def get_protein_and_manager(self, refseq, **kwargs):
protein = Protein.query.filter_by(refseq=refseq).first_or_404()
if kwargs:
user_datasets = current_user.datasets_names_by_uri()
filter_manager = self.filter_class(
protein, custom_datasets_ids=user_datasets.keys(), **kwargs)
else:
filter_manager = self.filter_manager
return protein, filter_manager
def before_request(self, name, *args, **kwargs):
user_datasets = current_user.datasets_names_by_uri()
refseq = kwargs.get('refseq', None)
protein = (Protein.query.filter_by(
refseq=refseq).first_or_404() if refseq else None)
filter_manager = self.filter_class(
protein, custom_datasets_ids=user_datasets.keys())
flask.g.filter_manager = filter_manager
endpoint = self.build_route_name(name)
return filter_manager.reformat_request_url(request, endpoint, *args,
**kwargs)
def show(self, refseq, predicted_interactions=False):
"""Show a protein network visualisation"""
protein, filter_manager = self.get_protein_and_manager(refseq)
user_datasets = current_user.datasets_names_by_uri()
return template(
'network/show.html',
protein=protein,
filters=filter_manager,
option_widgets=self._create_option_widgets(filter_manager),
widgets=create_widgets(
protein,
filter_manager.filters,
custom_datasets_names=user_datasets.values()),
mutation_types=Mutation.types,
predicted_interactions=predicted_interactions)
def show(self, refseq):
"""Show a protein by:
+ needleplot
+ tracks (sequence + data tracks)
"""
protein, filter_manager = self.get_protein_and_manager(refseq)
user_datasets = current_user.datasets_names_by_uri()
return template(
'protein/show.html',
protein=protein,
filters=filter_manager,
widgets=create_widgets(
protein,
filter_manager.filters,
custom_datasets_names=user_datasets.values()),
site_types=['multi_ptm'] + SiteType.available_types(),
mutation_types=Mutation.types,
)