region.start
viz_config['viewport']['end'] = gene_region.end
'''
FIXME:
if new_dataset is not None:
if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]:
new_dataset = None # Already in browser, so don't add
'''
# fill template
return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset_id )
